Class ID Preferred Label Synonyms Definitions Obsolete CUI Semantic Types Parents Citation Created in deprecation_candidate deprecation_comment Documentation Example File extension has format has function has identifier has input has output has topic http://data.bioontology.org/metadata/prefixIRI http://edamontology.org/comment_handle http://edamontology.org/next_id http://edamontology.org/ontology_used http://purl.obolibrary.org/obo/date http://purl.obolibrary.org/obo/default-relationship-id-prefix http://purl.obolibrary.org/obo/edam#data http://purl.obolibrary.org/obo/edam#edam http://purl.obolibrary.org/obo/edam#events http://purl.obolibrary.org/obo/edam#formats http://purl.obolibrary.org/obo/edam#identifiers http://purl.obolibrary.org/obo/edam#obsolete http://purl.obolibrary.org/obo/edam#operations http://purl.obolibrary.org/obo/edam#topics http://purl.obolibrary.org/obo/idspace http://purl.obolibrary.org/obo/is_anti_symmetric http://purl.obolibrary.org/obo/is_metadata_tag http://purl.obolibrary.org/obo/is_reflexive http://purl.obolibrary.org/obo/is_symmetric http://purl.obolibrary.org/obo/namespace http://purl.obolibrary.org/obo/remark http://purl.obolibrary.org/obo/transitive_over http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/format http://purl.org/dc/elements/1.1/title http://usefulinc.com/ns/doap#Version http://www.geneontology.org/formats/oboInOwl#comment http://www.geneontology.org/formats/oboInOwl#consider http://www.geneontology.org/formats/oboInOwl#hasAlternativeId http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym http://www.geneontology.org/formats/oboInOwl#hasDbXRef http://www.geneontology.org/formats/oboInOwl#hasDbXref http://www.geneontology.org/formats/oboInOwl#hasDefinition http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasSubset http://www.geneontology.org/formats/oboInOwl#inSubset http://www.geneontology.org/formats/oboInOwl#isCyclic http://www.geneontology.org/formats/oboInOwl#replacedBy http://www.geneontology.org/formats/oboInOwl#savedBy http://www.geneontology.org/formats/oboInOwl#SubsetProperty http://xmlns.com/foaf/0.1/page Information standard is format of is function of is identifier of is input of is output of is topic of isdebtag Media type Obsolete since old parent Organisation refactor_candidate refactor_comment Regular expression thematic_editor UI tip http://edamontology.org/data_0005 Resource type A type of computational resource used in bioinformatics. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0005 http://edamontology.org/data_2337 A type of computational resource used in bioinformatics. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0006 Data Data record|Data set|Datum "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." FALSE http://www.w3.org/2002/07/owl#Thing beta12orEarlier data_0006 "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." Data record Data set|Datum http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data Not recommended for annotation in bio.tools. http://edamontology.org/data_0007 Tool "A bioinformatics package or tool, e.g. a standalone application or web service." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0007 "A bioinformatics package or tool, e.g. a standalone application or web service." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0958 beta12orEarlier http://edamontology.org/data_0581 Database "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0581 "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0957 beta12orEarlier http://edamontology.org/data_0582 Ontology Ontologies "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." FALSE http://edamontology.org/data_2353 beta12orEarlier data_0582 "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." Ontologies http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0583 Directory metadata A directory on disk from which files are read. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0583 http://edamontology.org/data_3106 A directory on disk from which files are read. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0831 MeSH vocabulary Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0831 http://edamontology.org/data_0582 Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0832 HGNC vocabulary Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0832 http://edamontology.org/data_0582 Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0835 UMLS vocabulary Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0835 http://edamontology.org/data_0582 Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0842 Identifier ID|http://purl.org/dc/elements/1.1/identifier "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)." FALSE http://edamontology.org/data_0006 beta12orEarlier data_0842 "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)." ID http://purl.org/dc/elements/1.1/identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0843 Database entry An entry (retrievable via URL) from a biological database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0843 http://edamontology.org/data_0006 An entry (retrievable via URL) from a biological database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0844 Molecular mass Mass of a molecule. FALSE http://edamontology.org/data_2050 beta12orEarlier data_0844 Mass of a molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0845 Molecular charge Net charge of a molecule. FALSE http://edamontology.org/data_2050 beta12orEarlier data_0845 PDBML:pdbx_formal_charge Net charge of a molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0846 Chemical formula Chemical structure specification A specification of a chemical structure. FALSE http://edamontology.org/data_2050 beta12orEarlier data_0846 A specification of a chemical structure. Chemical structure specification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0847 QSAR descriptor A QSAR quantitative descriptor (name-value pair) of chemical structure.|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. FALSE http://edamontology.org/data_2050 beta12orEarlier data_0847 A QSAR quantitative descriptor (name-value pair) of chemical structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0848 Raw sequence "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.|Non-sequence characters may be used for example for gaps and translation stop." FALSE http://edamontology.org/data_2044 beta12orEarlier data_0848 "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0849 Sequence record A molecular sequence and associated metadata. FALSE http://edamontology.org/data_2044 beta12orEarlier data_0849 SO:2000061 A molecular sequence and associated metadata. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0850 Sequence set SO:0001260 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.|This concept may be used for arbitrary sequence sets and associated data arising from processing. FALSE http://edamontology.org/data_0006 beta12orEarlier data_0850 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. SO:0001260 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0851 Sequence mask character A character used to replace (mask) other characters in a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0851 A character used to replace (mask) other characters in a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0852 Sequence mask type "A label (text token) describing the type of sequence masking to perform.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0852 http://edamontology.org/data_0842 A label (text token) describing the type of sequence masking to perform. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0853 DNA sense specification Strand|DNA strand specification "The strand of a DNA sequence (forward or reverse).|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." FALSE http://edamontology.org/data_2534 beta12orEarlier data_0853 The strand of a DNA sequence (forward or reverse). Strand|DNA strand specification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0854 Sequence length specification A specification of sequence length(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0854 http://edamontology.org/data_1249 A specification of sequence length(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0855 Sequence metadata "Basic or general information concerning molecular sequences.|This is used for such things as a report including the sequence identifier, type and length." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0855 http://edamontology.org/data_2955 Basic or general information concerning molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0856 Sequence feature source "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.|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)." FALSE http://edamontology.org/data_2914 beta12orEarlier data_0856 How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0857 Sequence search results Sequence database search results||Sequence search hits|Database hits (sequence)|Sequence database hits "A report of sequence hits and associated data from searching a database of sequences (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.|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." FALSE http://edamontology.org/data_2080 beta12orEarlier data_0857 A report of sequence hits and associated data from searching a database of sequences (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. Sequence database search results||Sequence search hits|Database hits (sequence)|Sequence database hits http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0858 Sequence signature matches Sequence motif matches|Sequence profile matches|Protein secondary database search results|Search results (protein secondary database) "Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.|This ncluding reports of hits from a search of a protein secondary or domain database." FALSE http://edamontology.org/data_0860 beta12orEarlier data_0858 "Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures." Sequence motif matches|Sequence profile matches Protein secondary database search results|Search results (protein secondary database) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0859 Sequence signature model Data files used by motif or profile methods. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0859 http://edamontology.org/data_0950 Data files used by motif or profile methods. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0860 Sequence signature data "Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.|This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on." FALSE http://edamontology.org/data_0006 beta12orEarlier data_0860 "Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0861 Sequence alignment (words) Sequence word alignment Alignment of exact matches between subsequences (words) within two or more molecular sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0861 http://edamontology.org/data_0863 Alignment of exact matches between subsequences (words) within two or more molecular sequences. Sequence word alignment http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0862 Dotplot A dotplot of sequence similarities identified from word-matching or character comparison. FALSE http://edamontology.org/data_0867 beta12orEarlier data_0862 A dotplot of sequence similarities identified from word-matching or character comparison. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0863 Sequence alignment Alignment of multiple molecular sequences. FALSE http://edamontology.org/data_1916 beta12orEarlier data_0863 Alignment of multiple molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0864 Sequence alignment parameter Some simple value controlling a sequence alignment (or similar 'match') operation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0864 Some simple value controlling a sequence alignment (or similar 'match') operation. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0865 Sequence similarity score A value representing molecular sequence similarity. FALSE http://edamontology.org/data_1772 beta12orEarlier data_0865 A value representing molecular sequence similarity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0866 Sequence alignment metadata "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0866 http://edamontology.org/data_0867 "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0867 Sequence alignment report "An informative report of molecular sequence alignment-derived data or metadata.|Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score." FALSE http://edamontology.org/data_2048 beta12orEarlier data_0867 An informative report of molecular sequence alignment-derived data or metadata. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0868 Profile-profile alignment Sequence profile alignment A profile-profile alignment (each profile typically representing a sequence alignment). FALSE http://edamontology.org/data_1916 beta12orEarlier data_0868 A profile-profile alignment (each profile typically representing a sequence alignment). Sequence profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0869 Sequence-profile alignment "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).|Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores." FALSE http://edamontology.org/data_1916 beta12orEarlier data_0869 Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0870 Sequence distance matrix Phylogenetic distance matrix "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.|Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix." FALSE http://edamontology.org/data_2855 beta12orEarlier data_0870 Moby:phylogenetic_distance_matrix "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." Phylogenetic distance matrix http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0871 Phylogenetic character data "Basic character data from which a phylogenetic tree may be generated.|As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments" FALSE http://edamontology.org/data_2523 beta12orEarlier data_0871 Basic character data from which a phylogenetic tree may be generated. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0872 Phylogenetic tree Phylogeny "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.|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'." FALSE http://edamontology.org/data_2523 beta12orEarlier data_0872 Moby:Tree|Moby:myTree|Moby:phylogenetic_tree "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." Phylogeny http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0874 Comparison matrix Substitution matrix "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.|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)." FALSE http://edamontology.org/data_2082 beta12orEarlier data_0874 Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. Substitution matrix http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0875 Protein topology Predicted or actual protein topology represented as a string of protein secondary structure elements.|The location and size of the secondary structure elements and intervening loop regions is usually indicated. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0875 Predicted or actual protein topology represented as a string of protein secondary structure elements. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 beta12orEarlier http://edamontology.org/data_0876 Protein features report (secondary structure) Secondary structure (predicted or real) of a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0876 Secondary structure (predicted or real) of a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_0877 Protein features report (super-secondary) "Super-secondary structure of protein sequence(s).|Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0877 Super-secondary structure of protein sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_0878 Secondary structure alignment (protein) Alignment of the (1D representations of) secondary structure of two or more proteins. FALSE http://edamontology.org/data_2366|http://edamontology.org/data_3154 beta12orEarlier data_0878 Alignment of the (1D representations of) secondary structure of two or more proteins. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0879 Secondary structure alignment metadata (protein) An informative report on protein secondary structure alignment-derived data or metadata. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0879 http://edamontology.org/data_0867 An informative report on protein secondary structure alignment-derived data or metadata. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0880 RNA secondary structure Secondary structure (RNA) "An informative report of secondary structure (predicted or real) of an RNA molecule.|This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc." FALSE http://edamontology.org/data_1465 beta12orEarlier data_0880 Moby:RNAStructML An informative report of secondary structure (predicted or real) of an RNA molecule. Secondary structure (RNA) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0881 Secondary structure alignment (RNA) Alignment of the (1D representations of) secondary structure of two or more RNA molecules. FALSE http://edamontology.org/data_2366 beta12orEarlier data_0881 Moby:RNAStructAlignmentML Alignment of the (1D representations of) secondary structure of two or more RNA molecules. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0882 Secondary structure alignment metadata (RNA) An informative report of RNA secondary structure alignment-derived data or metadata. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0882 http://edamontology.org/data_0867 An informative report of RNA secondary structure alignment-derived data or metadata. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0883 Structure Coordinate model|Structure data 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.|The coordinate data may be predicted or real. FALSE http://edamontology.org/data_0006 beta12orEarlier data_0883 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. Coordinate model|Structure data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0884 Tertiary structure record An entry from a molecular tertiary (3D) structure database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0884 http://edamontology.org/data_0883 An entry from a molecular tertiary (3D) structure database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0885 Structure database search results Results (hits) from searching a database of tertiary structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0885 http://edamontology.org/data_2080 Results (hits) from searching a database of tertiary structure. http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/data_0886 Structure alignment "Alignment (superimposition) of molecular tertiary (3D) structures.|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." FALSE http://edamontology.org/data_1916 beta12orEarlier data_0886 Alignment (superimposition) of molecular tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0887 Structure alignment report "An informative report of molecular tertiary structure alignment-derived data.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_2048 beta12orEarlier data_0887 An informative report of molecular tertiary structure alignment-derived data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0888 Structure similarity score "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." FALSE http://edamontology.org/data_1772 beta12orEarlier data_0888 "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0889 Structural profile 3D profile|Structural (3D) profile Some type of structural (3D) profile or template (representing a structure or structure alignment). FALSE http://edamontology.org/data_0006 beta12orEarlier data_0889 Some type of structural (3D) profile or template (representing a structure or structure alignment). 3D profile|Structural (3D) profile http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0890 Structural (3D) profile alignment Structural profile alignment A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). FALSE http://edamontology.org/data_1916 beta12orEarlier data_0890 A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). Structural profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0891 Sequence-3D profile alignment Sequence-structural profile alignment An alignment of a sequence to a 3D profile (representing structures or a structure alignment). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0891 http://edamontology.org/data_0893 An alignment of a sequence to a 3D profile (representing structures or a structure alignment). Sequence-structural profile alignment http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0892 Protein sequence-structure scoring matrix Matrix of values used for scoring sequence-structure compatibility. FALSE http://edamontology.org/data_2082 beta12orEarlier data_0892 Matrix of values used for scoring sequence-structure compatibility. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0893 Sequence-structure alignment An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). FALSE http://edamontology.org/data_1916 beta12orEarlier data_0893 An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0894 Amino acid annotation An informative report about a specific amino acid. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0894 http://edamontology.org/data_0962 An informative report about a specific amino acid. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_0895 Peptide annotation An informative report about a specific peptide. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0895 http://edamontology.org/data_0962 An informative report about a specific peptide. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_0896 Protein report Gene product annotation "An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." FALSE http://edamontology.org/data_2048 beta12orEarlier data_0896 "An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." Gene product annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0897 Protein property Protein physicochemical property|Protein properties|Protein sequence statistics "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.|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." FALSE http://edamontology.org/data_2087 beta12orEarlier data_0897 "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." Protein physicochemical property|Protein properties Protein sequence statistics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0899 Protein structural motifs and surfaces 3D structural motifs in a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0899 3D structural motifs in a protein. http://edamontology.org/data_1277 1.8 http://edamontology.org/data_0900 Protein domain classification Data concerning the classification of the sequences and/or structures of protein structural domain(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0900 http://edamontology.org/data_2980 Data concerning the classification of the sequences and/or structures of protein structural domain(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0901 Protein features report (domains) structural domains or 3D folds in a protein or polypeptide chain. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0901 structural domains or 3D folds in a protein or polypeptide chain. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_0902 Protein architecture report An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0902 http://edamontology.org/data_1537 An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_0903 Protein folding report "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0903 "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1537 1.8 http://edamontology.org/data_0904 Protein features (mutation) "Data on the effect of (typically point) mutation on protein folding, stability, structure and function.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0904 http://edamontology.org/data_0896 "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_0905 Protein interaction raw data "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.|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." FALSE http://edamontology.org/data_3108 beta12orEarlier data_0905 "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0906 Protein interaction report Protein interaction record|Protein report (interaction)|Protein non-covalent interactions report|Atom interaction data|Residue interaction data "An informative report on interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc. " FALSE http://edamontology.org/data_1537 beta12orEarlier data_0906 "An informative report on interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc. " Protein interaction record|Protein report (interaction) Protein non-covalent interactions report|Atom interaction data|Residue interaction data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0907 Protein family report Protein classification data|Protein family annotation An informative report on a specific protein family or other classification or group of protein sequences or structures. FALSE http://edamontology.org/data_0896 beta12orEarlier data_0907 Protein classification data An informative report on a specific protein family or other classification or group of protein sequences or structures. Protein family annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0909 Vmax The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. FALSE http://edamontology.org/data_2024 beta12orEarlier data_0909 The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0910 Km Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. FALSE http://edamontology.org/data_2024 beta12orEarlier data_0910 Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0911 Nucleotide base annotation An informative report about a specific nucleotide base. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0911 http://edamontology.org/data_0962 An informative report about a specific nucleotide base. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_0912 Nucleic acid property Nucleic acid physicochemical property|GC-content "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.|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." FALSE http://edamontology.org/data_2087 beta12orEarlier data_0912 "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." Nucleic acid physicochemical property GC-content http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0914 Codon usage data "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_0914 Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0916 Gene report Gene annotation|Gene and transcript structure (report)|Gene function (report)|Gene structure (repot)|Nucleic acid features (gene and transcript structure)|Gene features report "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.|This includes any report on a particular locus or gene. 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)." FALSE http://edamontology.org/data_1276 beta12orEarlier data_0916 Moby_namespace:Human_Readable_Description|Moby:gene|Moby:GeneInfo "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." Gene annotation|Gene and transcript structure (report)|Gene function (report)|Gene structure (repot)|Nucleic acid features (gene and transcript structure)|Gene features report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0917 Gene classification A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0917 http://edamontology.org/data_0916 A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0918 DNA variation "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0918 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_0919 Chromosome report "An informative report on a specific chromosome.|This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc." FALSE http://edamontology.org/data_2084 beta12orEarlier data_0919 An informative report on a specific chromosome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0920 Genotype/phenotype report Genotype/phenotype annotation "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." FALSE http://edamontology.org/data_2048 beta12orEarlier data_0920 "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." Genotype/phenotype annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0922 Nucleic acid features report (primers) PCR primers and hybridisation oligos in a nucleic acid sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0922 PCR primers and hybridisation oligos in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_0923 PCR experiment report "PCR experiments, e.g. quantitative real-time PCR." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0923 "PCR experiments, e.g. quantitative real-time PCR." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_0924 Sequence trace "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.|This is the raw data produced by a DNA sequencing machine." FALSE http://edamontology.org/data_1234|http://edamontology.org/data_3108 beta12orEarlier data_0924 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0925 Sequence assembly Contigs|SO:0000353|SO:0001248 "An assembly of fragments of a (typically genomic) DNA sequence.|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." FALSE http://edamontology.org/data_1234 beta12orEarlier data_0925 An assembly of fragments of a (typically genomic) DNA sequence. Contigs|SO:0000353 SO:0001248 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0926 Radiation Hybrid (RH) scores Radiation hybrid scores (RH) scores for one or more markers.|Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. FALSE http://edamontology.org/data_3108 beta12orEarlier data_0926 Radiation hybrid scores (RH) scores for one or more markers. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0927 Genetic linkage report Gene annotation (linkage)|Linkage disequilibrium (report) An informative report on the linkage of alleles.|This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). FALSE http://edamontology.org/data_2084 beta12orEarlier data_0927 An informative report on the linkage of alleles. Gene annotation (linkage) Linkage disequilibrium (report) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0928 Gene expression profile Gene expression pattern "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." FALSE http://edamontology.org/data_2603 beta12orEarlier data_0928 "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." Gene expression pattern http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0931 Microarray experiment report "microarray experiments including conditions, protocol, sample:data relationships etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0931 "microarray experiments including conditions, protocol, sample:data relationships etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_0932 Oligonucleotide probe data Data on oligonucleotide probes (typically for use with DNA microarrays). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0932 http://edamontology.org/data_2717 Data on oligonucleotide probes (typically for use with DNA microarrays). http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_0933 SAGE experimental data Output from a serial analysis of gene expression (SAGE) experiment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0933 http://edamontology.org/data_2535 Output from a serial analysis of gene expression (SAGE) experiment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0934 MPSS experimental data Massively parallel signature sequencing (MPSS) data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0934 http://edamontology.org/data_2535 Massively parallel signature sequencing (MPSS) data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0935 SBS experimental data Sequencing by synthesis (SBS) data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0935 http://edamontology.org/data_2535 Sequencing by synthesis (SBS) data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0936 Sequence tag profile (with gene assignment) "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0936 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2535 1.14 http://edamontology.org/data_0937 Protein X-ray crystallographic data X-ray crystallography data. FALSE http://edamontology.org/data_2537 beta12orEarlier data_0937 X-ray crystallography data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0938 Protein NMR data Protein nuclear magnetic resonance (NMR) raw data. FALSE http://edamontology.org/data_2537 beta12orEarlier data_0938 Protein nuclear magnetic resonance (NMR) raw data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0939 Protein circular dichroism (CD) spectroscopic data Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. FALSE http://edamontology.org/data_2537 beta12orEarlier data_0939 Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0940 Electron microscopy volume map EM volume map Volume map data from electron microscopy. FALSE http://edamontology.org/data_3108 beta12orEarlier data_0940 Volume map data from electron microscopy. EM volume map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0941 Electron microscopy model Annotation on a structural 3D model (volume map) from electron microscopy.|This might include the location in the model of the known features of a particular macromolecule. FALSE http://edamontology.org/data_0883 beta12orEarlier data_0941 Annotation on a structural 3D model (volume map) from electron microscopy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0942 2D PAGE image Two-dimensional gel electrophoresis image FALSE http://edamontology.org/data_3424 beta12orEarlier data_0942 Two-dimensional gel electrophoresis image http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0943 Mass spectrometry spectra Spectra from mass spectrometry. FALSE http://edamontology.org/data_2536 beta12orEarlier data_0943 Spectra from mass spectrometry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0944 Peptide mass fingerprint Protein fingerprint|Peak list|Molecular weights standard fingerprint "A set of peptide masses (peptide mass fingerprint) from mass spectrometry.|A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides." FALSE http://edamontology.org/data_2536|http://edamontology.org/data_2979 beta12orEarlier data_0944 A set of peptide masses (peptide mass fingerprint) from mass spectrometry. Protein fingerprint|Peak list Molecular weights standard fingerprint http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0945 Peptide identification 'Protein identification' "Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer." FALSE http://edamontology.org/data_0897|http://edamontology.org/data_2979 beta12orEarlier data_0945 "Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer." 'Protein identification' http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0946 Pathway or network annotation "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0946 http://edamontology.org/data_2984 "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0947 Biological pathway map A map (typically a diagram) of a biological pathway. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0947 http://edamontology.org/data_2600 A map (typically a diagram) of a biological pathway. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0948 Data resource definition "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0948 http://edamontology.org/data_1883 "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0949 Workflow metadata "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." FALSE http://edamontology.org/data_2337 beta12orEarlier data_0949 "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0950 Mathematical model Biological model A biological model represented in mathematical terms. FALSE http://edamontology.org/data_0006 beta12orEarlier data_0950 A biological model represented in mathematical terms. Biological model http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0951 Statistical estimate score A value representing estimated statistical significance of some observed data; typically sequence database hits. FALSE http://edamontology.org/data_1772 beta12orEarlier data_0951 A value representing estimated statistical significance of some observed data; typically sequence database hits. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0952 EMBOSS database resource definition Resource definition for an EMBOSS database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0952 http://edamontology.org/data_0957 Resource definition for an EMBOSS database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0953 Version information "Information on a version of software or data, for example name, version number and release date.|Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0953 http://edamontology.org/data_2337 "Information on a version of software or data, for example name, version number and release date." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0954 Database cross-mapping "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.|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." FALSE http://edamontology.org/data_2093 beta12orEarlier data_0954 A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0955 Data index An index of data of biological relevance. FALSE http://edamontology.org/data_0006 beta12orEarlier data_0955 An index of data of biological relevance. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0956 Data index report Database index annotation A report of an analysis of an index of biological data. FALSE http://edamontology.org/data_2048 beta12orEarlier data_0956 A report of an analysis of an index of biological data. Database index annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0957 Database metadata "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." FALSE http://edamontology.org/data_2337 beta12orEarlier data_0957 "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0958 Tool metadata "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." FALSE http://edamontology.org/data_2337 beta12orEarlier data_0958 "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0959 Job metadata Textual metadata on a submitted or completed job. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0959 http://edamontology.org/data_3106 Textual metadata on a submitted or completed job. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0960 User metadata "Textual metadata on a software author or end-user, for example a person or other software." FALSE http://edamontology.org/data_2337 beta12orEarlier data_0960 "Textual metadata on a software author or end-user, for example a person or other software." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0962 Small molecule report Small molecule annotation|Chemical structure report|Chemical compound annotation An informative report on a specific chemical compound. FALSE http://edamontology.org/data_2085 beta12orEarlier data_0962 An informative report on a specific chemical compound. Small molecule annotation|Chemical structure report|Chemical compound annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0963 Cell line report Cell line annotation|Organism strain data "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." FALSE http://edamontology.org/data_2530 beta12orEarlier data_0963 "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." Cell line annotation|Organism strain data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0964 Scent annotation An informative report about a specific scent. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0964 http://edamontology.org/data_0962 An informative report about a specific scent. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_0966 Ontology term Ontology class name|Ontology terms A term (name) from an ontology. FALSE http://edamontology.org/data_0967 beta12orEarlier data_0966 A term (name) from an ontology. Ontology class name|Ontology terms http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0967 Ontology concept data Ontology class metadata|Ontology term metadata Data concerning or derived from a concept from a biological ontology. FALSE http://edamontology.org/data_2353 beta12orEarlier data_0967 Data concerning or derived from a concept from a biological ontology. Ontology class metadata|Ontology term metadata http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0968 Keyword Phrases|Term "Keyword(s) or phrase(s) used (typically) for text-searching purposes.|Boolean operators (AND, OR and NOT) and wildcard characters may be allowed." FALSE http://edamontology.org/data_0006 beta12orEarlier data_0968 Moby:BooleanQueryString|Moby:QueryString|Moby:Wildcard_Query|Moby:Global_Keyword Keyword(s) or phrase(s) used (typically) for text-searching purposes. Phrases|Term http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0970 Citation Bibliographic reference|Reference "Bibliographic data that uniquely identifies a scientific article, book or other published material.|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." FALSE http://edamontology.org/data_2526 beta12orEarlier data_0970 Moby:GCP_SimpleCitation|Moby:Publication "Bibliographic data that uniquely identifies a scientific article, book or other published material." Bibliographic reference|Reference http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0971 Article Article text|Scientific article "A scientific text, typically a full text article from a scientific journal." FALSE http://edamontology.org/data_2526|http://edamontology.org/data_3671 beta12orEarlier data_0971 "A scientific text, typically a full text article from a scientific journal." Article text|Scientific article http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0972 Text mining report Text mining output An abstract of the results of text mining.|A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. FALSE http://edamontology.org/data_2048|http://edamontology.org/data_2526 beta12orEarlier data_0972 An abstract of the results of text mining. Text mining output http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0974 Entity identifier An identifier of a biological entity or phenomenon. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0974 http://edamontology.org/data_0842 An identifier of a biological entity or phenomenon. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0975 Data resource identifier An identifier of a data resource. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0975 http://edamontology.org/data_0842 An identifier of a data resource. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0976 Identifier (typed) An identifier that identifies a particular type of data.|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'. FALSE http://edamontology.org/data_0842 beta12orEarlier data_0976 An identifier that identifies a particular type of data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0977 Tool identifier "An identifier of a bioinformatics tool, e.g. an application or web service." FALSE http://edamontology.org/data_0976 beta12orEarlier data_0977 "An identifier of a bioinformatics tool, e.g. an application or web service." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0978 Discrete entity identifier "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0978 http://edamontology.org/data_0842 "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0979 Entity feature identifier "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)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0979 http://edamontology.org/data_0842 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0980 Entity collection identifier Name or other identifier of a collection of discrete biological entities. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0980 http://edamontology.org/data_0842 Name or other identifier of a collection of discrete biological entities. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0981 Phenomenon identifier "Name or other identifier of a physical, observable biological occurrence or event." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0981 http://edamontology.org/data_0842 "Name or other identifier of a physical, observable biological occurrence or event." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0982 Molecule identifier Name or other identifier of a molecule. FALSE http://edamontology.org/data_0976 beta12orEarlier data_0982 Name or other identifier of a molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0983 Atom ID Atom identifier Identifier (e.g. character symbol) of a specific atom. FALSE http://edamontology.org/data_0976 beta12orEarlier data_0983 Identifier (e.g. character symbol) of a specific atom. Atom identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0984 Molecule name Name of a specific molecule. FALSE http://edamontology.org/data_0982|http://edamontology.org/data_2099 beta12orEarlier data_0984 Name of a specific molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0985 Molecule type "A label (text token) describing the type a molecule.|For example, 'Protein', 'DNA', 'RNA' etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier Protein|DNA|RNA data_0985 http://edamontology.org/data_0842 A label (text token) describing the type a molecule. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_0986 Chemical identifier Unique identifier of a chemical compound. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0986 http://edamontology.org/data_1086 Unique identifier of a chemical compound. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0987 Chromosome name Name of a chromosome. FALSE http://edamontology.org/data_0984|http://edamontology.org/data_2119 beta12orEarlier data_0987 Name of a chromosome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0988 Peptide identifier Identifier of a peptide chain. FALSE http://edamontology.org/data_0982 beta12orEarlier data_0988 Identifier of a peptide chain. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0989 Protein identifier Identifier of a protein. FALSE http://edamontology.org/data_0982 beta12orEarlier data_0989 Identifier of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0990 Compound name Chemical name Unique name of a chemical compound. FALSE http://edamontology.org/data_1086|http://edamontology.org/data_0984 beta12orEarlier data_0990 Unique name of a chemical compound. Chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0991 Chemical registry number Unique registry number of a chemical compound. FALSE http://edamontology.org/data_2894 beta12orEarlier data_0991 Unique registry number of a chemical compound. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0992 Ligand identifier "Code word for a ligand, for example from a PDB file." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_0992 http://edamontology.org/data_1086 "Code word for a ligand, for example from a PDB file." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_0993 Drug identifier Identifier of a drug. FALSE http://edamontology.org/data_1086 beta12orEarlier data_0993 Identifier of a drug. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0994 Amino acid identifier Residue identifier Identifier of an amino acid. FALSE http://edamontology.org/data_1086 beta12orEarlier data_0994 Identifier of an amino acid. Residue identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0995 Nucleotide identifier Name or other identifier of a nucleotide. FALSE http://edamontology.org/data_1086 beta12orEarlier data_0995 Name or other identifier of a nucleotide. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0996 Monosaccharide identifier Identifier of a monosaccharide. FALSE http://edamontology.org/data_1086 beta12orEarlier data_0996 Identifier of a monosaccharide. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0997 Chemical name (ChEBI) ChEBI chemical name Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.|This is the recommended chemical name for use for example in database annotation. FALSE http://edamontology.org/data_0990 beta12orEarlier data_0997 Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. ChEBI chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0998 Chemical name (IUPAC) IUPAC chemical name IUPAC recommended name of a chemical compound. FALSE http://edamontology.org/data_0990 beta12orEarlier data_0998 IUPAC recommended name of a chemical compound. IUPAC chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_0999 Chemical name (INN) INN chemical name "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO)." FALSE http://edamontology.org/data_0990 beta12orEarlier data_0999 "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO)." INN chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1000 Chemical name (brand) Brand chemical name Brand name of a chemical compound. FALSE http://edamontology.org/data_0990 beta12orEarlier data_1000 Brand name of a chemical compound. Brand chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1001 Chemical name (synonymous) Synonymous chemical name Synonymous name of a chemical compound. FALSE http://edamontology.org/data_0990 beta12orEarlier data_1001 Synonymous name of a chemical compound. Synonymous chemical name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1002 Chemical registry number (CAS) CAS chemical registry number CAS registry number of a chemical compound. FALSE http://edamontology.org/data_0991 beta12orEarlier data_1002 CAS registry number of a chemical compound. CAS chemical registry number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1003 Chemical registry number (Beilstein) Beilstein chemical registry number Beilstein registry number of a chemical compound. FALSE http://edamontology.org/data_0991 beta12orEarlier data_1003 Beilstein registry number of a chemical compound. Beilstein chemical registry number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1004 Chemical registry number (Gmelin) Gmelin chemical registry number Gmelin registry number of a chemical compound. FALSE http://edamontology.org/data_0991 beta12orEarlier data_1004 Gmelin registry number of a chemical compound. Gmelin chemical registry number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1005 HET group name Short ligand name|Component identifier code "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." FALSE http://edamontology.org/data_0990 beta12orEarlier data_1005 "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." Short ligand name|Component identifier code http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1006 Amino acid name String of one or more ASCII characters representing an amino acid. FALSE http://edamontology.org/data_0994 beta12orEarlier data_1006 String of one or more ASCII characters representing an amino acid. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1007 Nucleotide code String of one or more ASCII characters representing a nucleotide. FALSE http://edamontology.org/data_0995|http://edamontology.org/data_0990 beta12orEarlier data_1007 String of one or more ASCII characters representing a nucleotide. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1008 Polypeptide chain ID PDB chain identifier|Polypeptide chain identifier|PDB strand id|Protein chain identifier|Chain identifier "Identifier of a polypeptide chain from a protein.|This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA" FALSE http://edamontology.org/data_0988 beta12orEarlier data_1008 WHATIF: chain|PDBML:pdbx_PDB_strand_id Identifier of a polypeptide chain from a protein. PDB chain identifier|Polypeptide chain identifier|PDB strand id|Protein chain identifier|Chain identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1009 Protein name Name of a protein. FALSE http://edamontology.org/data_0989|http://edamontology.org/data_0984 beta12orEarlier data_1009 Name of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1010 Enzyme identifier Name or other identifier of an enzyme or record from a database of enzymes. FALSE http://edamontology.org/data_0989 beta12orEarlier data_1010 Name or other identifier of an enzyme or record from a database of enzymes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1011 EC number EC code|EC|Enzyme Commission number An Enzyme Commission (EC) number of an enzyme. FALSE http://edamontology.org/data_2321 beta12orEarlier data_1011 Moby:EC_Number|Moby:Annotated_EC_Number An Enzyme Commission (EC) number of an enzyme. EC code|EC|Enzyme Commission number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ http://edamontology.org/data_1012 Enzyme name Name of an enzyme. FALSE http://edamontology.org/data_1010|http://edamontology.org/data_1009 beta12orEarlier data_1012 Name of an enzyme. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1013 Restriction enzyme name Name of a restriction enzyme. FALSE http://edamontology.org/data_1012 beta12orEarlier data_1013 Name of a restriction enzyme. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1014 Sequence position specification A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1014 http://edamontology.org/data_1016 A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1015 Sequence feature ID "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." FALSE http://edamontology.org/data_3034|http://edamontology.org/data_2091 beta12orEarlier data_1015 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1016 Sequence position SO:0000735 "A position of one or more points (base or residue) in a sequence, or part of such a specification." FALSE http://edamontology.org/data_2534 beta12orEarlier data_1016 WHATIF: PDBx_atom_site|PDBML:_atom_site.id|WHATIF: number "A position of one or more points (base or residue) in a sequence, or part of such a specification." SO:0000735 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1017 Sequence range Specification of range(s) of sequence positions. FALSE http://edamontology.org/data_2534 beta12orEarlier data_1017 Specification of range(s) of sequence positions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1018 Nucleic acid feature identifier Name or other identifier of an nucleic acid feature. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1018 http://edamontology.org/data_1015 Name or other identifier of an nucleic acid feature. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1019 Protein feature identifier Name or other identifier of a protein feature. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1019 http://edamontology.org/data_1015 Name or other identifier of a protein feature. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1020 Sequence feature key Sequence feature method|Sequence feature type "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.|A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence." FALSE http://edamontology.org/data_2914 beta12orEarlier data_1020 "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." Sequence feature method|Sequence feature type http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1021 Sequence feature qualifier Typically one of the EMBL or Swiss-Prot feature qualifiers.|Feature qualifiers hold information about a feature beyond that provided by the feature key and location. FALSE http://edamontology.org/data_2914 beta12orEarlier data_1021 Typically one of the EMBL or Swiss-Prot feature qualifiers. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1022 Sequence feature label Sequence feature name "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label.|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." FALSE http://edamontology.org/data_3034|http://edamontology.org/data_2099|http://edamontology.org/data_2914 beta12orEarlier data_1022 "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label." Sequence feature name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1023 EMBOSS Uniform Feature Object UFO The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. FALSE http://edamontology.org/data_3034|http://edamontology.org/data_2099 beta12orEarlier data_1023 The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. UFO http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1024 Codon name String of one or more ASCII characters representing a codon. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1024 http://edamontology.org/data_1276 String of one or more ASCII characters representing a codon. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1025 Gene identifier "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." FALSE http://edamontology.org/data_0976 beta12orEarlier data_1025 Moby:GeneAccessionList "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1026 Gene symbol The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. FALSE http://edamontology.org/data_2299 beta12orEarlier data_1026 Moby_namespace:Global_GeneSymbol|Moby_namespace:Global_GeneCommonName 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1027 Gene ID (NCBI) Gene identifier (NCBI)|NCBI gene ID|Entrez gene ID|NCBI geneid|Gene identifier (Entrez) An NCBI unique identifier of a gene. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_1098 beta12orEarlier data_1027 http://www.geneontology.org/doc/GO.xrf_abbs:LocusID|http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene An NCBI unique identifier of a gene. Gene identifier (NCBI)|NCBI gene ID|Entrez gene ID|NCBI geneid|Gene identifier (Entrez) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1028 Gene identifier (NCBI RefSeq) An NCBI RefSeq unique identifier of a gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1028 http://edamontology.org/data_1027 An NCBI RefSeq unique identifier of a gene. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1029 Gene identifier (NCBI UniGene) An NCBI UniGene unique identifier of a gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1029 http://edamontology.org/data_1104 An NCBI UniGene unique identifier of a gene. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1030 Gene identifier (Entrez) An Entrez unique identifier of a gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1030 http://edamontology.org/data_1027 An Entrez unique identifier of a gene. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier [0-9]+ http://edamontology.org/data_1031 Gene ID (CGD) CGD ID Identifier of a gene or feature from the CGD database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1031 Identifier of a gene or feature from the CGD database. CGD ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1032 Gene ID (DictyBase) Identifier of a gene from DictyBase. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1032 Identifier of a gene from DictyBase. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1033 Ensembl gene ID Gene ID (Ensembl) Unique identifier for a gene (or other feature) from the Ensembl database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2610 beta12orEarlier data_1033 Unique identifier for a gene (or other feature) from the Ensembl database. Gene ID (Ensembl) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1034 Gene ID (SGD) SGD identifier Identifier of an entry from the SGD database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2632 beta12orEarlier data_1034 Identifier of an entry from the SGD database. SGD identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data S[0-9]+ http://edamontology.org/data_1035 Gene ID (GeneDB) GeneDB identifier Identifier of a gene from the GeneDB database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1035 Moby_namespace:GeneDB Identifier of a gene from the GeneDB database. GeneDB identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9.-]* http://edamontology.org/data_1036 TIGR identifier Identifier of an entry from the TIGR database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2109 beta12orEarlier data_1036 Identifier of an entry from the TIGR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1037 TAIR accession (gene) Identifier of an gene from the TAIR database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2387 beta12orEarlier data_1037 Identifier of an gene from the TAIR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data Gene:[0-9]{7} http://edamontology.org/data_1038 Protein domain ID Identifier of a protein structural domain.|This is typically a character or string concatenated with a PDB identifier and a chain identifier. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1038 Identifier of a protein structural domain. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1039 SCOP domain identifier Identifier of a protein domain (or other node) from the SCOP database. FALSE http://edamontology.org/data_1038 beta12orEarlier data_1039 Identifier of a protein domain (or other node) from the SCOP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1040 CATH domain ID CATH domain identifier Identifier of a protein domain from CATH. FALSE http://edamontology.org/data_2700 beta12orEarlier 1nr3A00 data_1040 Identifier of a protein domain from CATH. CATH domain identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1041 SCOP concise classification string (sccs) "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.|An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs." FALSE http://edamontology.org/data_1039 beta12orEarlier data_1041 A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1042 SCOP sunid SCOP unique identifier|sunid "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.|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." FALSE http://edamontology.org/data_1039 beta12orEarlier 33229 data_1042 "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." SCOP unique identifier|sunid http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1043 CATH node ID CATH node identifier|CATH code A code number identifying a node from the CATH database. FALSE http://edamontology.org/data_2700 beta12orEarlier 3.30.1190.10.1.1.1.1.1 data_1043 A code number identifying a node from the CATH database. CATH node identifier|CATH code http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1044 Kingdom name "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." FALSE http://edamontology.org/data_1868 beta12orEarlier data_1044 "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1045 Species name Organism species The name of a species (typically a taxonomic group) of organism. FALSE http://edamontology.org/data_1868 beta12orEarlier data_1045 The name of a species (typically a taxonomic group) of organism. Organism species http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1046 Strain name "The name of a strain of an organism variant, typically a plant, virus or bacterium." FALSE http://edamontology.org/data_2379|http://edamontology.org/data_2909 beta12orEarlier data_1046 "The name of a strain of an organism variant, typically a plant, virus or bacterium." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1047 URI URIs A string of characters that name or otherwise identify a resource on the Internet. FALSE http://edamontology.org/data_0842 beta12orEarlier data_1047 A string of characters that name or otherwise identify a resource on the Internet. URIs http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1048 Database ID Database identifier An identifier of a biological or bioinformatics database. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1048 An identifier of a biological or bioinformatics database. Database identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1049 Directory name The name of a directory. FALSE http://edamontology.org/data_2099 beta12orEarlier data_1049 The name of a directory. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1050 File name The name (or part of a name) of a file (of any type). FALSE http://edamontology.org/data_2099 beta12orEarlier data_1050 The name (or part of a name) of a file (of any type). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1051 Ontology name Name of an ontology of biological or bioinformatics concepts and relations. FALSE http://edamontology.org/data_2338|http://edamontology.org/data_2099 beta12orEarlier data_1051 Name of an ontology of biological or bioinformatics concepts and relations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1052 URL A Uniform Resource Locator (URL). FALSE http://edamontology.org/data_1047 beta12orEarlier data_1052 Moby:Link|Moby:URL A Uniform Resource Locator (URL). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1053 URN A Uniform Resource Name (URN). FALSE http://edamontology.org/data_1047 beta12orEarlier data_1053 A Uniform Resource Name (URN). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1055 LSID Life Science Identifier A Life Science Identifier (LSID) - a unique identifier of some data.|LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:::[:] FALSE http://edamontology.org/data_1053 beta12orEarlier data_1055 A Life Science Identifier (LSID) - a unique identifier of some data. Life Science Identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1056 Database name The name of a biological or bioinformatics database. FALSE http://edamontology.org/data_1048|http://edamontology.org/data_2099 beta12orEarlier data_1056 The name of a biological or bioinformatics database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1057 Sequence database name The name of a molecular sequence database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1057 http://edamontology.org/data_1056 The name of a molecular sequence database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1058 Enumerated file name The name of a file (of any type) with restricted possible values. FALSE http://edamontology.org/data_1050 beta12orEarlier data_1058 The name of a file (of any type) with restricted possible values. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1059 File name extension The extension of a file name.|A file extension is the characters appearing after the final '.' in the file name. FALSE http://edamontology.org/data_1050 beta12orEarlier data_1059 The extension of a file name. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1060 File base name The base name of a file.|A file base name is the file name stripped of its directory specification and extension. FALSE http://edamontology.org/data_1050 beta12orEarlier data_1060 The base name of a file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1061 QSAR descriptor name Name of a QSAR descriptor. FALSE http://edamontology.org/data_2110|http://edamontology.org/data_2099 beta12orEarlier data_1061 Name of a QSAR descriptor. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1062 Database entry identifier An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.|This concept is required for completeness. It should never have child concepts. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1062 http://edamontology.org/data_0842 An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1063 Sequence identifier An identifier of molecular sequence(s) or entries from a molecular sequence database. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1063 An identifier of molecular sequence(s) or entries from a molecular sequence database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1064 Sequence set ID An identifier of a set of molecular sequence(s). FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1064 An identifier of a set of molecular sequence(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1065 Sequence signature identifier Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1065 http://edamontology.org/data_1114|http://edamontology.org/data_1115 Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1066 Sequence alignment ID "Identifier of a molecular sequence alignment, for example a record from an alignment database." FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1066 "Identifier of a molecular sequence alignment, for example a record from an alignment database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1067 Phylogenetic distance matrix identifier Identifier of a phylogenetic distance matrix. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1067 http://edamontology.org/data_0976 Identifier of a phylogenetic distance matrix. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1068 Phylogenetic tree ID Identifier of a phylogenetic tree for example from a phylogenetic tree database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1068 Identifier of a phylogenetic tree for example from a phylogenetic tree database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1069 Comparison matrix identifier Substitution matrix identifier An identifier of a comparison matrix. FALSE http://edamontology.org/data_3036 beta12orEarlier data_1069 An identifier of a comparison matrix. Substitution matrix identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1070 Structure ID "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." FALSE http://edamontology.org/data_3035|http://edamontology.org/data_2091 beta12orEarlier data_1070 "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1071 Structural (3D) profile ID Structural profile identifier Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1071 Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). Structural profile identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1072 Structure alignment ID Identifier of an entry from a database of tertiary structure alignments. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1072 Identifier of an entry from a database of tertiary structure alignments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1073 Amino acid index ID Identifier of an index of amino acid physicochemical and biochemical property data. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_3036 beta12orEarlier data_1073 Identifier of an index of amino acid physicochemical and biochemical property data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1074 Protein interaction ID Molecular interaction ID Identifier of a report of protein interactions from a protein interaction database (typically). FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1074 Molecular interaction ID Identifier of a report of protein interactions from a protein interaction database (typically). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1075 Protein family identifier Protein secondary database record identifier Identifier of a protein family. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1075 Identifier of a protein family. Protein secondary database record identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1076 Codon usage table name Unique name of a codon usage table. FALSE http://edamontology.org/data_2111|http://edamontology.org/data_2099 beta12orEarlier data_1076 Unique name of a codon usage table. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1077 Transcription factor identifier Identifier of a transcription factor (or a TF binding site). FALSE http://edamontology.org/data_0989|http://edamontology.org/data_0976 beta12orEarlier data_1077 Identifier of a transcription factor (or a TF binding site). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1078 Experiment annotation ID Identifier of an entry from a database of microarray data. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1078 Identifier of an entry from a database of microarray data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1079 Electron microscopy model ID Identifier of an entry from a database of electron microscopy data. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1079 Identifier of an entry from a database of electron microscopy data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1080 Gene expression report ID Gene expression profile identifier Accession of a report of gene expression (e.g. a gene expression profile) from a database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1080 Accession of a report of gene expression (e.g. a gene expression profile) from a database. Gene expression profile identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1081 Genotype and phenotype annotation ID Identifier of an entry from a database of genotypes and phenotypes. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1081 Identifier of an entry from a database of genotypes and phenotypes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1082 Pathway or network identifier Identifier of an entry from a database of biological pathways or networks. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1082 Identifier of an entry from a database of biological pathways or networks. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1083 Workflow ID "Identifier of a biological or biomedical workflow, typically from a database of workflows." FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1083 "Identifier of a biological or biomedical workflow, typically from a database of workflows." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1084 Data resource definition ID Data resource definition identifier Identifier of a data type definition from some provider. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1084 Identifier of a data type definition from some provider. Data resource definition identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1085 Biological model ID Biological model identifier "Identifier of a mathematical model, typically an entry from a database." FALSE http://edamontology.org/data_0976 beta12orEarlier data_1085 "Identifier of a mathematical model, typically an entry from a database." Biological model identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1086 Compound identifier Small molecule identifier|Chemical compound identifier Identifier of an entry from a database of chemicals. FALSE http://edamontology.org/data_0982 beta12orEarlier data_1086 Identifier of an entry from a database of chemicals. Small molecule identifier|Chemical compound identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1087 Ontology concept ID A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. FALSE http://edamontology.org/data_3025|http://edamontology.org/data_2091 beta12orEarlier data_1087 A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1088 Article ID Article identifier Unique identifier of a scientific article. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1088 Unique identifier of a scientific article. Article identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1089 FlyBase ID Identifier of an object from the FlyBase database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_1089 Identifier of an object from the FlyBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data FB[a-zA-Z_0-9]{2}[0-9]{7} http://edamontology.org/data_1091 WormBase name "Name of an object from the WormBase database, usually a human-readable name." FALSE http://edamontology.org/data_2099|http://edamontology.org/data_2113 beta12orEarlier data_1091 "Name of an object from the WormBase database, usually a human-readable name." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1092 WormBase class Class of an object from the WormBase database.|A WormBase class describes the type of object such as 'sequence' or 'protein'. FALSE http://edamontology.org/data_2113 beta12orEarlier data_1092 Class of an object from the WormBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1093 Sequence accession Sequence accession number "A persistent, unique identifier of a molecular sequence database entry." FALSE http://edamontology.org/data_2091|http://edamontology.org/data_1063 beta12orEarlier data_1093 "A persistent, unique identifier of a molecular sequence database entry." Sequence accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1094 Sequence type "A label (text token) describing a type of molecular sequence.|Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1094 http://edamontology.org/data_0842 A label (text token) describing a type of molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1095 EMBOSS Uniform Sequence Address EMBOSS USA The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. FALSE http://edamontology.org/data_1063|http://edamontology.org/data_2099 beta12orEarlier data_1095 The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. EMBOSS USA http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1096 Sequence accession (protein) Protein sequence accession number Accession number of a protein sequence database entry. FALSE http://edamontology.org/data_1093 beta12orEarlier data_1096 Accession number of a protein sequence database entry. Protein sequence accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1097 Sequence accession (nucleic acid) Nucleotide sequence accession number Accession number of a nucleotide sequence database entry. FALSE http://edamontology.org/data_1093 beta12orEarlier data_1097 Accession number of a nucleotide sequence database entry. Nucleotide sequence accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1098 RefSeq accession RefSeq ID Accession number of a RefSeq database entry. FALSE http://edamontology.org/data_2362 beta12orEarlier data_1098 Accession number of a RefSeq database entry. RefSeq ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ http://edamontology.org/data_1099 UniProt accession (extended) Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier Q7M1G0|P43353-2|P01012.107 data_1099 http://edamontology.org/data_3021 Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. http://purl.obolibrary.org/obo/edam#obsolete 1.0 [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]+ http://edamontology.org/data_1100 PIR identifier PIR ID|PIR accession number An identifier of PIR sequence database entry. FALSE http://edamontology.org/data_1096 beta12orEarlier data_1100 An identifier of PIR sequence database entry. PIR ID|PIR accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1101 TREMBL accession Identifier of a TREMBL sequence database entry. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1101 Identifier of a TREMBL sequence database entry. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_3021 1.2 http://edamontology.org/data_1102 Gramene primary identifier Gramene primary ID Primary identifier of a Gramene database entry. FALSE http://edamontology.org/data_2915 beta12orEarlier data_1102 Primary identifier of a Gramene database entry. Gramene primary ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1103 EMBL/GenBank/DDBJ ID Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. FALSE http://edamontology.org/data_1097 beta12orEarlier data_1103 Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1104 Sequence cluster ID (UniGene) UniGene cluster ID|UniGene cluster id|UniGene identifier|UniGene ID A unique identifier of an entry (gene cluster) from the NCBI UniGene database. FALSE http://edamontology.org/data_1112 beta12orEarlier data_1104 A unique identifier of an entry (gene cluster) from the NCBI UniGene database. UniGene cluster ID|UniGene cluster id|UniGene identifier|UniGene ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1105 dbEST accession dbEST ID Identifier of a dbEST database entry. FALSE http://edamontology.org/data_2728|http://edamontology.org/data_2292 beta12orEarlier data_1105 Identifier of a dbEST database entry. dbEST ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1106 dbSNP ID dbSNP identifier Identifier of a dbSNP database entry. FALSE http://edamontology.org/data_2294 beta12orEarlier data_1106 Identifier of a dbSNP database entry. dbSNP identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1110 EMBOSS sequence type The EMBOSS type of a molecular sequence.|See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1110 The EMBOSS type of a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1111 EMBOSS listfile List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1111 http://edamontology.org/data_2872 List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1112 Sequence cluster ID An identifier of a cluster of molecular sequence(s). FALSE http://edamontology.org/data_1064 beta12orEarlier data_1112 An identifier of a cluster of molecular sequence(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1113 Sequence cluster ID (COG) COG ID Unique identifier of an entry from the COG database. FALSE http://edamontology.org/data_1112 beta12orEarlier data_1113 Unique identifier of an entry from the COG database. COG ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1114 Sequence motif identifier "Identifier of a sequence motif, for example an entry from a motif database." FALSE http://edamontology.org/data_0976 beta12orEarlier data_1114 "Identifier of a sequence motif, for example an entry from a motif database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1115 Sequence profile ID Identifier of a sequence profile.|A sequence profile typically represents a sequence alignment. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1115 Identifier of a sequence profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1116 ELM ID Identifier of an entry from the ELMdb database of protein functional sites. FALSE http://edamontology.org/data_1114 beta12orEarlier data_1116 Identifier of an entry from the ELMdb database of protein functional sites. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1117 Prosite accession number Prosite ID Accession number of an entry from the Prosite database. FALSE http://edamontology.org/data_1114 beta12orEarlier data_1117 Accession number of an entry from the Prosite database. Prosite ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PS[0-9]{5} http://edamontology.org/data_1118 HMMER hidden Markov model ID Unique identifier or name of a HMMER hidden Markov model. FALSE http://edamontology.org/data_1115 beta12orEarlier data_1118 Unique identifier or name of a HMMER hidden Markov model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1119 JASPAR profile ID Unique identifier or name of a profile from the JASPAR database. FALSE http://edamontology.org/data_1115 beta12orEarlier data_1119 Unique identifier or name of a profile from the JASPAR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1120 Sequence alignment type "A label (text token) describing the type of a sequence alignment.|Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1120 http://edamontology.org/data_0842 A label (text token) describing the type of a sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1121 BLAST sequence alignment type The type of a BLAST sequence alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1121 The type of a BLAST sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1122 Phylogenetic tree type "A label (text token) describing the type of a phylogenetic tree.|For example 'nj', 'upgmp' etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier nj|upgmp data_1122 http://edamontology.org/data_0842 A label (text token) describing the type of a phylogenetic tree. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1123 TreeBASE study accession number Accession number of an entry from the TreeBASE database. FALSE http://edamontology.org/data_1068 beta12orEarlier data_1123 Accession number of an entry from the TreeBASE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1124 TreeFam accession number Accession number of an entry from the TreeFam database. FALSE http://edamontology.org/data_1068 beta12orEarlier data_1124 Accession number of an entry from the TreeFam database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1125 Comparison matrix type "A label (text token) describing the type of a comparison matrix.|For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier blosum|pam|gonnet|id data_1125 http://edamontology.org/data_0842 A label (text token) describing the type of a comparison matrix. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1126 Comparison matrix name Substitution matrix name Unique name or identifier of a comparison matrix.|See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. FALSE http://edamontology.org/data_1069|http://edamontology.org/data_2099 beta12orEarlier data_1126 Unique name or identifier of a comparison matrix. Substitution matrix name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1127 PDB ID PDB identifier|PDBID An identifier of an entry from the PDB database. FALSE http://edamontology.org/data_1070 beta12orEarlier data_1127 An identifier of an entry from the PDB database. PDB identifier|PDBID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9]{4} http://edamontology.org/data_1128 AAindex ID Identifier of an entry from the AAindex database. FALSE http://edamontology.org/data_1073 beta12orEarlier data_1128 Identifier of an entry from the AAindex database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1129 BIND accession number Accession number of an entry from the BIND database. FALSE http://edamontology.org/data_1074 beta12orEarlier data_1129 Accession number of an entry from the BIND database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1130 IntAct accession number Accession number of an entry from the IntAct database. FALSE http://edamontology.org/data_1074 beta12orEarlier data_1130 Accession number of an entry from the IntAct database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data EBI-[0-9]+ http://edamontology.org/data_1131 Protein family name Name of a protein family. FALSE http://edamontology.org/data_1075|http://edamontology.org/data_2099 beta12orEarlier data_1131 Name of a protein family. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1132 InterPro entry name "Name of an InterPro entry, usually indicating the type of protein matches for that entry." FALSE http://edamontology.org/data_1131 beta12orEarlier data_1132 "Name of an InterPro entry, usually indicating the type of protein matches for that entry." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1133 InterPro accession InterPro primary accession|InterPro primary accession number Primary accession number of an InterPro entry.|Every InterPro entry has a unique accession number to provide a persistent citation of database records. FALSE http://edamontology.org/data_2910 beta12orEarlier IPR015590 data_1133 Primary accession number of an InterPro entry. InterPro primary accession|InterPro primary accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data IPR[0-9]{6} http://edamontology.org/data_1134 InterPro secondary accession InterPro secondary accession number Secondary accession number of an InterPro entry. FALSE http://edamontology.org/data_1133 beta12orEarlier data_1134 Secondary accession number of an InterPro entry. InterPro secondary accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1135 Gene3D ID Unique identifier of an entry from the Gene3D database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1135 Unique identifier of an entry from the Gene3D database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1136 PIRSF ID Unique identifier of an entry from the PIRSF database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1136 Unique identifier of an entry from the PIRSF database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PIRSF[0-9]{6} http://edamontology.org/data_1137 PRINTS code The unique identifier of an entry in the PRINTS database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1137 The unique identifier of an entry in the PRINTS database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PR[0-9]{5} http://edamontology.org/data_1138 Pfam accession number Accession number of a Pfam entry. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1138 Accession number of a Pfam entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PF[0-9]{5} http://edamontology.org/data_1139 SMART accession number Accession number of an entry from the SMART database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1139 Accession number of an entry from the SMART database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data SM[0-9]{5} http://edamontology.org/data_1140 Superfamily hidden Markov model number Unique identifier (number) of a hidden Markov model from the Superfamily database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1140 Unique identifier (number) of a hidden Markov model from the Superfamily database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1141 TIGRFam ID TIGRFam accession number Accession number of an entry (family) from the TIGRFam database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1141 Accession number of an entry (family) from the TIGRFam database. TIGRFam accession number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1142 ProDom accession number A ProDom domain family accession number.|ProDom is a protein domain family database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_1142 A ProDom domain family accession number. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PD[0-9]+ http://edamontology.org/data_1143 TRANSFAC accession number Identifier of an entry from the TRANSFAC database. FALSE http://edamontology.org/data_2911 beta12orEarlier data_1143 Identifier of an entry from the TRANSFAC database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1144 ArrayExpress accession number ArrayExpress experiment ID Accession number of an entry from the ArrayExpress database. FALSE http://edamontology.org/data_1078 beta12orEarlier data_1144 Accession number of an entry from the ArrayExpress database. ArrayExpress experiment ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ http://edamontology.org/data_1145 PRIDE experiment accession number PRIDE experiment accession number. FALSE http://edamontology.org/data_1078 beta12orEarlier data_1145 PRIDE experiment accession number. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_1146 EMDB ID Identifier of an entry from the EMDB electron microscopy database. FALSE http://edamontology.org/data_1079 beta12orEarlier data_1146 Identifier of an entry from the EMDB electron microscopy database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1147 GEO accession number Accession number of an entry from the GEO database. FALSE http://edamontology.org/data_1080 beta12orEarlier data_1147 Accession number of an entry from the GEO database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data o^GDS[0-9]+ http://edamontology.org/data_1148 GermOnline ID Identifier of an entry from the GermOnline database. FALSE http://edamontology.org/data_1080 beta12orEarlier data_1148 Identifier of an entry from the GermOnline database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1149 EMAGE ID Identifier of an entry from the EMAGE database. FALSE http://edamontology.org/data_1080 beta12orEarlier data_1149 Identifier of an entry from the EMAGE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1150 Disease ID Accession number of an entry from a database of disease. FALSE http://edamontology.org/data_3667|http://edamontology.org/data_2091 beta12orEarlier data_1150 Accession number of an entry from a database of disease. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1151 HGVbase ID Identifier of an entry from the HGVbase database. FALSE http://edamontology.org/data_1081 beta12orEarlier data_1151 Identifier of an entry from the HGVbase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1152 HIVDB identifier Identifier of an entry from the HIVDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1152 http://edamontology.org/data_0842 Identifier of an entry from the HIVDB database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1153 OMIM ID Identifier of an entry from the OMIM database. FALSE http://edamontology.org/data_1081 beta12orEarlier data_1153 Identifier of an entry from the OMIM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [*#+%^]?[0-9]{6} http://edamontology.org/data_1154 KEGG object identifier Unique identifier of an object from one of the KEGG databases (excluding the GENES division). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_1154 Unique identifier of an object from one of the KEGG databases (excluding the GENES division). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1155 Pathway ID (reactome) Reactome ID Identifier of an entry from the Reactome database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_1155 Identifier of an entry from the Reactome database. Reactome ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data REACT_[0-9]+(.[0-9]+)? http://edamontology.org/data_1156 Pathway ID (aMAZE) aMAZE ID Identifier of an entry from the aMAZE database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1156 http://edamontology.org/data_1082 Identifier of an entry from the aMAZE database. aMAZE ID http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1157 Pathway ID (BioCyc) BioCyc pathway ID Identifier of an pathway from the BioCyc biological pathways database. FALSE http://edamontology.org/data_2365|http://edamontology.org/data_2104 beta12orEarlier data_1157 Identifier of an pathway from the BioCyc biological pathways database. BioCyc pathway ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1158 Pathway ID (INOH) INOH identifier Identifier of an entry from the INOH database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_1158 Identifier of an entry from the INOH database. INOH identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1159 Pathway ID (PATIKA) PATIKA ID Identifier of an entry from the PATIKA database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_1159 Identifier of an entry from the PATIKA database. PATIKA ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1160 Pathway ID (CPDB) CPDB ID "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.|This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined." FALSE http://edamontology.org/data_2365 beta12orEarlier data_1160 "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." CPDB ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1161 Pathway ID (Panther) Panther Pathways ID Identifier of a biological pathway from the Panther Pathways database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_1161 Identifier of a biological pathway from the Panther Pathways database. Panther Pathways ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PTHR[0-9]{5} http://edamontology.org/data_1162 MIRIAM identifier Unique identifier of a MIRIAM data resource.|This is the identifier used internally by MIRIAM for a data type. FALSE http://edamontology.org/data_2902 beta12orEarlier MIR:00100005 data_1162 Unique identifier of a MIRIAM data resource. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data MIR:[0-9]{8} http://edamontology.org/data_1163 MIRIAM data type name The name of a data type from the MIRIAM database. FALSE http://edamontology.org/data_2253 beta12orEarlier data_1163 The name of a data type from the MIRIAM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1164 MIRIAM URI identifiers.org synonym "The URI (URL or URN) of a data entity from the MIRIAM database.|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." FALSE http://edamontology.org/data_1047|http://edamontology.org/data_2902 beta12orEarlier urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 data_1164 The URI (URL or URN) of a data entity from the MIRIAM database. identifiers.org synonym http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1165 MIRIAM data type primary name The primary name of a data type from the MIRIAM database.|The primary name of a MIRIAM data type is taken from a controlled vocabulary. FALSE http://edamontology.org/data_1163 beta12orEarlier UniProt|Enzyme Nomenclature data_1165 The primary name of a data type from the MIRIAM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1166 MIRIAM data type synonymous name A synonymous name of a data type from the MIRIAM database.|A synonymous name for a MIRIAM data type taken from a controlled vocabulary. FALSE http://edamontology.org/data_1163 beta12orEarlier data_1166 A synonymous name of a data type from the MIRIAM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1167 Taverna workflow ID Unique identifier of a Taverna workflow. FALSE http://edamontology.org/data_1083 beta12orEarlier data_1167 Unique identifier of a Taverna workflow. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1170 Biological model name Name of a biological (mathematical) model. FALSE http://edamontology.org/data_1085|http://edamontology.org/data_2099 beta12orEarlier data_1170 Name of a biological (mathematical) model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1171 BioModel ID Unique identifier of an entry from the BioModel database. FALSE http://edamontology.org/data_2891 beta12orEarlier data_1171 Unique identifier of an entry from the BioModel database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data (BIOMD|MODEL)[0-9]{10} http://edamontology.org/data_1172 PubChem CID PubChem compound accession identifier "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." FALSE http://edamontology.org/data_2639|http://edamontology.org/data_2894 beta12orEarlier data_1172 "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." PubChem compound accession identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_1173 ChemSpider ID Identifier of an entry from the ChemSpider database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_1173 Identifier of an entry from the ChemSpider database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_1174 ChEBI ID ChEBI IDs|ChEBI identifier Identifier of an entry from the ChEBI database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_1174 Identifier of an entry from the ChEBI database. ChEBI IDs|ChEBI identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data CHEBI:[0-9]+ http://edamontology.org/data_1175 BioPax concept ID An identifier of a concept from the BioPax ontology. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1175 An identifier of a concept from the BioPax ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1176 GO concept ID GO concept identifier An identifier of a concept from The Gene Ontology. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1176 An identifier of a concept from The Gene Ontology. GO concept identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]{7}|GO:[0-9]{7} http://edamontology.org/data_1177 MeSH concept ID An identifier of a concept from the MeSH vocabulary. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1177 An identifier of a concept from the MeSH vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1178 HGNC concept ID An identifier of a concept from the HGNC controlled vocabulary. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1178 An identifier of a concept from the HGNC controlled vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1179 NCBI taxonomy ID NCBI taxonomy identifier|NCBI tax ID "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." FALSE http://edamontology.org/data_2908|http://edamontology.org/data_1087 beta12orEarlier 9662|3483|182682 data_1179 "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." NCBI taxonomy identifier|NCBI tax ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[1-9][0-9]{0,8}" http://edamontology.org/data_1180 Plant Ontology concept ID An identifier of a concept from the Plant Ontology (PO). FALSE http://edamontology.org/data_1087 beta12orEarlier data_1180 An identifier of a concept from the Plant Ontology (PO). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1181 UMLS concept ID An identifier of a concept from the UMLS vocabulary. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1181 An identifier of a concept from the UMLS vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1182 FMA concept ID "An identifier of a concept from Foundational Model of Anatomy.|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." FALSE http://edamontology.org/data_1087 beta12orEarlier data_1182 An identifier of a concept from Foundational Model of Anatomy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data FMA:[0-9]+ http://edamontology.org/data_1183 EMAP concept ID An identifier of a concept from the EMAP mouse ontology. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1183 An identifier of a concept from the EMAP mouse ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1184 ChEBI concept ID An identifier of a concept from the ChEBI ontology. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1184 An identifier of a concept from the ChEBI ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1185 MGED concept ID An identifier of a concept from the MGED ontology. FALSE http://edamontology.org/data_1087 beta12orEarlier data_1185 An identifier of a concept from the MGED ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1186 myGrid concept ID "An identifier of a concept from the myGrid ontology.|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." FALSE http://edamontology.org/data_1087 beta12orEarlier data_1186 An identifier of a concept from the myGrid ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1187 PubMed ID PMID PubMed unique identifier of an article. FALSE http://edamontology.org/data_1088 beta12orEarlier 4963447 data_1187 PubMed unique identifier of an article. PMID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[1-9][0-9]{0,8}" http://edamontology.org/data_1188 DOI Digital Object Identifier Digital Object Identifier (DOI) of a published article. FALSE http://edamontology.org/data_1088 beta12orEarlier data_1188 Digital Object Identifier (DOI) of a published article. Digital Object Identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data (doi:)?[0-9]{2}\.[0-9]{4}/.* http://edamontology.org/data_1189 Medline UI Medline unique identifier Medline UI (unique identifier) of an article.|The use of Medline UI has been replaced by the PubMed unique identifier. FALSE http://edamontology.org/data_1088 beta12orEarlier data_1189 Medline UI (unique identifier) of an article. Medline unique identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1190 Tool name "The name of a computer package, application, method or function." FALSE http://edamontology.org/data_0977 beta12orEarlier data_1190 "The name of a computer package, application, method or function." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1191 Tool name (signature) "The unique name of a signature (sequence classifier) method.|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." FALSE http://edamontology.org/data_1190 beta12orEarlier data_1191 The unique name of a signature (sequence classifier) method. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1192 Tool name (BLAST) BLAST name "The name of a BLAST tool.|This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'." FALSE http://edamontology.org/data_1190 beta12orEarlier data_1192 The name of a BLAST tool. BLAST name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1193 Tool name (FASTA) "The name of a FASTA tool.|This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'." FALSE http://edamontology.org/data_1190 beta12orEarlier data_1193 The name of a FASTA tool. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1194 Tool name (EMBOSS) The name of an EMBOSS application. FALSE http://edamontology.org/data_1190 beta12orEarlier data_1194 The name of an EMBOSS application. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1195 Tool name (EMBASSY package) The name of an EMBASSY package. FALSE http://edamontology.org/data_1190 beta12orEarlier data_1195 The name of an EMBASSY package. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1201 QSAR descriptor (constitutional) QSAR constitutional descriptor A QSAR constitutional descriptor. FALSE http://edamontology.org/data_0847 beta12orEarlier data_1201 A QSAR constitutional descriptor. QSAR constitutional descriptor http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1202 QSAR descriptor (electronic) QSAR electronic descriptor A QSAR electronic descriptor. FALSE http://edamontology.org/data_0847 beta12orEarlier data_1202 A QSAR electronic descriptor. QSAR electronic descriptor http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1203 QSAR descriptor (geometrical) QSAR geometrical descriptor A QSAR geometrical descriptor. FALSE http://edamontology.org/data_0847 beta12orEarlier data_1203 A QSAR geometrical descriptor. QSAR geometrical descriptor http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1204 QSAR descriptor (topological) QSAR topological descriptor A QSAR topological descriptor. FALSE http://edamontology.org/data_0847 beta12orEarlier data_1204 A QSAR topological descriptor. QSAR topological descriptor http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1205 QSAR descriptor (molecular) QSAR molecular descriptor A QSAR molecular descriptor. FALSE http://edamontology.org/data_0847 beta12orEarlier data_1205 A QSAR molecular descriptor. QSAR molecular descriptor http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1233 Sequence set (protein) Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. FALSE http://edamontology.org/data_0850 beta12orEarlier data_1233 Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1234 Sequence set (nucleic acid) Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. FALSE http://edamontology.org/data_0850 beta12orEarlier data_1234 Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1235 Sequence cluster "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.|The cluster might include sequences identifiers, short descriptions, alignment and summary information." FALSE http://edamontology.org/data_0850 beta12orEarlier data_1235 A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1236 Psiblast checkpoint file A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.|A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1236 http://edamontology.org/data_0850 A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1237 HMMER synthetic sequences set Sequences generated by HMMER package in FASTA-style format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1237 http://edamontology.org/data_0850 Sequences generated by HMMER package in FASTA-style format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1238 Proteolytic digest A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. FALSE http://edamontology.org/data_1233 beta12orEarlier data_1238 A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1239 Restriction digest Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. FALSE http://edamontology.org/data_1234 beta12orEarlier data_1239 SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1240 PCR primers "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." FALSE http://edamontology.org/data_1234 beta12orEarlier data_1240 "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1241 vectorstrip cloning vector definition file "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1241 http://edamontology.org/data_0850 "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1242 Primer3 internal oligo mishybridizing library "A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1242 http://edamontology.org/data_0850 "A library of nucleotide sequences to avoid during hybridisation events. Hybridisation 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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1243 Primer3 mispriming library file "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1243 http://edamontology.org/data_0850 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1244 primersearch primer pairs sequence record "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1244 http://edamontology.org/data_0850 "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1245 Sequence cluster (protein) Protein sequence cluster "A cluster of protein sequences.|The sequences are typically related, for example a family of sequences." FALSE http://edamontology.org/data_1233|http://edamontology.org/data_1235 beta12orEarlier data_1245 A cluster of protein sequences. Protein sequence cluster http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1246 Sequence cluster (nucleic acid) Nucleotide sequence cluster "A cluster of nucleotide sequences.|The sequences are typically related, for example a family of sequences." FALSE http://edamontology.org/data_1234|http://edamontology.org/data_1235 beta12orEarlier data_1246 A cluster of nucleotide sequences. Nucleotide sequence cluster http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1249 Sequence length "The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths." FALSE http://edamontology.org/data_2534 beta12orEarlier data_1249 "The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1250 Word size Size of a sequence word.|Word size is used for example in word-based sequence database search methods. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1250 http://edamontology.org/data_1249 Size of a sequence word. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1251 Window size Size of a sequence window.|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. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1251 http://edamontology.org/data_1249 Size of a sequence window. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1252 Sequence length range Specification of range(s) of length of sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1252 http://edamontology.org/data_1249 Specification of range(s) of length of sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1253 Sequence information report "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1253 "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2955 beta12orEarlier http://edamontology.org/data_1254 Sequence property Sequence properties report "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." FALSE http://edamontology.org/data_2955 beta12orEarlier data_1254 "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." Sequence properties report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1255 Sequence features Feature record|Sequence features report|General sequence features|Features|SO:0000110 "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.|This includes annotation of positional sequence features, organised 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." FALSE http://edamontology.org/data_0006 beta12orEarlier data_1255 "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." Feature record|Sequence features report|General sequence features|Features SO:0000110 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1256 Sequence features (comparative) "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1256 http://edamontology.org/data_1255 "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1257 Sequence property (protein) A report of general sequence properties derived from protein sequence data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1257 http://edamontology.org/data_0897 A report of general sequence properties derived from protein sequence data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1258 Sequence property (nucleic acid) A report of general sequence properties derived from nucleotide sequence data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1258 http://edamontology.org/data_0912 A report of general sequence properties derived from nucleotide sequence data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1259 Sequence complexity report Sequence property (complexity) "A report on sequence complexity, for example low-complexity or repeat regions in sequences." FALSE http://edamontology.org/data_1254 beta12orEarlier data_1259 "A report on sequence complexity, for example low-complexity or repeat regions in sequences." Sequence property (complexity) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1260 Sequence ambiguity report Sequence property (ambiguity) A report on ambiguity in molecular sequence(s). FALSE http://edamontology.org/data_1254 beta12orEarlier data_1260 A report on ambiguity in molecular sequence(s). Sequence property (ambiguity) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1261 Sequence composition report Sequence property (composition) A report (typically a table) on character or word composition / frequency of a molecular sequence(s). FALSE http://edamontology.org/data_1254 beta12orEarlier data_1261 A report (typically a table) on character or word composition / frequency of a molecular sequence(s). Sequence property (composition) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1262 Peptide molecular weight hits A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. FALSE http://edamontology.org/data_1233 beta12orEarlier data_1262 A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1263 Base position variability plot A plot of third base position variability in a nucleotide sequence. FALSE http://edamontology.org/data_1261 beta12orEarlier data_1263 A plot of third base position variability in a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1264 Sequence composition table A table of character or word composition / frequency of a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1264 http://edamontology.org/data_1261 A table of character or word composition / frequency of a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1265 Base frequencies table A table of base frequencies of a nucleotide sequence. FALSE http://edamontology.org/data_2082|http://edamontology.org/data_1261 beta12orEarlier data_1265 A table of base frequencies of a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1266 Base word frequencies table A table of word composition of a nucleotide sequence. FALSE http://edamontology.org/data_2082|http://edamontology.org/data_1261 beta12orEarlier data_1266 A table of word composition of a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1267 Amino acid frequencies table Sequence composition (amino acid frequencies) A table of amino acid frequencies of a protein sequence. FALSE http://edamontology.org/data_2082|http://edamontology.org/data_1261 beta12orEarlier data_1267 A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1268 Amino acid word frequencies table Sequence composition (amino acid words) A table of amino acid word composition of a protein sequence. FALSE http://edamontology.org/data_2082|http://edamontology.org/data_1261 beta12orEarlier data_1268 A table of amino acid word composition of a protein sequence. Sequence composition (amino acid words) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1269 DAS sequence feature annotation Annotation of a molecular sequence in DAS format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1269 http://edamontology.org/format_1978 Annotation of a molecular sequence in DAS format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1270 Feature table Sequence feature table "Annotation of positional sequence features, organised into a standard feature table." FALSE http://edamontology.org/data_1255 beta12orEarlier data_1270 "Annotation of positional sequence features, organised into a standard feature table." Sequence feature table http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1274 Map DNA map A map of (typically one) DNA sequence annotated with positional or non-positional features. FALSE http://edamontology.org/data_2019 beta12orEarlier data_1274 A map of (typically one) DNA sequence annotated with positional or non-positional features. DNA map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1276 Nucleic acid features Nucleic acid feature table|Feature table (nucleic acid)|Genome features|Genomic features An informative report on intrinsic positional features of a nucleotide sequence.|This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. FALSE http://edamontology.org/data_1255|http://edamontology.org/data_2084 beta12orEarlier data_1276 An informative report on intrinsic positional features of a nucleotide sequence. Nucleic acid feature table|Feature table (nucleic acid) Genome features|Genomic features http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1277 Protein features Protein feature table|Feature table (protein) An informative report on intrinsic positional features of a protein sequence.|This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. FALSE http://edamontology.org/data_1255|http://edamontology.org/data_0896 beta12orEarlier data_1277 An informative report on intrinsic positional features of a protein sequence. Protein feature table|Feature table (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1278 Genetic map Linkage map "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.|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." FALSE http://edamontology.org/data_1274 beta12orEarlier data_1278 Moby:GeneticMap "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." Linkage map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1279 Sequence map "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.|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." FALSE http://edamontology.org/data_1280 beta12orEarlier data_1279 "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1280 Physical map "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.|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." FALSE http://edamontology.org/data_1274 beta12orEarlier data_1280 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1281 Sequence signature map "Image of a sequence with matches to signatures, motifs or profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1281 "Image of a sequence with matches to signatures, motifs or profiles." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2969 beta12orEarlier http://edamontology.org/data_1283 Cytogenetic map Cytogenic map|Chromosome map|Cytologic map "A map showing banding patterns derived from direct observation of a stained chromosome.|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." FALSE http://edamontology.org/data_1280 beta12orEarlier data_1283 A map showing banding patterns derived from direct observation of a stained chromosome. Cytogenic map|Chromosome map|Cytologic map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1284 DNA transduction map A gene map showing distances between loci based on relative cotransduction frequencies. FALSE http://edamontology.org/data_1278 beta12orEarlier data_1284 A gene map showing distances between loci based on relative cotransduction frequencies. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1285 Gene map "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." FALSE http://edamontology.org/data_1279 beta12orEarlier data_1285 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1286 Plasmid map Sequence map of a plasmid (circular DNA). FALSE http://edamontology.org/data_1279 beta12orEarlier data_1286 Sequence map of a plasmid (circular DNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1288 Genome map Sequence map of a whole genome. FALSE http://edamontology.org/data_1279 beta12orEarlier data_1288 Sequence map of a whole genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1289 Restriction map Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. FALSE http://edamontology.org/data_1279|http://edamontology.org/data_2969 beta12orEarlier data_1289 Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1290 InterPro compact match image "Image showing matches between protein sequence(s) and InterPro Entries.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1290 Image showing matches between protein sequence(s) and InterPro Entries. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2969 beta12orEarlier http://edamontology.org/data_1291 InterPro detailed match image "Image showing detailed information on matches between protein sequence(s) and InterPro Entries.|The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1291 Image showing detailed information on matches between protein sequence(s) and InterPro Entries. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2969 beta12orEarlier http://edamontology.org/data_1292 InterPro architecture image "Image showing the architecture of InterPro domains in a protein sequence.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1292 Image showing the architecture of InterPro domains in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2969 beta12orEarlier http://edamontology.org/data_1293 SMART protein schematic SMART protein schematic in PNG format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1293 http://edamontology.org/data_2969 SMART protein schematic in PNG format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1294 GlobPlot domain image Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1294 Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2969 beta12orEarlier http://edamontology.org/data_1298 Sequence motif matches "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1298 "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0858 1.8 http://edamontology.org/data_1299 Sequence features (repeats) "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.|The report might include derived data map such as classification, annotation, organisation, periodicity etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1299 http://edamontology.org/data_1255 Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1300 Gene and transcript structure (report) "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1300 http://edamontology.org/data_0916 "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://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1301 Mobile genetic elements regions of a nucleic acid sequence containing mobile genetic elements. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1301 regions of a nucleic acid sequence containing mobile genetic elements. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1302 Nucleic acid features report (PolyA signal or site) regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1302 regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1303 Nucleic acid features (quadruplexes) A report on quadruplex-forming motifs in a nucleotide sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1303 http://edamontology.org/data_3128 A report on quadruplex-forming motifs in a nucleotide sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1304 Nucleic acid features report (CpG island and isochore) CpG rich regions (isochores) in a nucleotide sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1304 CpG rich regions (isochores) in a nucleotide sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1305 Nucleic acid features report (restriction sites) restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1305 restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1306 Nucleosome exclusion sequences Report on nucleosome formation potential or exclusion sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1306 Report on nucleosome formation potential or exclusion sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1307 Nucleic acid features report (splice sites) splice sites in a nucleotide sequence or alternative RNA splicing events. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1307 splice sites in a nucleotide sequence or alternative RNA splicing events. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1308 Nucleic acid features report (matrix/scaffold attachment sites) matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1308 matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1309 Gene features (exonic splicing enhancer) A report on exonic splicing enhancers (ESE) in an exon. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1309 A report on exonic splicing enhancers (ESE) in an exon. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 beta13 http://edamontology.org/data_1310 Nucleic acid features (microRNA) "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1310 http://edamontology.org/data_1276 "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1311 Gene features report (operon) "operons (operators, promoters and genes) from a bacterial genome." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1311 "operons (operators, promoters and genes) from a bacterial genome." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1312 Nucleic acid features report (promoters) "whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1312 "whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1313 Coding region "protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1313 "protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1314 Gene features (SECIS element) A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1314 http://edamontology.org/data_0916 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1315 Transcription factor binding sites transcription factor binding sites (TFBS) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1315 transcription factor binding sites (TFBS) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_1321 Protein features (sites) "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.|Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1321 http://edamontology.org/data_1277 "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1322 Protein features report (signal peptides) signal peptides or signal peptide cleavage sites in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1322 signal peptides or signal peptide cleavage sites in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1323 Protein features report (cleavage sites) cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1323 cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1324 Protein features (post-translation modifications) "post-translation modifications in a protein sequence, typically describing the specific sites involved." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1324 "post-translation modifications in a protein sequence, typically describing the specific sites involved." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1325 Protein features report (active sites) catalytic residues (active site) of an enzyme. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1325 catalytic residues (active site) of an enzyme. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1326 Protein features report (binding sites) "ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1326 "ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1327 Protein features (epitopes) "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.|Epitope mapping is commonly done during vaccine design." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1327 "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 beta13 http://edamontology.org/data_1328 Protein features report (nucleic acid binding sites) RNA and DNA-binding proteins and binding sites in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1328 RNA and DNA-binding proteins and binding sites in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1329 MHC Class I epitopes report A report on epitopes that bind to MHC class I molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1329 http://edamontology.org/data_1277 A report on epitopes that bind to MHC class I molecules. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1330 MHC Class II epitopes report A report on predicted epitopes that bind to MHC class II molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1330 http://edamontology.org/data_1277 A report on predicted epitopes that bind to MHC class II molecules. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1331 Protein features (PEST sites) A report or plot of PEST sites in a protein sequence.|'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1331 A report or plot of PEST sites in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 beta13 http://edamontology.org/data_1338 Sequence database hits scores list Scores from a sequence database search (for example a BLAST search). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1338 http://edamontology.org/data_0857 Scores from a sequence database search (for example a BLAST search). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1339 Sequence database hits alignments list Alignments from a sequence database search (for example a BLAST search). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1339 http://edamontology.org/data_0857 Alignments from a sequence database search (for example a BLAST search). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1340 Sequence database hits evaluation data A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1340 http://edamontology.org/data_0857 A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1344 MEME motif alphabet Alphabet for the motifs (patterns) that MEME will search for. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1344 http://edamontology.org/data_0950 Alphabet for the motifs (patterns) that MEME will search for. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1345 MEME background frequencies file MEME background frequencies file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1345 http://edamontology.org/data_0950 MEME background frequencies file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1346 MEME motifs directive file File of directives for ordering and spacing of MEME motifs. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1346 http://edamontology.org/data_0950 File of directives for ordering and spacing of MEME motifs. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1347 Dirichlet distribution Dirichlet distribution used by hidden Markov model analysis programs. FALSE http://edamontology.org/data_0950 beta12orEarlier data_1347 Dirichlet distribution used by hidden Markov model analysis programs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1348 HMM emission and transition counts "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1348 http://edamontology.org/data_3355|http://edamontology.org/data_3354 "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://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1352 Regular expression Regular expression pattern. FALSE http://edamontology.org/data_0006 beta12orEarlier data_1352 Regular expression pattern. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1353 Sequence motif Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. FALSE http://edamontology.org/data_0860 beta12orEarlier data_1353 Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1354 Sequence profile Some type of statistical model representing a (typically multiple) sequence alignment. FALSE http://edamontology.org/data_0860 beta12orEarlier data_1354 Some type of statistical model representing a (typically multiple) sequence alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1355 Protein signature Protein site signature|Protein repeat signature|Protein family signature|Protein domain signature|InterPro entry|Protein region signature An informative report about a specific or conserved protein sequence pattern. FALSE http://edamontology.org/data_2762 beta12orEarlier data_1355 An informative report about a specific or conserved protein sequence pattern. Protein site signature|Protein repeat signature|Protein family signature|Protein domain signature|InterPro entry|Protein region signature http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1358 Prosite nucleotide pattern A nucleotide regular expression pattern from the Prosite database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1358 http://edamontology.org/data_1353 A nucleotide regular expression pattern from the Prosite database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1359 Prosite protein pattern A protein regular expression pattern from the Prosite database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1359 http://edamontology.org/data_1353 A protein regular expression pattern from the Prosite database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1361 Position frequency matrix PFM A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. FALSE http://edamontology.org/data_2854 beta12orEarlier data_1361 A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. PFM http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1362 Position weight matrix PWM A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.|Contributions of individual sequences to the matrix might be uneven (weighted). FALSE http://edamontology.org/data_2854 beta12orEarlier data_1362 A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. PWM http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1363 Information content matrix ICM 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. FALSE http://edamontology.org/data_2854 beta12orEarlier data_1363 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. ICM http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1364 Hidden Markov model HMM "A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences." FALSE http://edamontology.org/data_0950|http://edamontology.org/data_1354 beta12orEarlier data_1364 "A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences." HMM http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1365 Fingerprint One or more fingerprints (sequence classifiers) as used in the PRINTS database. FALSE http://edamontology.org/data_2854 beta12orEarlier data_1365 One or more fingerprints (sequence classifiers) as used in the PRINTS database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1368 Domainatrix signature A protein signature of the type used in the EMBASSY Signature package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1368 http://edamontology.org/data_1354 A protein signature of the type used in the EMBASSY Signature package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1371 HMMER NULL hidden Markov model NULL hidden Markov model representation used by the HMMER package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1371 http://edamontology.org/data_1364 NULL hidden Markov model representation used by the HMMER package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1372 Protein family signature A protein family signature (sequence classifier) from the InterPro database.|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. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1372 http://edamontology.org/data_1355 A protein family signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1373 Protein domain signature A protein domain signature (sequence classifier) from the InterPro database.|Protein domain signatures identify structural or functional domains or other units with defined boundaries. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1373 http://edamontology.org/data_1355 A protein domain signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1374 Protein region signature A protein region signature (sequence classifier) from the InterPro database.|A protein region signature defines a region which cannot be described as a protein family or domain signature. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1374 http://edamontology.org/data_1355 A protein region signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1375 Protein repeat signature "A protein repeat signature (sequence classifier) from the InterPro database.|A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1375 http://edamontology.org/data_1355 A protein repeat signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1376 Protein site signature A protein site signature (sequence classifier) from the InterPro database.|A protein site signature is a classifier for a specific site in a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1376 http://edamontology.org/data_1355 A protein site signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1377 Protein conserved site signature "A protein conserved site signature (sequence classifier) from the InterPro database.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1377 http://edamontology.org/data_2071 A protein conserved site signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1378 Protein active site signature "A protein active site signature (sequence classifier) from the InterPro database.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1378 http://edamontology.org/data_2071 A protein active site signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1379 Protein binding site signature "A protein binding site signature (sequence classifier) from the InterPro database.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1379 http://edamontology.org/data_2071 A protein binding site signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1380 Protein post-translational modification signature "A protein post-translational modification signature (sequence classifier) from the InterPro database.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1380 http://edamontology.org/data_2071 A protein post-translational modification signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1381 Sequence alignment (pair) Alignment of exactly two molecular sequences. FALSE http://edamontology.org/data_0863 beta12orEarlier data_1381 Alignment of exactly two molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1382 Sequence alignment (multiple) Alignment of more than two molecular sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1382 http://edamontology.org/data_0863 Alignment of more than two molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1383 Sequence alignment (nucleic acid) Alignment of multiple nucleotide sequences. FALSE http://edamontology.org/data_0863 beta12orEarlier data_1383 Alignment of multiple nucleotide sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1384 Sequence alignment (protein) Alignment of multiple protein sequences. FALSE http://edamontology.org/data_3154|http://edamontology.org/data_0863 beta12orEarlier data_1384 Alignment of multiple protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1385 Sequence alignment (hybrid) "Alignment of multiple molecular sequences of different types.|Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA." FALSE http://edamontology.org/data_0863 beta12orEarlier data_1385 Alignment of multiple molecular sequences of different types. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1386 Sequence alignment (nucleic acid pair) Alignment of exactly two nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1386 http://edamontology.org/data_1383|http://edamontology.org/data_1381 Alignment of exactly two nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/data_1387 Sequence alignment (protein pair) Alignment of exactly two protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1387 http://edamontology.org/data_1384|http://edamontology.org/data_1381 Alignment of exactly two protein sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/data_1388 Hybrid sequence alignment (pair) Alignment of exactly two molecular sequences of different types. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1388 http://edamontology.org/data_1385 Alignment of exactly two molecular sequences of different types. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1389 Multiple nucleotide sequence alignment Alignment of more than two nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1389 http://edamontology.org/data_0863 Alignment of more than two nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1390 Multiple protein sequence alignment Alignment of more than two protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1390 http://edamontology.org/data_0863 Alignment of more than two protein sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1394 Alignment score or penalty A simple floating point number defining the penalty for opening or extending a gap in an alignment. FALSE http://edamontology.org/data_1772 beta12orEarlier data_1394 A simple floating point number defining the penalty for opening or extending a gap in an alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1395 Score end gaps control Whether end gaps are scored or not. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1395 Whether end gaps are scored or not. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1396 Aligned sequence order Controls the order of sequences in an output sequence alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1396 Controls the order of sequences in an output sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1397 Gap opening penalty A penalty for opening a gap in an alignment. FALSE http://edamontology.org/data_2137 beta12orEarlier data_1397 A penalty for opening a gap in an alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1398 Gap extension penalty A penalty for extending a gap in an alignment. FALSE http://edamontology.org/data_2137 beta12orEarlier data_1398 A penalty for extending a gap in an alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1399 Gap separation penalty A penalty for gaps that are close together in an alignment. FALSE http://edamontology.org/data_2137 beta12orEarlier data_1399 A penalty for gaps that are close together in an alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1400 Terminal gap penalty "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1400 http://edamontology.org/data_1411|http://edamontology.org/data_1410 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1401 Match reward score The score for a 'match' used in various sequence database search applications with simple scoring schemes. FALSE http://edamontology.org/data_1394 beta12orEarlier data_1401 The score for a 'match' used in various sequence database search applications with simple scoring schemes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1402 Mismatch penalty score The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. FALSE http://edamontology.org/data_1394 beta12orEarlier data_1402 The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1403 Drop off score This is the threshold drop in score at which extension of word alignment is halted. FALSE http://edamontology.org/data_1394 beta12orEarlier data_1403 This is the threshold drop in score at which extension of word alignment is halted. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1404 Gap opening penalty (integer) A simple floating point number defining the penalty for opening a gap in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1404 http://edamontology.org/data_1397 A simple floating point number defining the penalty for opening a gap in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1405 Gap opening penalty (float) A simple floating point number defining the penalty for opening a gap in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1405 http://edamontology.org/data_1397 A simple floating point number defining the penalty for opening a gap in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1406 Gap extension penalty (integer) A simple floating point number defining the penalty for extending a gap in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1406 http://edamontology.org/data_1398 A simple floating point number defining the penalty for extending a gap in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1407 Gap extension penalty (float) A simple floating point number defining the penalty for extending a gap in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1407 http://edamontology.org/data_1398 A simple floating point number defining the penalty for extending a gap in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1408 Gap separation penalty (integer) A simple floating point number defining the penalty for gaps that are close together in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1408 http://edamontology.org/data_1399 A simple floating point number defining the penalty for gaps that are close together in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1409 Gap separation penalty (float) A simple floating point number defining the penalty for gaps that are close together in an alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1409 http://edamontology.org/data_1399 A simple floating point number defining the penalty for gaps that are close together in an alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1410 Terminal gap opening penalty "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." FALSE http://edamontology.org/data_1397 beta12orEarlier data_1410 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1411 Terminal gap extension penalty "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." FALSE http://edamontology.org/data_1398 beta12orEarlier data_1411 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1412 Sequence identity Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. FALSE http://edamontology.org/data_0865 beta12orEarlier data_1412 Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1413 Sequence similarity "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.|Data Type is float probably." FALSE http://edamontology.org/data_0865 beta12orEarlier data_1413 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1414 Sequence alignment metadata (quality report) Data on molecular sequence alignment quality (estimated accuracy). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1414 http://edamontology.org/data_0867 Data on molecular sequence alignment quality (estimated accuracy). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1415 Sequence alignment report (site conservation) "Data on character conservation in a molecular sequence alignment.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1415 http://edamontology.org/data_2161 Data on character conservation in a molecular sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1416 Sequence alignment report (site correlation) "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1416 http://edamontology.org/data_0867 "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://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1417 Sequence-profile alignment (Domainatrix signature) Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1417 http://edamontology.org/data_0869 Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1418 Sequence-profile alignment (HMM) Alignment of molecular sequence(s) to a hidden Markov model(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1418 http://edamontology.org/data_0869 Alignment of molecular sequence(s) to a hidden Markov model(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1420 Sequence-profile alignment (fingerprint) Alignment of molecular sequences to a protein fingerprint from the PRINTS database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1420 http://edamontology.org/data_0869 Alignment of molecular sequences to a protein fingerprint from the PRINTS database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1426 Phylogenetic continuous quantitative data Quantitative traits|Phylogenetic continuous quantitative characters Continuous quantitative data that may be read during phylogenetic tree calculation. FALSE http://edamontology.org/data_0871 beta12orEarlier data_1426 Continuous quantitative data that may be read during phylogenetic tree calculation. Quantitative traits|Phylogenetic continuous quantitative characters http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1427 Phylogenetic discrete data Discrete characters|Phylogenetic discrete states|Discretely coded characters Character data with discrete states that may be read during phylogenetic tree calculation. FALSE http://edamontology.org/data_0871 beta12orEarlier data_1427 Character data with discrete states that may be read during phylogenetic tree calculation. Discrete characters|Phylogenetic discrete states|Discretely coded characters http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1428 Phylogenetic character cliques Phylogenetic report (cliques) "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." FALSE http://edamontology.org/data_2523 beta12orEarlier data_1428 "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." Phylogenetic report (cliques) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1429 Phylogenetic invariants Phylogenetic report (invariants) Phylogenetic invariants data for testing alternative tree topologies. FALSE http://edamontology.org/data_2523 beta12orEarlier data_1429 Phylogenetic invariants data for testing alternative tree topologies. Phylogenetic report (invariants) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1438 Phylogenetic report "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.|This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1438 http://edamontology.org/data_2523 "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1439 DNA substitution model Phylogenetic tree report (DNA substitution model)|Substitution model|Sequence alignment report (DNA substitution model) "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." FALSE http://edamontology.org/data_0950 beta12orEarlier data_1439 "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." Phylogenetic tree report (DNA substitution model)|Substitution model|Sequence alignment report (DNA substitution model) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1440 Phylogenetic tree report (tree shape) Data about the shape of a phylogenetic tree. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1440 http://edamontology.org/data_2523 Data about the shape of a phylogenetic tree. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1441 Phylogenetic tree report (tree evaluation) Data on the confidence of a phylogenetic tree. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1441 http://edamontology.org/data_2523 Data on the confidence of a phylogenetic tree. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1442 Phylogenetic tree distances Phylogenetic tree report (tree distances) "Distances, such as Branch Score distance, between two or more phylogenetic trees." FALSE http://edamontology.org/data_2523 beta12orEarlier data_1442 "Distances, such as Branch Score distance, between two or more phylogenetic trees." Phylogenetic tree report (tree distances) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1443 Phylogenetic tree report (tree stratigraphic) Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1443 http://edamontology.org/data_2523 Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1444 Phylogenetic character contrasts Phylogenetic report (character contrasts) "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." FALSE http://edamontology.org/data_2523 beta12orEarlier data_1444 "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." Phylogenetic report (character contrasts) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1446 Comparison matrix (integers) Matrix of integer numbers for sequence comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1446 http://edamontology.org/data_0874 Matrix of integer numbers for sequence comparison. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1447 Comparison matrix (floats) Matrix of floating point numbers for sequence comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1447 http://edamontology.org/data_0874 Matrix of floating point numbers for sequence comparison. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1448 Comparison matrix (nucleotide) Nucleotide substitution matrix Matrix of integer or floating point numbers for nucleotide comparison. FALSE http://edamontology.org/data_0874 beta12orEarlier data_1448 Matrix of integer or floating point numbers for nucleotide comparison. Nucleotide substitution matrix http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1449 Comparison matrix (amino acid) Amino acid comparison matrix|Amino acid substitution matrix Matrix of integer or floating point numbers for amino acid comparison. FALSE http://edamontology.org/data_2016|http://edamontology.org/data_0874 beta12orEarlier data_1449 Matrix of integer or floating point numbers for amino acid comparison. Amino acid comparison matrix|Amino acid substitution matrix http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1450 Nucleotide comparison matrix (integers) Nucleotide substitution matrix (integers) Matrix of integer numbers for nucleotide comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1450 http://edamontology.org/data_1448 Matrix of integer numbers for nucleotide comparison. Nucleotide substitution matrix (integers) http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1451 Nucleotide comparison matrix (floats) Nucleotide substitution matrix (floats) Matrix of floating point numbers for nucleotide comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1451 http://edamontology.org/data_1448 Matrix of floating point numbers for nucleotide comparison. Nucleotide substitution matrix (floats) http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1452 Amino acid comparison matrix (integers) Matrix of integer numbers for amino acid comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1452 http://edamontology.org/data_1449 Matrix of integer numbers for amino acid comparison. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1453 Amino acid comparison matrix (floats) Matrix of floating point numbers for amino acid comparison. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1453 http://edamontology.org/data_1449 Matrix of floating point numbers for amino acid comparison. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1456 Protein features report (membrane regions) "trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1456 "trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_1459 Nucleic acid structure 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. FALSE http://edamontology.org/data_0883 beta12orEarlier data_1459 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1460 Protein structure Protein structures 3D coordinate and associated data for a protein tertiary (3D) structure. FALSE http://edamontology.org/data_0883 beta12orEarlier data_1460 3D coordinate and associated data for a protein tertiary (3D) structure. Protein structures http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1461 Protein-ligand complex "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.|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." FALSE http://edamontology.org/data_1460 beta12orEarlier data_1461 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1462 Carbohydrate structure 3D coordinate and associated data for a carbohydrate (3D) structure. FALSE http://edamontology.org/data_0883 beta12orEarlier data_1462 3D coordinate and associated data for a carbohydrate (3D) structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1463 Small molecule structure CHEBI:23367 "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." FALSE http://edamontology.org/data_0883 beta12orEarlier data_1463 "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." CHEBI:23367 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1464 DNA structure 3D coordinate and associated data for a DNA tertiary (3D) structure. FALSE http://edamontology.org/data_1459 beta12orEarlier data_1464 3D coordinate and associated data for a DNA tertiary (3D) structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1465 RNA structure 3D coordinate and associated data for an RNA tertiary (3D) structure. FALSE http://edamontology.org/data_1459 beta12orEarlier data_1465 3D coordinate and associated data for an RNA tertiary (3D) structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1466 tRNA structure "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." FALSE http://edamontology.org/data_1465 beta12orEarlier data_1466 "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1467 Protein chain 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. FALSE http://edamontology.org/data_1460 beta12orEarlier data_1467 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1468 Protein domain 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. FALSE http://edamontology.org/data_1460 beta12orEarlier data_1468 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1469 Protein structure (all atoms) 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1469 http://edamontology.org/data_1460 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1470 C-alpha trace Protein structure (C-alpha atoms) 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).|C-beta atoms from amino acid side-chains may be included. FALSE http://edamontology.org/data_1460 beta12orEarlier data_1470 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). Protein structure (C-alpha atoms) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1471 Protein chain (all atoms) 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1471 http://edamontology.org/data_1467 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1472 Protein chain (C-alpha atoms) 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).|C-beta atoms from amino acid side-chains may be included. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1472 http://edamontology.org/data_1467 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1473 Protein domain (all atoms) 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1473 http://edamontology.org/data_1468 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1474 Protein domain (C-alpha atoms) 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).|C-beta atoms from amino acid side-chains may be included. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1474 http://edamontology.org/data_1468 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1479 Structure alignment (pair) Pair structure alignment Alignment (superimposition) of exactly two molecular tertiary (3D) structures. FALSE http://edamontology.org/data_0886 beta12orEarlier data_1479 Alignment (superimposition) of exactly two molecular tertiary (3D) structures. Pair structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1480 Structure alignment (multiple) Alignment (superimposition) of more than two molecular tertiary (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1480 http://edamontology.org/data_0886 Alignment (superimposition) of more than two molecular tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1481 Structure alignment (protein) Protein structure alignment Alignment (superimposition) of protein tertiary (3D) structures. FALSE http://edamontology.org/data_3154|http://edamontology.org/data_0886 beta12orEarlier data_1481 Alignment (superimposition) of protein tertiary (3D) structures. Protein structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1482 Structure alignment (nucleic acid) Nucleic acid structure alignment Alignment (superimposition) of nucleic acid tertiary (3D) structures. FALSE http://edamontology.org/data_0886 beta12orEarlier data_1482 Alignment (superimposition) of nucleic acid tertiary (3D) structures. Nucleic acid structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1483 Structure alignment (protein pair) Alignment (superimposition) of exactly two protein tertiary (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1483 http://edamontology.org/data_1481|http://edamontology.org/data_1479 Alignment (superimposition) of exactly two protein tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/data_1484 Multiple protein tertiary structure alignment Alignment (superimposition) of more than two protein tertiary (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1484 http://edamontology.org/data_1481 Alignment (superimposition) of more than two protein tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1485 Structure alignment (protein all atoms) Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1485 http://edamontology.org/data_1481 Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1486 Structure alignment (protein C-alpha atoms) Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).|C-beta atoms from amino acid side-chains may be considered. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1486 http://edamontology.org/data_1481 Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1487 Pairwise protein tertiary structure alignment (all atoms) Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1487 http://edamontology.org/data_1481 Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1488 Pairwise protein tertiary structure alignment (C-alpha atoms) Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).|C-beta atoms from amino acid side-chains may be included. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1488 http://edamontology.org/data_1481 Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1489 Multiple protein tertiary structure alignment (all atoms) Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1489 http://edamontology.org/data_1481 Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1490 Multiple protein tertiary structure alignment (C-alpha atoms) Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).|C-beta atoms from amino acid side-chains may be included. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1490 http://edamontology.org/data_1481 Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1491 Structure alignment (nucleic acid pair) Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1491 http://edamontology.org/data_1479|http://edamontology.org/data_1482 Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/data_1492 Multiple nucleic acid tertiary structure alignment Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1492 http://edamontology.org/data_1482 Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1493 Structure alignment (RNA) RNA structure alignment Alignment (superimposition) of RNA tertiary (3D) structures. FALSE http://edamontology.org/data_1482 beta12orEarlier data_1493 Alignment (superimposition) of RNA tertiary (3D) structures. RNA structure alignment http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1494 Structural transformation matrix "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." FALSE http://edamontology.org/data_2082 beta12orEarlier data_1494 "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1495 DaliLite hit table "DaliLite hit table of protein chain tertiary structure alignment data.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1495 http://edamontology.org/data_0887 DaliLite hit table of protein chain tertiary structure alignment data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1496 Molecular similarity score A score reflecting structural similarities of two molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1496 http://edamontology.org/data_0888 A score reflecting structural similarities of two molecules. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1497 Root-mean-square deviation RMSD Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. FALSE http://edamontology.org/data_0888 beta12orEarlier data_1497 Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. RMSD http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1498 Tanimoto similarity score "A measure of the similarity between two ligand fingerprints.|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." FALSE http://edamontology.org/data_0888 beta12orEarlier data_1498 A measure of the similarity between two ligand fingerprints. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1499 3D-1D scoring matrix A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. FALSE http://edamontology.org/data_0892 beta12orEarlier data_1499 A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1501 Amino acid index A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. FALSE http://edamontology.org/data_2016|http://edamontology.org/data_2082 beta12orEarlier data_1501 A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1502 Amino acid index (chemical classes) Chemical classes (amino acids) "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." FALSE http://edamontology.org/data_1501 beta12orEarlier data_1502 "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." Chemical classes (amino acids) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1503 Amino acid pair-wise contact potentials Contact potentials (amino acid pair-wise) Statistical protein contact potentials. FALSE http://edamontology.org/data_2016 beta12orEarlier data_1503 Statistical protein contact potentials. Contact potentials (amino acid pair-wise) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1505 Amino acid index (molecular weight) Molecular weight (amino acids) Molecular weights of amino acids. FALSE http://edamontology.org/data_1501 beta12orEarlier data_1505 Molecular weights of amino acids. Molecular weight (amino acids) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1506 Amino acid index (hydropathy) Hydropathy (amino acids) "Hydrophobic, hydrophilic or charge properties of amino acids." FALSE http://edamontology.org/data_1501 beta12orEarlier data_1506 "Hydrophobic, hydrophilic or charge properties of amino acids." Hydropathy (amino acids) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1507 Amino acid index (White-Wimley data) White-Wimley data (amino acids) Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. FALSE http://edamontology.org/data_1501 beta12orEarlier data_1507 Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. White-Wimley data (amino acids) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1508 Amino acid index (van der Waals radii) van der Waals radii (amino acids) Van der Waals radii of atoms for different amino acid residues. FALSE http://edamontology.org/data_1501 beta12orEarlier data_1508 Van der Waals radii of atoms for different amino acid residues. van der Waals radii (amino acids) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1509 Enzyme report An informative report on a specific enzyme. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1509 http://edamontology.org/data_0896 An informative report on a specific enzyme. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1517 Restriction enzyme report "An informative report on a specific restriction enzyme such as enzyme reference data.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1517 http://edamontology.org/data_0896 An informative report on a specific restriction enzyme such as enzyme reference data. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1519 Peptide molecular weights "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.|The report might include associated data such as frequency of peptide fragment molecular weights." FALSE http://edamontology.org/data_0897 beta12orEarlier data_1519 "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1520 Peptide hydrophobic moment Report on the hydrophobic moment of a polypeptide sequence.|Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. FALSE http://edamontology.org/data_2970 beta12orEarlier data_1520 Report on the hydrophobic moment of a polypeptide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1521 Protein aliphatic index The aliphatic index of a protein.|The aliphatic index is the relative protein volume occupied by aliphatic side chains. FALSE http://edamontology.org/data_2970 beta12orEarlier data_1521 The aliphatic index of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1522 Protein sequence hydropathy plot "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.|Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation." FALSE http://edamontology.org/data_2970 beta12orEarlier data_1522 "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1523 Protein charge plot 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. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1523 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1524 Protein solubility Protein solubility data The solubility or atomic solvation energy of a protein sequence or structure. FALSE http://edamontology.org/data_2970 beta12orEarlier data_1524 The solubility or atomic solvation energy of a protein sequence or structure. Protein solubility data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1525 Protein crystallizability Protein crystallizability data Data on the crystallizability of a protein sequence. FALSE http://edamontology.org/data_2970 beta12orEarlier data_1525 Data on the crystallizability of a protein sequence. Protein crystallizability data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1526 Protein globularity Protein globularity data "Data on the stability, intrinsic disorder or globularity of a protein sequence." FALSE http://edamontology.org/data_2970 beta12orEarlier data_1526 "Data on the stability, intrinsic disorder or globularity of a protein sequence." Protein globularity data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1527 Protein titration curve The titration curve of a protein. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_0897 beta12orEarlier data_1527 The titration curve of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1528 Protein isoelectric point The isoelectric point of one proteins. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1528 The isoelectric point of one proteins. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1529 Protein pKa value The pKa value of a protein. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1529 The pKa value of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1530 Protein hydrogen exchange rate The hydrogen exchange rate of a protein. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1530 The hydrogen exchange rate of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1531 Protein extinction coefficient The extinction coefficient of a protein. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1531 The extinction coefficient of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1532 Protein optical density The optical density of a protein. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1532 The optical density of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1533 Protein subcellular localisation Protein report (subcellular localisation) "An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1533 http://edamontology.org/data_0896 "An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." Protein report (subcellular localisation) http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1534 Peptide immunogenicity data Peptide immunogenicity|Peptide immunogenicity report "An report on allergenicity / immunogenicity of peptides and proteins.|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." FALSE http://edamontology.org/data_0897 beta12orEarlier data_1534 An report on allergenicity / immunogenicity of peptides and proteins. Peptide immunogenicity|Peptide immunogenicity report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1536 MHC peptide immunogenicity report A report on the immunogenicity of MHC class I or class II binding peptides. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1536 http://edamontology.org/data_1534 A report on the immunogenicity of MHC class I or class II binding peptides. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1537 Protein structure report Protein structure report (domain)|Protein structure-derived report|Protein structural property|Protein property (structural)|Protein report (structure) "Annotation about, or structural information derived from, one or more specific protein 3D structure(s) or structural domains.|This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure)." FALSE http://edamontology.org/data_2085|http://edamontology.org/data_0896 beta12orEarlier data_1537 "Annotation about, or structural information derived from, one or more specific protein 3D structure(s) or structural domains." Protein structure report (domain)|Protein structure-derived report|Protein structural property|Protein property (structural)|Protein report (structure) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1539 Protein structural quality report Protein structure report (quality evaluation)|Protein structure validation report|Protein property (structural quality)|Protein report (structural quality) "Report on the quality of a protein three-dimensional model.|Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc." FALSE http://edamontology.org/data_1537 beta12orEarlier data_1539 Report on the quality of a protein three-dimensional model. Protein structure report (quality evaluation)|Protein structure validation report|Protein property (structural quality)|Protein report (structural quality) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1540 Protein non-covalent interactions report "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1540 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0906 1.12 http://edamontology.org/data_1541 Protein flexibility or motion report "Informative report on flexibility or motion of a protein structure.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1541 http://edamontology.org/data_1537 Informative report on flexibility or motion of a protein structure. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1542 Protein solvent accessibility report "Data on the solvent accessible or buried surface area of a protein structure.|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." FALSE http://edamontology.org/data_1537 beta12orEarlier data_1542 Data on the solvent accessible or buried surface area of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1543 Protein surface report "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1543 http://edamontology.org/data_1537 "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1544 Ramachandran plot Phi/psi angle data or a Ramachandran plot of a protein structure. FALSE http://edamontology.org/data_2991 beta12orEarlier data_1544 Phi/psi angle data or a Ramachandran plot of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1545 Protein dipole moment Data on the net charge distribution (dipole moment) of a protein structure. FALSE http://edamontology.org/data_0897 beta12orEarlier data_1545 Data on the net charge distribution (dipole moment) of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1546 Protein distance matrix A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. FALSE http://edamontology.org/data_0906|http://edamontology.org/data_2855 beta12orEarlier data_1546 A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1547 Protein contact map An amino acid residue contact map for a protein structure. FALSE http://edamontology.org/data_0906 beta12orEarlier data_1547 An amino acid residue contact map for a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1548 Protein residue 3D cluster Report on clusters of contacting residues in protein structures such as a key structural residue network. FALSE http://edamontology.org/data_0906 beta12orEarlier data_1548 Report on clusters of contacting residues in protein structures such as a key structural residue network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1549 Protein hydrogen bonds Patterns of hydrogen bonding in protein structures. FALSE http://edamontology.org/data_0906 beta12orEarlier data_1549 Patterns of hydrogen bonding in protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1550 Protein non-canonical interactions Non-canonical atomic interactions in protein structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1550 http://edamontology.org/data_1537 Non-canonical atomic interactions in protein structures. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1553 CATH node "Information on a node from the CATH database.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1553 http://edamontology.org/data_2980 Information on a node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1554 SCOP node Information on a node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1554 http://edamontology.org/data_2980 Information on a node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1555 EMBASSY domain classification "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1555 "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0907 beta12orEarlier http://edamontology.org/data_1556 CATH class Information on a protein 'class' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1556 http://edamontology.org/data_2980 Information on a protein 'class' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1557 CATH architecture Information on a protein 'architecture' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1557 http://edamontology.org/data_2980 Information on a protein 'architecture' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1558 CATH topology Information on a protein 'topology' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1558 http://edamontology.org/data_2980 Information on a protein 'topology' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1559 CATH homologous superfamily Information on a protein 'homologous superfamily' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1559 http://edamontology.org/data_2980 Information on a protein 'homologous superfamily' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1560 CATH structurally similar group Information on a protein 'structurally similar group' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1560 http://edamontology.org/data_2980 Information on a protein 'structurally similar group' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1561 CATH functional category Information on a protein 'functional category' node from the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1561 http://edamontology.org/data_2980 Information on a protein 'functional category' node from the CATH database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1564 Protein fold recognition report "A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s).|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1564 http://edamontology.org/data_1277 A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1565 Protein-protein interaction report "protein-protein interaction(s), including interactions between protein domains." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1565 "protein-protein interaction(s), including interactions between protein domains." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0906 1.8 http://edamontology.org/data_1566 Protein-ligand interaction report Protein-drug interaction report An informative report on protein-ligand (small molecule) interaction(s). FALSE http://edamontology.org/data_0906 beta12orEarlier data_1566 An informative report on protein-ligand (small molecule) interaction(s). Protein-drug interaction report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1567 Protein-nucleic acid interactions report protein-DNA/RNA interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1567 protein-DNA/RNA interaction(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0906 1.8 http://edamontology.org/data_1583 Nucleic acid melting profile Nucleic acid stability profile "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.|A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence." FALSE http://edamontology.org/data_2985 beta12orEarlier data_1583 Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. Nucleic acid stability profile http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1584 Nucleic acid enthalpy Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). FALSE http://edamontology.org/data_2985 beta12orEarlier data_1584 Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1585 Nucleic acid entropy Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). FALSE http://edamontology.org/data_2985 beta12orEarlier data_1585 Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1586 Nucleic acid melting temperature Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1586 http://edamontology.org/data_2139 Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1587 Nucleic acid stitch profile "Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA).|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." FALSE http://edamontology.org/data_1583 beta12orEarlier data_1587 Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1588 DNA base pair stacking energies data DNA base pair stacking energies data. FALSE http://edamontology.org/data_2088 beta12orEarlier data_1588 DNA base pair stacking energies data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1589 DNA base pair twist angle data DNA base pair twist angle data. FALSE http://edamontology.org/data_2088 beta12orEarlier data_1589 DNA base pair twist angle data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1590 DNA base trimer roll angles data DNA base trimer roll angles data. FALSE http://edamontology.org/data_2088 beta12orEarlier data_1590 DNA base trimer roll angles data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1591 Vienna RNA parameters RNA parameters used by the Vienna package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1591 RNA parameters used by the Vienna package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1592 Vienna RNA structure constraints Structure constraints used by the Vienna package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1592 Structure constraints used by the Vienna package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1593 Vienna RNA concentration data RNA concentration data used by the Vienna package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1593 RNA concentration data used by the Vienna package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1594 Vienna RNA calculated energy RNA calculated energy data generated by the Vienna package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1594 http://edamontology.org/data_1584 RNA calculated energy data generated by the Vienna package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1595 Base pairing probability matrix dotplot Dotplot of RNA base pairing probability matrix.|Such as generated by the Vienna package. FALSE http://edamontology.org/data_2088|http://edamontology.org/data_2884 beta12orEarlier data_1595 Dotplot of RNA base pairing probability matrix. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1596 Nucleic acid folding report Nucleic acid report (folding model)|Nucleic acid report (folding)|RNA secondary structure folding probablities|RNA secondary structure folding classification "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." FALSE http://edamontology.org/data_2084 beta12orEarlier data_1596 "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." Nucleic acid report (folding model)|Nucleic acid report (folding) RNA secondary structure folding probablities|RNA secondary structure folding classification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1597 Codon usage table "Table of codon usage data calculated from one or more nucleic acid sequences.|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." FALSE http://edamontology.org/data_0914 beta12orEarlier data_1597 Table of codon usage data calculated from one or more nucleic acid sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1598 Genetic code A genetic code for an organism.|A genetic code need not include detailed codon usage information. FALSE http://edamontology.org/data_0914 beta12orEarlier data_1598 A genetic code for an organism. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1599 Codon adaptation index A simple measure of synonymous codon usage bias often used to predict gene expression levels. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1599 http://edamontology.org/data_2865 A simple measure of synonymous codon usage bias often used to predict gene expression levels. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1600 Codon usage bias plot Synonymous codon usage statistic plot A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. FALSE http://edamontology.org/data_0914 beta12orEarlier data_1600 A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. Synonymous codon usage statistic plot http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1601 Nc statistic 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. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1601 http://edamontology.org/data_2865 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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1602 Codon usage fraction difference The differences in codon usage fractions between two codon usage tables. FALSE http://edamontology.org/data_0914 beta12orEarlier data_1602 The differences in codon usage fractions between two codon usage tables. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1621 Pharmacogenomic test report Data on the influence of genotype on drug response.|The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. FALSE http://edamontology.org/data_0920 beta12orEarlier data_1621 Data on the influence of genotype on drug response. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1622 Disease report "An informative report on a specific disease.|For example, 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." FALSE http://edamontology.org/data_0920 beta12orEarlier data_1622 An informative report on a specific disease. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1634 Linkage disequilibrium (report) A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1634 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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0927 1.8 http://edamontology.org/data_1636 Heat map "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.|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." FALSE http://edamontology.org/data_2968|http://edamontology.org/data_3768 beta12orEarlier data_1636 "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1642 Affymetrix probe sets library file Affymetrix library file of information about which probes belong to which probe set. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1642 http://edamontology.org/data_2717 Affymetrix library file of information about which probes belong to which probe set. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1643 Affymetrix probe sets information library file GIN file Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1643 http://edamontology.org/data_2717 Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. GIN file http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1646 Molecular weights standard fingerprint "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1646 "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0944 1.12 http://edamontology.org/data_1656 Metabolic pathway report "A report typically including a map (diagram) of a metabolic pathway.|This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1656 A report typically including a map (diagram) of a metabolic pathway. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_1657 Genetic information processing pathway report genetic information processing pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1657 genetic information processing pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_1658 Environmental information processing pathway report environmental information processing pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1658 environmental information processing pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_1659 Signal transduction pathway report A report typically including a map (diagram) of a signal transduction pathway. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1659 A report typically including a map (diagram) of a signal transduction pathway. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_1660 Cellular process pathways report Topic concernning cellular process pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1660 Topic concernning cellular process pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_1661 Disease pathway or network report "disease pathways, typically of human disease." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1661 "disease pathways, typically of human disease." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0906 1.8 http://edamontology.org/data_1662 Drug structure relationship map A report typically including a map (diagram) of drug structure relationships. FALSE http://edamontology.org/data_1696 beta12orEarlier data_1662 A report typically including a map (diagram) of drug structure relationships. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1663 Protein interaction networks networks of protein interactions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1663 http://edamontology.org/data_2600 networks of protein interactions. http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/data_1664 MIRIAM datatype "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1664 http://edamontology.org/data_1883 An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1667 E-value Expectation value A simple floating point number defining the lower or upper limit of an expectation value (E-value).|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. FALSE http://edamontology.org/data_0951 beta12orEarlier data_1667 A simple floating point number defining the lower or upper limit of an expectation value (E-value). Expectation value http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1668 Z-value The z-value is the number of standard deviations a data value is above or below a mean value.|A z-value might be specified as a threshold for reporting hits from database searches. FALSE http://edamontology.org/data_0951 beta12orEarlier data_1668 The z-value is the number of standard deviations a data value is above or below a mean value. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1669 P-value "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.|A z-value might be specified as a threshold for reporting hits from database searches." FALSE http://edamontology.org/data_0951 beta12orEarlier data_1669 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1670 Database version information "Information on a database (or ontology) version, for example name, version number and release date." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1670 http://edamontology.org/data_0957 "Information on a database (or ontology) version, for example name, version number and release date." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1671 Tool version information "Information on an application version, for example name, version number and release date." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1671 http://edamontology.org/data_0958 "Information on an application version, for example name, version number and release date." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1672 CATH version information Information on a version of the CATH database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1672 http://edamontology.org/data_2337 Information on a version of the CATH database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1673 Swiss-Prot to PDB mapping Cross-mapping of Swiss-Prot codes to PDB identifiers. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1673 http://edamontology.org/data_0954 Cross-mapping of Swiss-Prot codes to PDB identifiers. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1674 Sequence database cross-references Cross-references from a sequence record to other databases. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1674 http://edamontology.org/data_2093 Cross-references from a sequence record to other databases. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1675 Job status "Metadata on the status of a submitted job.|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)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1675 http://edamontology.org/data_3106 Metadata on the status of a submitted job. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1676 Job ID The (typically numeric) unique identifier of a submitted job. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1676 http://edamontology.org/data_3106 The (typically numeric) unique identifier of a submitted job. http://purl.obolibrary.org/obo/edam#obsolete 1.0 http://edamontology.org/data_1677 Job type "A label (text token) describing the type of job, for example interactive or non-interactive." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1677 http://edamontology.org/data_0842 "A label (text token) describing the type of job, for example interactive or non-interactive." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1678 Tool log "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1678 http://edamontology.org/data_3106 "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1679 DaliLite log file DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1679 http://edamontology.org/data_2048 DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1680 STRIDE log file STRIDE log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1680 http://edamontology.org/data_2048 STRIDE log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1681 NACCESS log file NACCESS log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1681 http://edamontology.org/data_2048 NACCESS log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1682 EMBOSS wordfinder log file EMBOSS wordfinder log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1682 http://edamontology.org/data_2048 EMBOSS wordfinder log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1683 EMBOSS domainatrix log file EMBOSS (EMBASSY) domainatrix application log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1683 http://edamontology.org/data_2048 EMBOSS (EMBASSY) domainatrix application log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1684 EMBOSS sites log file EMBOSS (EMBASSY) sites application log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1684 http://edamontology.org/data_2048 EMBOSS (EMBASSY) sites application log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1685 EMBOSS supermatcher error file EMBOSS (EMBASSY) supermatcher error file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1685 http://edamontology.org/data_2048 EMBOSS (EMBASSY) supermatcher error file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1686 EMBOSS megamerger log file EMBOSS megamerger log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1686 http://edamontology.org/data_2048 EMBOSS megamerger log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1687 EMBOSS whichdb log file EMBOSS megamerger log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1687 http://edamontology.org/data_2048 EMBOSS megamerger log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1688 EMBOSS vectorstrip log file EMBOSS vectorstrip log file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1688 http://edamontology.org/data_2048 EMBOSS vectorstrip log file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1689 Username A username on a computer system. FALSE http://edamontology.org/data_2101 beta12orEarlier data_1689 A username on a computer system. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1690 Password A password on a computer system. FALSE http://edamontology.org/data_2101 beta12orEarlier data_1690 A password on a computer system. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1691 Email address A valid email address of an end-user. FALSE http://edamontology.org/data_2101 beta12orEarlier data_1691 Moby:Email|Moby:EmailAddress A valid email address of an end-user. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1692 Person name The name of a person. FALSE http://edamontology.org/data_2118 beta12orEarlier data_1692 The name of a person. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1693 Number of iterations Number of iterations of an algorithm. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1693 Number of iterations of an algorithm. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1694 Number of output entities "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1694 "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1695 Hit sort order Controls the order of hits (reported matches) in an output file from a database search. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1695 Controls the order of hits (reported matches) in an output file from a database search. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1696 Drug report Drug annotation An informative report on a specific drug. FALSE http://edamontology.org/data_0962 beta12orEarlier data_1696 http://edamontology.org/data_0962 An informative report on a specific drug. Drug annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1707 Phylogenetic tree image "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.|See also 'Phylogenetic tree'" FALSE http://edamontology.org/data_2968 beta12orEarlier data_1707 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1708 RNA secondary structure image "Image of RNA secondary structure, knots, pseudoknots etc." FALSE http://edamontology.org/data_2968 beta12orEarlier data_1708 "Image of RNA secondary structure, knots, pseudoknots etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1709 Protein secondary structure image Image of protein secondary structure. FALSE http://edamontology.org/data_3153 beta12orEarlier data_1709 Image of protein secondary structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1710 Structure image Image of one or more molecular tertiary (3D) structures. FALSE http://edamontology.org/data_2968 beta12orEarlier data_1710 Image of one or more molecular tertiary (3D) structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1711 Sequence alignment image Image of two or more aligned molecular sequences possibly annotated with alignment features. FALSE http://edamontology.org/data_2968 beta12orEarlier data_1711 Image of two or more aligned molecular sequences possibly annotated with alignment features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1712 Chemical structure image Small molecule structure image An image of the structure of a small chemical compound.|The molecular identifier and formula are typically included. FALSE http://edamontology.org/data_1710 beta12orEarlier data_1712 An image of the structure of a small chemical compound. Small molecule structure image http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1713 Fate map " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." FALSE http://edamontology.org/data_2968|http://edamontology.org/data_2530 beta12orEarlier data_1713 " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1714 Microarray spots image An image of spots from a microarray experiment. FALSE http://edamontology.org/data_2603|http://edamontology.org/data_3424 beta12orEarlier data_1714 An image of spots from a microarray experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1715 BioPax term A term from the BioPax ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1715 http://edamontology.org/data_0966 A term from the BioPax ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1716 GO A term definition from The Gene Ontology (GO). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1716 http://edamontology.org/data_0966 A term definition from The Gene Ontology (GO). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1717 MeSH A term from the MeSH vocabulary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1717 http://edamontology.org/data_0966 A term from the MeSH vocabulary. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1718 HGNC A term from the HGNC controlled vocabulary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1718 http://edamontology.org/data_0966 A term from the HGNC controlled vocabulary. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1719 NCBI taxonomy vocabulary A term from the NCBI taxonomy vocabulary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1719 http://edamontology.org/data_0966 A term from the NCBI taxonomy vocabulary. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1720 Plant ontology term A term from the Plant Ontology (PO). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1720 http://edamontology.org/data_0966 A term from the Plant Ontology (PO). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1721 UMLS A term from the UMLS vocabulary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1721 http://edamontology.org/data_0966 A term from the UMLS vocabulary. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1722 FMA "A term from Foundational Model of Anatomy.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1722 http://edamontology.org/data_0966 A term from Foundational Model of Anatomy. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1723 EMAP A term from the EMAP mouse ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1723 http://edamontology.org/data_0966 A term from the EMAP mouse ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1724 ChEBI A term from the ChEBI ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1724 http://edamontology.org/data_0966 A term from the ChEBI ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1725 MGED A term from the MGED ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1725 http://edamontology.org/data_0966 A term from the MGED ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1726 myGrid "A term from the myGrid ontology.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1726 http://edamontology.org/data_0966 A term from the myGrid ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1727 GO (biological process) A term definition for a biological process from the Gene Ontology (GO).|Data Type is an enumerated string. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1727 http://edamontology.org/data_2858 A term definition for a biological process from the Gene Ontology (GO). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1728 GO (molecular function) A term definition for a molecular function from the Gene Ontology (GO).|Data Type is an enumerated string. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1728 http://edamontology.org/data_2858 A term definition for a molecular function from the Gene Ontology (GO). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1729 GO (cellular component) A term definition for a cellular component from the Gene Ontology (GO).|Data Type is an enumerated string. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1729 http://edamontology.org/data_2858 A term definition for a cellular component from the Gene Ontology (GO). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1730 Ontology relation type A relation type defined in an ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1730 http://edamontology.org/data_0967 A relation type defined in an ontology. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1731 Ontology concept definition Ontology class definition The definition of a concept from an ontology. FALSE http://edamontology.org/data_0967 beta12orEarlier data_1731 The definition of a concept from an ontology. Ontology class definition http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1732 Ontology concept comment A comment on a concept from an ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1732 http://edamontology.org/data_0967 A comment on a concept from an ontology. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_1733 Ontology concept reference Reference for a concept from an ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1733 http://edamontology.org/data_2093 Reference for a concept from an ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1738 doc2loc document information "Information on a published article provided by the doc2loc program.|The doc2loc output includes the url, format, type and availability code of a document for every service provider." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1738 http://edamontology.org/data_0970 Information on a published article provided by the doc2loc program. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1742 PDB residue number A residue identifier (a string) from a PDB file. FALSE http://edamontology.org/data_1016 beta12orEarlier data_1742 PDBML:PDB_residue_no|WHATIF: pdb_number A residue identifier (a string) from a PDB file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1743 Atomic coordinate Cartesian coordinate Cartesian coordinate of an atom (in a molecular structure). FALSE http://edamontology.org/data_1917 beta12orEarlier data_1743 Cartesian coordinate of an atom (in a molecular structure). Cartesian coordinate http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1744 Atomic x coordinate Cartesian x coordinate Cartesian x coordinate of an atom (in a molecular structure). FALSE http://edamontology.org/data_1743 beta12orEarlier data_1744 WHATIF: PDBx_Cartn_x|PDBML:_atom_site.Cartn_x in PDBML Cartesian x coordinate of an atom (in a molecular structure). Cartesian x coordinate http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1745 Atomic y coordinate Cartesian y coordinate Cartesian y coordinate of an atom (in a molecular structure). FALSE http://edamontology.org/data_1743 beta12orEarlier data_1745 PDBML:_atom_site.Cartn_y in PDBML|WHATIF: PDBx_Cartn_y Cartesian y coordinate of an atom (in a molecular structure). Cartesian y coordinate http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1746 Atomic z coordinate Cartesian z coordinate Cartesian z coordinate of an atom (in a molecular structure). FALSE http://edamontology.org/data_1743 beta12orEarlier data_1746 WHATIF: PDBx_Cartn_z|PDBML:_atom_site.Cartn_z Cartesian z coordinate of an atom (in a molecular structure). Cartesian z coordinate http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1748 PDB atom name Identifier (a string) of a specific atom from a PDB file for a molecular structure. FALSE http://edamontology.org/data_1757 beta12orEarlier data_1748 WHATIF: PDBx_type_symbol|WHATIF: PDBx_auth_atom_id|WHATIF: alternate_atom|PDBML:pdbx_PDB_atom_name|WHATIF: atom_type Identifier (a string) of a specific atom from a PDB file for a molecular structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1755 Protein atom Atom data|CHEBI:33250 "Data on a single atom from a protein structure.|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." FALSE http://edamontology.org/data_1460 beta12orEarlier data_1755 Data on a single atom from a protein structure. Atom data CHEBI:33250 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1756 Protein residue Residue "Data on a single amino acid residue position in a protein structure.|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." FALSE http://edamontology.org/data_1460 beta12orEarlier data_1756 Data on a single amino acid residue position in a protein structure. Residue http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1757 Atom name Name of an atom. FALSE http://edamontology.org/data_0983|http://edamontology.org/data_2099 beta12orEarlier data_1757 Name of an atom. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1758 PDB residue name Three-letter amino acid residue names as used in PDB files. FALSE http://edamontology.org/data_2564 beta12orEarlier data_1758 WHATIF: type Three-letter amino acid residue names as used in PDB files. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1759 PDB model number Model number Identifier of a model structure from a PDB file. FALSE http://edamontology.org/data_3035 beta12orEarlier data_1759 WHATIF: model_number|PDBML:pdbx_PDB_model_num Identifier of a model structure from a PDB file. Model number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1762 CATH domain report "Summary of domain classification information for a CATH domain.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1762 http://edamontology.org/data_0907 Summary of domain classification information for a CATH domain. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1764 CATH representative domain sequences (ATOM) FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1764 http://edamontology.org/data_1235 FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1765 CATH representative domain sequences (COMBS) FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1765 http://edamontology.org/data_1235 FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1766 CATH domain sequences (ATOM) FASTA sequence database for all CATH domains (based on PDB ATOM records). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1766 http://edamontology.org/data_0850 FASTA sequence database for all CATH domains (based on PDB ATOM records). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1767 CATH domain sequences (COMBS) FASTA sequence database for all CATH domains (based on COMBS sequence data). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1767 http://edamontology.org/data_0850 FASTA sequence database for all CATH domains (based on COMBS sequence data). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1771 Sequence version Sequence version information Information on an molecular sequence version. FALSE http://edamontology.org/data_2534 beta12orEarlier data_1771 Information on an molecular sequence version. Sequence version information http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1772 Score "A numerical value, that is some type of scored value arising for example from a prediction method." FALSE http://edamontology.org/data_0006 beta12orEarlier data_1772 "A numerical value, that is some type of scored value arising for example from a prediction method." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1776 Protein report (function) "Report on general functional properties of specific protein(s).|For properties that can be mapped to a sequence, use 'Sequence report' instead." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1776 http://edamontology.org/data_0896 Report on general functional properties of specific protein(s). http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1783 Gene name (ASPGD) Name of a gene from Aspergillus Genome Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1783 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS Name of a gene from Aspergillus Genome Database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1784 Gene name (CGD) Name of a gene from Candida Genome Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1784 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS Name of a gene from Candida Genome Database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1785 Gene name (dictyBase) Name of a gene from dictyBase database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1785 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase Name of a gene from dictyBase database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1786 Gene name (EcoGene primary) EcoGene primary gene name Primary name of a gene from EcoGene Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1786 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G Primary name of a gene from EcoGene Database. EcoGene primary gene name http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1787 Gene name (MaizeGDB) Name of a gene from MaizeGDB (maize genes) database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1787 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus Name of a gene from MaizeGDB (maize genes) database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1788 Gene name (SGD) Name of a gene from Saccharomyces Genome Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1788 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS Name of a gene from Saccharomyces Genome Database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1789 Gene name (TGD) Name of a gene from Tetrahymena Genome Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1789 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS Name of a gene from Tetrahymena Genome Database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1790 Gene name (CGSC) Symbol of a gene from E.coli Genetic Stock Center. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1790 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs: CGSC Symbol of a gene from E.coli Genetic Stock Center. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1791 Gene name (HGNC) Symbol of a gene approved by the HUGO Gene Nomenclature Committee. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1791 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene Symbol of a gene approved by the HUGO Gene Nomenclature Committee. http://purl.obolibrary.org/obo/edam#obsolete 1.3 "HGNC:[0-9]{1,5}" http://edamontology.org/data_1792 Gene name (MGD) Symbol of a gene from the Mouse Genome Database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1792 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs: MGD Symbol of a gene from the Mouse Genome Database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 MGI:[0-9]+ http://edamontology.org/data_1793 Gene name (Bacillus subtilis) Symbol of a gene from Bacillus subtilis Genome Sequence Project. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1793 http://edamontology.org/data_1026 http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG Symbol of a gene from Bacillus subtilis Genome Sequence Project. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1794 Gene ID (PlasmoDB) Identifier of a gene from PlasmoDB Plasmodium Genome Resource. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1794 http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB Identifier of a gene from PlasmoDB Plasmodium Genome Resource. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1795 Gene ID (EcoGene) EcoGene ID|EcoGene Accession Identifier of a gene from EcoGene Database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1795 Identifier of a gene from EcoGene Database. EcoGene ID|EcoGene Accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1796 Gene ID (FlyBase) Gene identifier from FlyBase database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1796 http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase|http://www.geneontology.org/doc/GO.xrf_abbs: FB Gene identifier from FlyBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1797 Gene ID (GeneDB Glossina morsitans) Gene identifier from Glossina morsitans GeneDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1797 http://edamontology.org/data_1035 Gene identifier from Glossina morsitans GeneDB database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1798 Gene ID (GeneDB Leishmania major) Gene identifier from Leishmania major GeneDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1798 http://edamontology.org/data_1035 Gene identifier from Leishmania major GeneDB database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1799 Gene ID (GeneDB Plasmodium falciparum) Gene identifier from Plasmodium falciparum GeneDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1799 http://edamontology.org/data_1035 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum Gene identifier from Plasmodium falciparum GeneDB database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1800 Gene ID (GeneDB Schizosaccharomyces pombe) Gene identifier from Schizosaccharomyces pombe GeneDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1800 http://edamontology.org/data_1035 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe Gene identifier from Schizosaccharomyces pombe GeneDB database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1801 Gene ID (GeneDB Trypanosoma brucei) Gene identifier from Trypanosoma brucei GeneDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1801 http://edamontology.org/data_1035 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei Gene identifier from Trypanosoma brucei GeneDB database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1802 Gene ID (Gramene) Gene identifier from Gramene database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1802 http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene|http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE Gene identifier from Gramene database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1803 Gene ID (Virginia microbial) Gene identifier from Virginia Bioinformatics Institute microbial database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1803 http://www.geneontology.org/doc/GO.xrf_abbs: VMD|http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD Gene identifier from Virginia Bioinformatics Institute microbial database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1804 Gene ID (SGN) Gene identifier from Sol Genomics Network. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1804 http://www.geneontology.org/doc/GO.xrf_abbs: SGN Gene identifier from Sol Genomics Network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1805 Gene ID (WormBase) Gene identifier used by WormBase database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2113 beta12orEarlier data_1805 http://www.geneontology.org/doc/GO.xrf_abbs: WormBase|http://www.geneontology.org/doc/GO.xrf_abbs: WB Gene identifier used by WormBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data WBGene[0-9]{8} http://edamontology.org/data_1806 Gene synonym Any name (other than the recommended one) for a gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1806 http://edamontology.org/data_1026 Any name (other than the recommended one) for a gene. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1807 ORF name The name of an open reading frame attributed by a sequencing project. FALSE http://edamontology.org/data_2795|http://edamontology.org/data_2099 beta12orEarlier data_1807 The name of an open reading frame attributed by a sequencing project. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1852 Sequence assembly component A component of a larger sequence assembly. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1852 http://edamontology.org/data_0925 A component of a larger sequence assembly. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1853 Chromosome annotation (aberration) A report on a chromosome aberration such as abnormalities in chromosome structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1853 http://edamontology.org/data_0919 A report on a chromosome aberration such as abnormalities in chromosome structure. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1855 Clone ID An identifier of a clone (cloned molecular sequence) from a database. FALSE http://edamontology.org/data_2769 beta12orEarlier data_1855 An identifier of a clone (cloned molecular sequence) from a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1856 PDB insertion code An insertion code (part of the residue number) for an amino acid residue from a PDB file. FALSE http://edamontology.org/data_1016 beta12orEarlier data_1856 WHATIF: insertion_code|PDBML:pdbx_PDB_ins_code An insertion code (part of the residue number) for an amino acid residue from a PDB file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1857 Atomic occupancy The fraction of an atom type present at a site in a molecular structure.|The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. FALSE http://edamontology.org/data_1917 beta12orEarlier data_1857 WHATIF: PDBx_occupancy The fraction of an atom type present at a site in a molecular structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1858 Isotropic B factor Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. FALSE http://edamontology.org/data_1917 beta12orEarlier data_1858 WHATIF: PDBx_B_iso_or_equiv Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1859 Deletion map Deletion-based cytogenetic map A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.|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. FALSE http://edamontology.org/data_1283 beta12orEarlier data_1859 A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. Deletion-based cytogenetic map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1860 QTL map Quantitative trait locus map A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. FALSE http://edamontology.org/data_1278 beta12orEarlier data_1860 A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. Quantitative trait locus map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1863 Haplotype map "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." FALSE http://edamontology.org/data_1278 beta12orEarlier data_1863 Moby:Haplotyping_Study_obj "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1864 Map set data "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." FALSE http://edamontology.org/data_2019 beta12orEarlier data_1864 Moby:GCP_CorrelatedMapSet|Moby:GCP_CorrelatedLinkageMapSet "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1865 Map feature A feature which may mapped (positioned) on a genetic or other type of map.|Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1865 http://edamontology.org/data_1255|http://edamontology.org/data_2019|http://edamontology.org/data_1276 A feature which may mapped (positioned) on a genetic or other type of map. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1866 Map type "A designation of the type of map (genetic map, physical map, sequence map etc) or map set.|Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1866 http://edamontology.org/data_0842 "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_1867 Protein fold name The name of a protein fold. FALSE http://edamontology.org/data_2099 beta12orEarlier data_1867 The name of a protein fold. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1868 Taxon Taxonomy rank|Taxonomic rank The name of a group of organisms belonging to the same taxonomic rank.|For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. FALSE http://edamontology.org/data_2909 beta12orEarlier data_1868 Moby:PotentialTaxon|Moby:BriefTaxonConcept The name of a group of organisms belonging to the same taxonomic rank. Taxonomy rank|Taxonomic rank http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1869 Organism identifier A unique identifier of a (group of) organisms. FALSE http://edamontology.org/data_0976 beta12orEarlier data_1869 A unique identifier of a (group of) organisms. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1870 Genus name The name of a genus of organism. FALSE http://edamontology.org/data_1868 beta12orEarlier data_1870 The name of a genus of organism. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1872 Taxonomic classification Taxonomic information|Taxonomic name "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.|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." FALSE http://edamontology.org/data_2909 beta12orEarlier data_1872 Moby:TaxonScientificName|Moby:GCP_Taxon|Moby:TaxonName|Moby:iANT_organism-xml|Moby:TaxonTCS "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." Taxonomic information|Taxonomic name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1873 iHOP organism ID A unique identifier for an organism used in the iHOP database. FALSE http://edamontology.org/data_2908 beta12orEarlier data_1873 Moby_namespace:iHOPorganism A unique identifier for an organism used in the iHOP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1874 Genbank common name Common name for an organism as used in the GenBank database. FALSE http://edamontology.org/data_2909 beta12orEarlier data_1874 Common name for an organism as used in the GenBank database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1875 NCBI taxon The name of a taxon from the NCBI taxonomy database. FALSE http://edamontology.org/data_1868 beta12orEarlier data_1875 The name of a taxon from the NCBI taxonomy database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1877 Synonym An alternative for a word. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1877 http://edamontology.org/data_0968 An alternative for a word. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1878 Misspelling A common misspelling of a word. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1878 http://edamontology.org/data_0968 A common misspelling of a word. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1879 Acronym An abbreviation of a phrase or word. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1879 http://edamontology.org/data_0968 An abbreviation of a phrase or word. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1880 Misnomer A term which is likely to be misleading of its meaning. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1880 http://edamontology.org/data_0968 A term which is likely to be misleading of its meaning. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1881 Author ID Information on the authors of a published work. FALSE http://edamontology.org/data_2118 beta12orEarlier data_1881 Moby:Author Information on the authors of a published work. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1882 DragonDB author identifier An identifier representing an author in the DragonDB database. FALSE http://edamontology.org/data_1881 beta12orEarlier data_1882 An identifier representing an author in the DragonDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1883 Annotated URI A URI along with annotation describing the data found at the address. FALSE http://edamontology.org/data_2093 beta12orEarlier data_1883 Moby:DescribedLink A URI along with annotation describing the data found at the address. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1884 UniProt keywords A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1884 http://edamontology.org/data_0582 A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1885 Gene ID (GeneFarm) Identifier of a gene from the GeneFarm database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1885 Moby_namespace:GENEFARM_GeneID Identifier of a gene from the GeneFarm database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1886 Blattner number The blattner identifier for a gene. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1886 Moby_namespace:Blattner_number The blattner identifier for a gene. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1887 Gene ID (MIPS Maize) Identifier for genetic elements in MIPS Maize database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1887 http://edamontology.org/data_2285 Moby_namespace:MIPS_GE_Maize Identifier for genetic elements in MIPS Maize database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1888 Gene ID (MIPS Medicago) Identifier for genetic elements in MIPS Medicago database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1888 http://edamontology.org/data_2285 Moby_namespace:MIPS_GE_Medicago Identifier for genetic elements in MIPS Medicago database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_1889 Gene name (DragonDB) The name of an Antirrhinum Gene from the DragonDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1889 http://edamontology.org/data_1026 Moby_namespace:DragonDB_Gene The name of an Antirrhinum Gene from the DragonDB database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1890 Gene name (Arabidopsis) "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1890 http://edamontology.org/data_1026 "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1891 iHOP symbol A unique identifier of a protein or gene used in the iHOP database. FALSE http://edamontology.org/data_2295|http://edamontology.org/data_2907|http://edamontology.org/data_2109 beta12orEarlier data_1891 Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1892 Gene name (GeneFarm) GeneFarm gene ID Name of a gene from the GeneFarm database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1892 http://edamontology.org/data_1026 Name of a gene from the GeneFarm database. GeneFarm gene ID http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_1893 Locus ID Locus name|Locus identifier "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." FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_1893 "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." Locus name|Locus identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1895 Locus ID (AGI) AGI ID|AGI locus code|AGI identifier|Arabidopsis gene loci number "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" FALSE http://edamontology.org/data_1893 beta12orEarlier data_1895 http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" AGI ID|AGI locus code|AGI identifier|Arabidopsis gene loci number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data AT[1-5]G[0-9]{5} http://edamontology.org/data_1896 Locus ID (ASPGD) Identifier for loci from ASPGD (Aspergillus Genome Database). FALSE http://edamontology.org/data_1893 beta12orEarlier data_1896 http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID|http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD Identifier for loci from ASPGD (Aspergillus Genome Database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1897 Locus ID (MGG) Identifier for loci from Magnaporthe grisea Database at the Broad Institute. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1897 http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG Identifier for loci from Magnaporthe grisea Database at the Broad Institute. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1898 Locus ID (CGD) CGDID|CGD locus identifier Identifier for loci from CGD (Candida Genome Database). FALSE http://edamontology.org/data_1893 beta12orEarlier data_1898 http://www.geneontology.org/doc/GO.xrf_abbs: CGD|http://www.geneontology.org/doc/GO.xrf_abbs: CGDID Identifier for loci from CGD (Candida Genome Database). CGDID|CGD locus identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1899 Locus ID (CMR) Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1899 http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR|http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1900 NCBI locus tag Locus ID (NCBI) Identifier for loci from NCBI database. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1900 Moby_namespace:LocusID|http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag Identifier for loci from NCBI database. Locus ID (NCBI) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1901 Locus ID (SGD) SGDID Identifier for loci from SGD (Saccharomyces Genome Database). FALSE http://edamontology.org/data_2632|http://edamontology.org/data_1893 beta12orEarlier data_1901 http://www.geneontology.org/doc/GO.xrf_abbs: SGD|http://www.geneontology.org/doc/GO.xrf_abbs: SGDID Identifier for loci from SGD (Saccharomyces Genome Database). SGDID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1902 Locus ID (MMP) Identifier of loci from Maize Mapping Project. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1902 Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1903 Locus ID (DictyBase) Identifier of locus from DictyBase (Dictyostelium discoideum). FALSE http://edamontology.org/data_1893 beta12orEarlier data_1903 Moby_namespace:DDB_gene Identifier of locus from DictyBase (Dictyostelium discoideum). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1904 Locus ID (EntrezGene) Identifier of a locus from EntrezGene database. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1904 Moby_namespace:EntrezGene_ID|Moby_namespace:EntrezGene_EntrezGeneID Identifier of a locus from EntrezGene database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1905 Locus ID (MaizeGDB) Identifier of locus from MaizeGDB (Maize genome database). FALSE http://edamontology.org/data_1893 beta12orEarlier data_1905 Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1906 Quantitative trait locus 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).|A QTL sometimes but does not necessarily correspond to a gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_1906 http://edamontology.org/data_2012 Moby:SO_QTL 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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_1907 Gene ID (KOME) Identifier of a gene from the KOME database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_1907 Moby_namespace:GeneId Identifier of a gene from the KOME database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1908 Locus ID (Tropgene) Identifier of a locus from the Tropgene database. FALSE http://edamontology.org/data_1893 beta12orEarlier data_1908 Moby:Tropgene_locus Identifier of a locus from the Tropgene database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1916 Alignment "An alignment of molecular sequences, structures or profiles derived from them." FALSE http://edamontology.org/data_0006 beta12orEarlier data_1916 "An alignment of molecular sequences, structures or profiles derived from them." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_1917 Atomic property General atomic property Data for an atom (in a molecular structure). FALSE http://edamontology.org/data_2087 beta12orEarlier data_1917 Data for an atom (in a molecular structure). General atomic property http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2007 UniProt keyword A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. FALSE http://edamontology.org/data_0968 beta12orEarlier data_2007 http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW|Moby_namespace:SP_KW A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2009 Ordered locus name "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2009 http://edamontology.org/data_1893 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2012 Sequence coordinates Sequence co-ordinates|Locus|Map position "A position in a map (for example a genetic map), either a single position (point) or a region / interval.|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. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position." FALSE http://edamontology.org/data_1016|http://edamontology.org/data_2019|http://edamontology.org/data_1017 beta12orEarlier data_2012 Moby:GenePosition|Moby:HitPosition|PDBML:_atom_site.id|Moby:GCP_MapPosition|Moby:GCP_MapInterval|Moby:Position|Moby:Locus|Moby:GCP_MapPoint|Moby:MapPosition "A position in a map (for example a genetic map), either a single position (point) or a region / interval." Sequence co-ordinates|Locus|Map position http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2016 Amino acid property Amino acid data "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." FALSE http://edamontology.org/data_2087 beta12orEarlier data_2016 "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." Amino acid data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2018 Annotation "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.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2018 http://edamontology.org/data_2048 "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://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2019 Map data Map attribute "A molecular map (genetic or physical), an attribute of such a map, or data extracted from or derived from the analysis of such a map.|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." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2019 "A molecular map (genetic or physical), an attribute of such a map, or data extracted from or derived from the analysis of such a map." Map attribute http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2022 Vienna RNA structural data Data used by the Vienna RNA analysis package. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2022 Data used by the Vienna RNA analysis package. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2023 Sequence mask parameter Data used to replace (mask) characters in a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2023 Data used to replace (mask) characters in a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2024 Enzyme kinetics data "Data concerning chemical reaction(s) catalysed by enzyme(s).|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0897|http://edamontology.org/data_2978 beta12orEarlier data_2024 Data concerning chemical reaction(s) catalysed by enzyme(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2025 Michaelis Menten plot "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." FALSE http://edamontology.org/data_2024 beta12orEarlier data_2025 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2026 Hanes Woolf plot 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). FALSE http://edamontology.org/data_2024 beta12orEarlier data_2026 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2028 Experimental data "Raw data from or annotation on laboratory experiments.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2028 http://edamontology.org/data_2531|http://edamontology.org/data_3108 Raw data from or annotation on laboratory experiments. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2041 Genome version information Information on a genome version. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2041 http://edamontology.org/data_2711 Information on a genome version. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2042 Evidence "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." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2042 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2043 Sequence record lite "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2043 "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2044 Sequence Sequences "One or more molecular sequences, possibly with associated annotation.|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." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2044 "One or more molecular sequences, possibly with associated annotation." Sequences http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2046 Nucleic acid sequence record (lite) "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2046 "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2047 Protein sequence record (lite) Sequence record lite (protein) "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2047 "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." Sequence record lite (protein) http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2048 Report Document "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.|You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2048 "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself." Document http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2050 Molecular property (general) General molecular property General data for a molecule. FALSE http://edamontology.org/data_2087 beta12orEarlier data_2050 General data for a molecule. General molecular property http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2053 Structural data "Data concerning molecular structural data.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2053 http://edamontology.org/data_2085|http://edamontology.org/data_0883 Data concerning molecular structural data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2070 Sequence motif (nucleic acid) Nucleic acid sequence motif|RNA sequence motif|DNA sequence motif A nucleotide sequence motif. FALSE http://edamontology.org/data_1353 beta12orEarlier data_2070 A nucleotide sequence motif. Nucleic acid sequence motif RNA sequence motif|DNA sequence motif http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2071 Sequence motif (protein) Protein sequence motif An amino acid sequence motif. FALSE http://edamontology.org/data_1353 beta12orEarlier data_2071 An amino acid sequence motif. Protein sequence motif http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2079 Search parameter "Some simple value controlling a search operation, typically a search of a database." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2079 "Some simple value controlling a search operation, typically a search of a database." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2080 Database search results Database hits|Search results A report of hits from searching a database of some type. FALSE http://edamontology.org/data_0006 beta12orEarlier data_2080 A report of hits from searching a database of some type. Database hits|Search results http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2081 Secondary structure The secondary structure assignment (predicted or real) of a nucleic acid or protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2081 http://edamontology.org/data_0883 The secondary structure assignment (predicted or real) of a nucleic acid or protein. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2082 Matrix Array "An array of numerical values.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2082 An array of numerical values. Array http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2083 Alignment data "Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2083 http://edamontology.org/data_1394 "Data concerning, extracted from, or derived from the analysis of molecular alignment of some type." http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/data_2084 Nucleic acid report "An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2084 "An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2085 Structure report Structure-derived report "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2085 "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." Structure-derived report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2086 Nucleic acid structure data Nucleic acid structural property|Nucleic acid property (structural) "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).|This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties." FALSE http://edamontology.org/data_0912 beta12orEarlier data_2086 "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)." Nucleic acid structural property|Nucleic acid property (structural) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2087 Molecular property Physicochemical property|SO:0000400 "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2087 "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." Physicochemical property SO:0000400 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2088 DNA base structural data "Structural data for DNA base pairs or runs of bases, such as energy or angle data." FALSE http://edamontology.org/data_2086 beta12orEarlier data_2088 "Structural data for DNA base pairs or runs of bases, such as energy or angle data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2090 Database entry version information "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2090 http://edamontology.org/data_0957 "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://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2091 Accession "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." FALSE http://edamontology.org/data_0842 beta12orEarlier data_2091 "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2092 SNP single nucleotide polymorphism (SNP) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2092 single nucleotide polymorphism (SNP) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2093 Data reference "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.|A list of database accessions or identifiers are usually included." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2093 "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2098 Job identifier An identifier of a submitted job. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2098 An identifier of a submitted job. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2099 Name http://www.w3.org/2000/01/rdf-schema#label|Symbolic name "A name of a thing, which need not necessarily uniquely identify it." FALSE http://edamontology.org/data_0842 beta12orEarlier data_2099 http://www.w3.org/2000/01/rdf-schema#label "A name of a thing, which need not necessarily uniquely identify it." Symbolic name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2100 Type "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2100 http://edamontology.org/data_0842 "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://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2101 User ID An identifier of a software end-user (typically a person). FALSE http://edamontology.org/data_2118 beta12orEarlier data_2101 An identifier of a software end-user (typically a person). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2102 KEGG organism code A three-letter code used in the KEGG databases to uniquely identify organisms. FALSE http://edamontology.org/data_1154|http://edamontology.org/data_2909 beta12orEarlier data_2102 A three-letter code used in the KEGG databases to uniquely identify organisms. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2103 Gene name (KEGG GENES) Name of an entry (gene) from the KEGG GENES database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2103 http://edamontology.org/data_1026 Moby_namespace:GeneId Name of an entry (gene) from the KEGG GENES database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 [a-zA-Z_0-9]+:[a-zA-Z_0-9.-]* http://edamontology.org/data_2104 BioCyc ID Identifier of an object from one of the BioCyc databases. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2104 Identifier of an object from one of the BioCyc databases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2105 Compound ID (BioCyc) BioCyc compound identifier|BioCyc compound ID Identifier of a compound from the BioCyc chemical compounds database. FALSE http://edamontology.org/data_2104|http://edamontology.org/data_2894 beta12orEarlier data_2105 Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound identifier|BioCyc compound ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2106 Reaction ID (BioCyc) Identifier of a biological reaction from the BioCyc reactions database. FALSE http://edamontology.org/data_2104|http://edamontology.org/data_2108 beta12orEarlier data_2106 Identifier of a biological reaction from the BioCyc reactions database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2107 Enzyme ID (BioCyc) BioCyc enzyme ID Identifier of an enzyme from the BioCyc enzymes database. FALSE http://edamontology.org/data_2321|http://edamontology.org/data_2104 beta12orEarlier data_2107 Identifier of an enzyme from the BioCyc enzymes database. BioCyc enzyme ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2108 Reaction ID Identifier of a biological reaction from a database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2108 Identifier of a biological reaction from a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2109 Identifier (hybrid) An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).|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'. FALSE http://edamontology.org/data_0842 beta12orEarlier data_2109 An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2110 Molecular property identifier Identifier of a molecular property. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2110 Identifier of a molecular property. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2111 Codon usage table ID Codon usage table identifier "Identifier of a codon usage table, for example a genetic code." FALSE http://edamontology.org/data_0976 beta12orEarlier data_2111 "Identifier of a codon usage table, for example a genetic code." Codon usage table identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2112 FlyBase primary identifier Primary identifier of an object from the FlyBase database. FALSE http://edamontology.org/data_1089 beta12orEarlier data_2112 Primary identifier of an object from the FlyBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2113 WormBase identifier Identifier of an object from the WormBase database. FALSE http://edamontology.org/data_2109 beta12orEarlier data_2113 Identifier of an object from the WormBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2114 WormBase wormpep ID Protein identifier used by WormBase database. FALSE http://edamontology.org/data_2907|http://edamontology.org/data_2113 beta12orEarlier data_2114 Protein identifier used by WormBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data CE[0-9]{5} http://edamontology.org/data_2116 Nucleic acid features (codon) "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2116 http://edamontology.org/data_1276 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2117 Map identifier An identifier of a map of a molecular sequence. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2117 An identifier of a map of a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2118 Person identifier An identifier of a software end-user (typically a person). FALSE http://edamontology.org/data_0976 beta12orEarlier data_2118 An identifier of a software end-user (typically a person). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2119 Nucleic acid identifier Name or other identifier of a nucleic acid molecule. FALSE http://edamontology.org/data_0982 beta12orEarlier data_2119 Name or other identifier of a nucleic acid molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2126 Translation frame specification Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). FALSE http://edamontology.org/data_2534 beta12orEarlier data_2126 Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2127 Genetic code identifier An identifier of a genetic code. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2127 An identifier of a genetic code. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2128 Genetic code name "Informal name for a genetic code, typically an organism name." FALSE http://edamontology.org/data_2127|http://edamontology.org/data_2099 beta12orEarlier data_2128 "Informal name for a genetic code, typically an organism name." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2129 File format name "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." FALSE http://edamontology.org/data_3358|http://edamontology.org/data_2099 beta12orEarlier data_2129 "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2130 Sequence profile type "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2130 http://edamontology.org/data_0842 "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2131 Operating system name "Name of a computer operating system such as Linux, PC or Mac." FALSE http://edamontology.org/data_2099 beta12orEarlier data_2131 "Name of a computer operating system such as Linux, PC or Mac." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2132 Mutation type "A type of point or block mutation, including insertion, deletion, change, duplication and moves." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2132 "A type of point or block mutation, including insertion, deletion, change, duplication and moves." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2133 Logical operator "A logical operator such as OR, AND, XOR, and NOT." FALSE http://edamontology.org/data_2099 beta12orEarlier data_2133 "A logical operator such as OR, AND, XOR, and NOT." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2134 Results sort order "A control of the order of data that is output, for example the order of sequences in an alignment.|Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2134 "A control of the order of data that is output, for example the order of sequences in an alignment." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2135 Toggle "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2135 "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2136 Sequence width The width of an output sequence or alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2136 http://edamontology.org/data_1249 The width of an output sequence or alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2137 Gap penalty A penalty for introducing or extending a gap in an alignment. FALSE http://edamontology.org/data_1394 beta12orEarlier data_2137 A penalty for introducing or extending a gap in an alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2139 Nucleic acid melting temperature Melting temperature "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." FALSE http://edamontology.org/data_2985 beta12orEarlier data_2139 "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." Melting temperature http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2140 Concentration The concentration of a chemical compound. FALSE http://edamontology.org/data_2050 beta12orEarlier data_2140 The concentration of a chemical compound. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2141 Window step size Size of the incremental 'step' a sequence window is moved over a sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2141 http://edamontology.org/data_1249 Size of the incremental 'step' a sequence window is moved over a sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2142 EMBOSS graph An image of a graph generated by the EMBOSS suite. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2142 http://edamontology.org/data_2968 An image of a graph generated by the EMBOSS suite. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2143 EMBOSS report An application report generated by the EMBOSS suite. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2143 http://edamontology.org/data_2048 An application report generated by the EMBOSS suite. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2145 Sequence offset An offset for a single-point sequence position. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2145 An offset for a single-point sequence position. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2146 Threshold A value that serves as a threshold for a tool (usually to control scoring or output). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2146 A value that serves as a threshold for a tool (usually to control scoring or output). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2147 Protein report (transcription factor) "An informative report on a transcription factor protein.|This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2147 http://edamontology.org/data_0896 An informative report on a transcription factor protein. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2149 Database category name The name of a category of biological or bioinformatics database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2149 http://edamontology.org/data_0957 The name of a category of biological or bioinformatics database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2150 Sequence profile name Name of a sequence profile. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2150 http://edamontology.org/data_1115 Name of a sequence profile. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2151 Color Specification of one or more colors. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2151 Specification of one or more colors. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2152 Rendering parameter A parameter that is used to control rendering (drawing) to a device or image. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2152 A parameter that is used to control rendering (drawing) to a device or image. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2154 Sequence name Any arbitrary name of a molecular sequence. FALSE http://edamontology.org/data_1063|http://edamontology.org/data_2099 beta12orEarlier data_2154 Any arbitrary name of a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2156 Date A temporal date. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2156 A temporal date. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2157 Word composition Word composition data for a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2157 http://edamontology.org/data_1268|http://edamontology.org/data_1266 Word composition data for a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2160 Fickett testcode plot A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. FALSE http://edamontology.org/data_2884 beta12orEarlier data_2160 A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2161 Sequence similarity plot Sequence conservation report "A plot of sequence similarities identified from word-matching or character comparison.|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." FALSE http://edamontology.org/data_0867|http://edamontology.org/data_2884 beta12orEarlier data_2161 A plot of sequence similarities identified from word-matching or character comparison. Sequence conservation report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2162 Helical wheel An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. FALSE http://edamontology.org/data_1709 beta12orEarlier data_2162 An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2163 Helical net "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.|Useful for highlighting amphipathicity and other properties." FALSE http://edamontology.org/data_1709 beta12orEarlier data_2163 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2164 Protein sequence properties plot A plot of general physicochemical properties of a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2164 http://edamontology.org/data_0897 A plot of general physicochemical properties of a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2165 Protein ionisation curve A plot of pK versus pH for a protein. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_0897 beta12orEarlier data_2165 A plot of pK versus pH for a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2166 Sequence composition plot A plot of character or word composition / frequency of a molecular sequence. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_1261 beta12orEarlier data_2166 A plot of character or word composition / frequency of a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2167 Nucleic acid density plot Density plot (of base composition) for a nucleotide sequence. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_1261 beta12orEarlier data_2167 Density plot (of base composition) for a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2168 Sequence trace image Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). FALSE http://edamontology.org/data_2969 beta12orEarlier data_2168 Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2169 Nucleic acid features (siRNA) A report on siRNA duplexes in mRNA. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2169 http://edamontology.org/data_1276 A report on siRNA duplexes in mRNA. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2173 Sequence set (stream) A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.|This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2173 http://edamontology.org/data_0850 A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2174 FlyBase secondary identifier Secondary identifier of an object from the FlyBase database.|Secondary identifier are used to handle entries that were merged with or split from other entries in the database. FALSE http://edamontology.org/data_1089 beta12orEarlier data_2174 Secondary identifier of an object from the FlyBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2176 Cardinality The number of a certain thing. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2176 The number of a certain thing. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2177 Exactly 1 A single thing. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2177 http://edamontology.org/data_2337 A single thing. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2178 1 or more One or more things. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2178 http://edamontology.org/data_2337 One or more things. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2179 Exactly 2 Exactly two things. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2179 http://edamontology.org/data_2337 Exactly two things. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2180 2 or more Two or more things. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2180 http://edamontology.org/data_2337 Two or more things. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2190 Sequence checksum Hash code|Hash value|Hash|Hash sum "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." FALSE http://edamontology.org/data_2534 beta12orEarlier data_2190 "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." Hash code|Hash value|Hash|Hash sum http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2191 Protein features report (chemical modifications) chemical modification of a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2191 chemical modification of a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_2192 Error Data on an error generated by computer system or tool. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2192 http://edamontology.org/data_3106 Data on an error generated by computer system or tool. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2193 Database entry metadata Basic information on any arbitrary database entry. FALSE http://edamontology.org/data_2337 beta12orEarlier data_2193 Basic information on any arbitrary database entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2198 Gene cluster A cluster of similar genes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2198 http://edamontology.org/data_1246 A cluster of similar genes. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2201 Sequence record full "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2201 "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2208 Plasmid identifier An identifier of a plasmid in a database. FALSE http://edamontology.org/data_2119 beta12orEarlier data_2208 An identifier of a plasmid in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2209 Mutation ID A unique identifier of a specific mutation catalogued in a database. FALSE http://edamontology.org/data_2538|http://edamontology.org/data_2091 beta12orEarlier data_2209 A unique identifier of a specific mutation catalogued in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2212 Mutation annotation (basic) "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2212 http://edamontology.org/data_1276 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2213 Mutation annotation (prevalence) "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2213 http://edamontology.org/data_1276 "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2214 Mutation annotation (prognostic) "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2214 http://edamontology.org/data_1276 "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2215 Mutation annotation (functional) "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2215 http://edamontology.org/data_1276 "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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2216 Codon number "The number of a codon, for instance, at which a mutation is located." FALSE http://edamontology.org/data_1016 beta12orEarlier data_2216 "The number of a codon, for instance, at which a mutation is located." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2217 Tumor annotation "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2217 http://edamontology.org/data_1622 "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://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2218 Server metadata "Basic information about a server on the web, such as an SRS server." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2218 http://edamontology.org/data_3106 "Basic information about a server on the web, such as an SRS server." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2219 Database field name The name of a field in a database. FALSE http://edamontology.org/data_2099 beta12orEarlier data_2219 The name of a field in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2220 Sequence cluster ID (SYSTERS) SYSTERS cluster ID Unique identifier of a sequence cluster from the SYSTERS database. FALSE http://edamontology.org/data_1112 beta12orEarlier data_2220 Unique identifier of a sequence cluster from the SYSTERS database. SYSTERS cluster ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2223 Ontology metadata Data concerning a biological ontology. FALSE http://edamontology.org/data_2337 beta12orEarlier data_2223 Data concerning a biological ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2235 Raw SCOP domain classification Raw SCOP domain classification data files.|These are the parsable data files provided by SCOP. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2235 http://edamontology.org/data_0907 Raw SCOP domain classification data files. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2236 Raw CATH domain classification Raw CATH domain classification data files.|These are the parsable data files provided by CATH. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2236 http://edamontology.org/data_0907 Raw CATH domain classification data files. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2240 Heterogen annotation An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2240 http://edamontology.org/data_0962 An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2242 Phylogenetic property values Phylogenetic property values data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2242 http://edamontology.org/data_0871 Phylogenetic property values data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2245 Sequence set (bootstrapped) A collection of sequences output from a bootstrapping (resampling) procedure.|Bootstrapping is often performed in phylogenetic analysis. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2245 http://edamontology.org/data_0850 A collection of sequences output from a bootstrapping (resampling) procedure. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2247 Phylogenetic consensus tree A consensus phylogenetic tree derived from comparison of multiple trees. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2247 http://edamontology.org/data_0872 A consensus phylogenetic tree derived from comparison of multiple trees. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2248 Schema A data schema for organising or transforming data of some type. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2248 http://edamontology.org/data_2048 A data schema for organising or transforming data of some type. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2249 DTD A DTD (document type definition). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2249 http://edamontology.org/data_2048 A DTD (document type definition). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2250 XML Schema An XML Schema. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2250 http://edamontology.org/data_2048 An XML Schema. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2251 Relax-NG schema A relax-NG schema. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2251 http://edamontology.org/data_2048 A relax-NG schema. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2252 XSLT stylesheet An XSLT stylesheet. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2252 http://edamontology.org/data_2048 An XSLT stylesheet. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2253 Data resource definition name The name of a data type. FALSE http://edamontology.org/data_1084|http://edamontology.org/data_2099 beta12orEarlier data_2253 The name of a data type. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2254 OBO file format name "Name of an OBO file format such as OBO-XML, plain and so on." FALSE http://edamontology.org/data_2129 beta12orEarlier data_2254 "Name of an OBO file format such as OBO-XML, plain and so on." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2285 Gene ID (MIPS) MIPS genetic element identifier Identifier for genetic elements in MIPS database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2285 Identifier for genetic elements in MIPS database. MIPS genetic element identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2288 Sequence identifier (protein) An identifier of protein sequence(s) or protein sequence database entries. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2288 http://edamontology.org/data_1096 An identifier of protein sequence(s) or protein sequence database entries. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2289 Sequence identifier (nucleic acid) An identifier of nucleotide sequence(s) or nucleotide sequence database entries. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2289 http://edamontology.org/data_1097 An identifier of nucleotide sequence(s) or nucleotide sequence database entries. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2290 EMBL accession EMBL accession number|EMBL identifier|EMBL ID An accession number of an entry from the EMBL sequence database. FALSE http://edamontology.org/data_1103 beta12orEarlier data_2290 An accession number of an entry from the EMBL sequence database. EMBL accession number|EMBL identifier|EMBL ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2291 UniProt ID UniProtKB identifier|UniProt entry name|UniProtKB entry name|UniProt identifier An identifier of a polypeptide in the UniProt database. FALSE http://edamontology.org/data_2154 beta12orEarlier data_2291 An identifier of a polypeptide in the UniProt database. UniProtKB identifier|UniProt entry name|UniProtKB entry name|UniProt identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2292 GenBank accession GenBank accession number|GenBank identifier|GenBank ID Accession number of an entry from the GenBank sequence database. FALSE http://edamontology.org/data_1103 beta12orEarlier data_2292 Accession number of an entry from the GenBank sequence database. GenBank accession number|GenBank identifier|GenBank ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2293 Gramene secondary identifier Gramene internal ID|Gramene internal identifier|Gramene secondary ID Secondary (internal) identifier of a Gramene database entry. FALSE http://edamontology.org/data_2915 beta12orEarlier data_2293 Secondary (internal) identifier of a Gramene database entry. Gramene internal ID|Gramene internal identifier|Gramene secondary ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2294 Sequence variation ID An identifier of an entry from a database of molecular sequence variation. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2294 An identifier of an entry from a database of molecular sequence variation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2295 Gene ID Gene accession|Gene code "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." FALSE http://edamontology.org/data_1025|http://edamontology.org/data_1893 beta12orEarlier data_2295 "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." Gene accession|Gene code http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2296 Gene name (AceView) Name of an entry (gene) from the AceView genes database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2296 http://edamontology.org/data_1026 Name of an entry (gene) from the AceView genes database. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_2297 Gene ID (ECK) E. coli K-12 gene identifier|ECK accession Identifier of an E. coli K-12 gene from EcoGene Database. FALSE http://edamontology.org/data_1795 beta12orEarlier data_2297 http://www.geneontology.org/doc/GO.xrf_abbs: ECK Identifier of an E. coli K-12 gene from EcoGene Database. E. coli K-12 gene identifier|ECK accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2298 Gene ID (HGNC) HGNC ID Identifier for a gene approved by the HUGO Gene Nomenclature Committee. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2298 Identifier for a gene approved by the HUGO Gene Nomenclature Committee. HGNC ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2299 Gene name Allele name "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." FALSE http://edamontology.org/data_1025|http://edamontology.org/data_2099 beta12orEarlier data_2299 "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." Allele name http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2300 Gene name (NCBI) NCBI gene name Name of an entry (gene) from the NCBI genes database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2300 http://edamontology.org/data_1026 Name of an entry (gene) from the NCBI genes database. NCBI gene name http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_2301 SMILES string A specification of a chemical structure in SMILES format. FALSE http://edamontology.org/data_0846 beta12orEarlier data_2301 A specification of a chemical structure in SMILES format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2302 STRING ID Unique identifier of an entry from the STRING database of protein-protein interactions. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2302 Unique identifier of an entry from the STRING database of protein-protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2307 Virus annotation An informative report on a specific virus. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2307 http://edamontology.org/data_2530 An informative report on a specific virus. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2308 Virus annotation (taxonomy) An informative report on the taxonomy of a specific virus. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2308 http://edamontology.org/data_2530 An informative report on the taxonomy of a specific virus. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2309 Reaction ID (SABIO-RK) Identifier of a biological reaction from the SABIO-RK reactions database. FALSE http://edamontology.org/data_2108 beta12orEarlier data_2309 Identifier of a biological reaction from the SABIO-RK reactions database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2313 Carbohydrate report Annotation on or information derived from one or more specific carbohydrate 3D structure(s). FALSE http://edamontology.org/data_2085 beta12orEarlier data_2313 Annotation on or information derived from one or more specific carbohydrate 3D structure(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2314 GI number gi number|NCBI GI number "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.|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." FALSE http://edamontology.org/data_2362 beta12orEarlier data_2314 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. gi number|NCBI GI number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2315 NCBI version NCBI accession.version|accession.version "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.|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." FALSE http://edamontology.org/data_2362 beta12orEarlier data_2315 "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." NCBI accession.version|accession.version http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2316 Cell line name The name of a cell line. FALSE http://edamontology.org/data_1046 beta12orEarlier data_2316 The name of a cell line. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2317 Cell line name (exact) The name of a cell line. FALSE http://edamontology.org/data_2316 beta12orEarlier data_2317 The name of a cell line. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2318 Cell line name (truncated) The name of a cell line. FALSE http://edamontology.org/data_2316 beta12orEarlier data_2318 The name of a cell line. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2319 Cell line name (no punctuation) The name of a cell line. FALSE http://edamontology.org/data_2316 beta12orEarlier data_2319 The name of a cell line. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2320 Cell line name (assonant) The name of a cell line. FALSE http://edamontology.org/data_2316 beta12orEarlier data_2320 The name of a cell line. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2321 Enzyme ID Enzyme accession "A unique, persistent identifier of an enzyme." FALSE http://edamontology.org/data_1010|http://edamontology.org/data_2907 beta12orEarlier data_2321 "A unique, persistent identifier of an enzyme." Enzyme accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2325 REBASE enzyme number Identifier of an enzyme from the REBASE enzymes database. FALSE http://edamontology.org/data_2321 beta12orEarlier data_2325 Identifier of an enzyme from the REBASE enzymes database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2326 DrugBank ID Unique identifier of a drug from the DrugBank database. FALSE http://edamontology.org/data_2895 beta12orEarlier data_2326 Unique identifier of a drug from the DrugBank database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data DB[0-9]{5} http://edamontology.org/data_2327 GI number (protein) protein gi|protein gi number "A unique identifier assigned to NCBI protein sequence records.|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." FALSE http://edamontology.org/data_2314 beta12orEarlier data_2327 A unique identifier assigned to NCBI protein sequence records. protein gi|protein gi number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2335 Bit score "A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system.|Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches." FALSE http://edamontology.org/data_1413 beta12orEarlier data_2335 "A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2336 Translation phase specification Phase "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." FALSE http://edamontology.org/data_2534 beta12orEarlier data_2336 "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." Phase http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2337 Resource metadata Provenance metadata "Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2337 "Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing." Provenance metadata http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2338 Ontology identifier Any arbitrary identifier of an ontology. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2338 Any arbitrary identifier of an ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2339 Ontology concept name The name of a concept in an ontology. FALSE http://edamontology.org/data_3025|http://edamontology.org/data_2099 beta12orEarlier data_2339 The name of a concept in an ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2340 Genome build identifier An identifier of a build of a particular genome. FALSE http://edamontology.org/data_2749 beta12orEarlier data_2340 An identifier of a build of a particular genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2342 Pathway or network name The name of a biological pathway or network. FALSE http://edamontology.org/data_1082 beta12orEarlier data_2342 The name of a biological pathway or network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2343 Pathway ID (KEGG) KEGG pathway ID Identifier of a pathway from the KEGG pathway database. FALSE http://edamontology.org/data_2365|http://edamontology.org/data_1154 beta12orEarlier data_2343 Identifier of a pathway from the KEGG pathway database. KEGG pathway ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[a-zA-Z_0-9]{2,3}[0-9]{5}" http://edamontology.org/data_2344 Pathway ID (NCI-Nature) Identifier of a pathway from the NCI-Nature pathway database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_2344 Identifier of a pathway from the NCI-Nature pathway database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9]+ http://edamontology.org/data_2345 Pathway ID (ConsensusPathDB) Identifier of a pathway from the ConsensusPathDB pathway database. FALSE http://edamontology.org/data_2365|http://edamontology.org/data_2917 beta12orEarlier data_2345 Identifier of a pathway from the ConsensusPathDB pathway database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2346 Sequence cluster ID (UniRef) UniRef entry accession|UniRef cluster id Unique identifier of an entry from the UniRef database. FALSE http://edamontology.org/data_1112 beta12orEarlier data_2346 Unique identifier of an entry from the UniRef database. UniRef entry accession|UniRef cluster id http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2347 Sequence cluster ID (UniRef100) UniRef100 cluster id|UniRef100 entry accession Unique identifier of an entry from the UniRef100 database. FALSE http://edamontology.org/data_2346 beta12orEarlier data_2347 Unique identifier of an entry from the UniRef100 database. UniRef100 cluster id|UniRef100 entry accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2348 Sequence cluster ID (UniRef90) UniRef90 cluster id|UniRef90 entry accession Unique identifier of an entry from the UniRef90 database. FALSE http://edamontology.org/data_2346 beta12orEarlier data_2348 Unique identifier of an entry from the UniRef90 database. UniRef90 cluster id|UniRef90 entry accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2349 Sequence cluster ID (UniRef50) UniRef50 entry accession|UniRef50 cluster id Unique identifier of an entry from the UniRef50 database. FALSE http://edamontology.org/data_2346 beta12orEarlier data_2349 Unique identifier of an entry from the UniRef50 database. UniRef50 entry accession|UniRef50 cluster id http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2353 Ontology data Ontological data "Data concerning or derived from an ontology.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2353 Data concerning or derived from an ontology. Ontological data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2354 RNA family report RNA family annotation An informative report on a specific RNA family or other group of classified RNA sequences. FALSE http://edamontology.org/data_3148 beta12orEarlier data_2354 An informative report on a specific RNA family or other group of classified RNA sequences. RNA family annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2355 RNA family identifier "Identifier of an RNA family, typically an entry from a RNA sequence classification database." FALSE http://edamontology.org/data_0976 beta12orEarlier data_2355 "Identifier of an RNA family, typically an entry from a RNA sequence classification database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2356 RFAM accession Stable accession number of an entry (RNA family) from the RFAM database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2355 beta12orEarlier data_2356 Stable accession number of an entry (RNA family) from the RFAM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2357 Protein signature type A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2357 http://edamontology.org/data_0842 A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2358 Domain-nucleic acid interaction report An informative report on protein domain-DNA/RNA interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2358 http://edamontology.org/data_0906 An informative report on protein domain-DNA/RNA interaction(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2359 Domain-domain interactions An informative report on protein domain-protein domain interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2359 http://edamontology.org/data_0906 An informative report on protein domain-protein domain interaction(s). http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/data_2360 Domain-domain interaction (indirect) Data on indirect protein domain-protein domain interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2360 http://edamontology.org/data_0906 Data on indirect protein domain-protein domain interaction(s). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2362 Sequence accession (hybrid) Accession number of a nucleotide or protein sequence database entry. FALSE http://edamontology.org/data_1093 beta12orEarlier data_2362 Accession number of a nucleotide or protein sequence database entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2363 2D PAGE data "Data concerning two-dimensional polygel electrophoresis.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2363 Data concerning two-dimensional polygel electrophoresis. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 beta13 http://edamontology.org/data_2364 2D PAGE report "two-dimensional gel electrophoresis experiments, gels or spots in a gel." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2364 "two-dimensional gel electrophoresis experiments, gels or spots in a gel." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_2365 Pathway or network accession "A persistent, unique identifier of a biological pathway or network (typically a database entry)." FALSE http://edamontology.org/data_1082|http://edamontology.org/data_2091 beta12orEarlier data_2365 "A persistent, unique identifier of a biological pathway or network (typically a database entry)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2366 Secondary structure alignment Alignment of the (1D representations of) secondary structure of two or more molecules. FALSE http://edamontology.org/data_1916 beta12orEarlier data_2366 Alignment of the (1D representations of) secondary structure of two or more molecules. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2367 ASTD ID Identifier of an object from the ASTD database. FALSE http://edamontology.org/data_1097|http://edamontology.org/data_2109 beta12orEarlier data_2367 Identifier of an object from the ASTD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2368 ASTD ID (exon) Identifier of an exon from the ASTD database. FALSE http://edamontology.org/data_2367 beta12orEarlier data_2368 Identifier of an exon from the ASTD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2369 ASTD ID (intron) Identifier of an intron from the ASTD database. FALSE http://edamontology.org/data_2367 beta12orEarlier data_2369 Identifier of an intron from the ASTD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2370 ASTD ID (polya) Identifier of a polyA signal from the ASTD database. FALSE http://edamontology.org/data_2367 beta12orEarlier data_2370 Identifier of a polyA signal from the ASTD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2371 ASTD ID (tss) Identifier of a transcription start site from the ASTD database. FALSE http://edamontology.org/data_2367 beta12orEarlier data_2371 Identifier of a transcription start site from the ASTD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2372 2D PAGE spot report An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2372 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_2373 Spot ID Unique identifier of a spot from a two-dimensional (protein) gel. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2373 Unique identifier of a spot from a two-dimensional (protein) gel. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2374 Spot serial number Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. FALSE http://edamontology.org/data_2373 beta12orEarlier data_2374 Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2375 Spot ID (HSC-2DPAGE) Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. FALSE http://edamontology.org/data_2373 beta12orEarlier data_2375 Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2378 Protein-motif interaction Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2378 http://edamontology.org/data_0906 Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2379 Strain identifier "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." FALSE http://edamontology.org/data_1869 beta12orEarlier data_2379 "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2380 CABRI accession A unique identifier of an item from the CABRI database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2380 A unique identifier of an item from the CABRI database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2381 Experiment report (genotyping) "Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2381 "Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_2382 Genotype experiment ID Identifier of an entry from a database of genotype experiment metadata. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2382 Identifier of an entry from a database of genotype experiment metadata. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2383 EGA accession Identifier of an entry from the EGA database. FALSE http://edamontology.org/data_2382 beta12orEarlier data_2383 Identifier of an entry from the EGA database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2384 IPI protein ID Identifier of a protein entry catalogued in the International Protein Index (IPI) database. FALSE http://edamontology.org/data_1096 beta12orEarlier data_2384 Identifier of a protein entry catalogued in the International Protein Index (IPI) database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data IPI[0-9]{8} http://edamontology.org/data_2385 RefSeq accession (protein) RefSeq protein ID Accession number of a protein from the RefSeq database. FALSE http://edamontology.org/data_1098 beta12orEarlier data_2385 Accession number of a protein from the RefSeq database. RefSeq protein ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2386 EPD ID EPD identifier Identifier of an entry (promoter) from the EPD database. FALSE http://edamontology.org/data_2727 beta12orEarlier data_2386 Identifier of an entry (promoter) from the EPD database. EPD identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2387 TAIR accession Identifier of an entry from the TAIR database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2387 Identifier of an entry from the TAIR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2388 TAIR accession (At gene) Identifier of an Arabidopsis thaliana gene from the TAIR database. FALSE http://edamontology.org/data_1037 beta12orEarlier data_2388 Identifier of an Arabidopsis thaliana gene from the TAIR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2389 UniSTS accession Identifier of an entry from the UniSTS database. FALSE http://edamontology.org/data_1097 beta12orEarlier data_2389 Identifier of an entry from the UniSTS database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2390 UNITE accession Identifier of an entry from the UNITE database. FALSE http://edamontology.org/data_1097 beta12orEarlier data_2390 Identifier of an entry from the UNITE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2391 UTR accession Identifier of an entry from the UTR database. FALSE http://edamontology.org/data_1097 beta12orEarlier data_2391 Identifier of an entry from the UTR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2392 UniParc accession UPI|UniParc ID Accession number of a UniParc (protein sequence) database entry. FALSE http://edamontology.org/data_1096 beta12orEarlier data_2392 Accession number of a UniParc (protein sequence) database entry. UPI|UniParc ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data UPI[A-F0-9]{10} http://edamontology.org/data_2393 mFLJ/mKIAA number Identifier of an entry from the Rouge or HUGE databases. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2393 Identifier of an entry from the Rouge or HUGE databases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2395 Fungi annotation An informative report on a specific fungus. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2395 http://edamontology.org/data_2530 An informative report on a specific fungus. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2396 Fungi annotation (anamorph) An informative report on a specific fungus anamorph. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2396 http://edamontology.org/data_2530 An informative report on a specific fungus anamorph. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2397 Gene features report (exon) exons in a nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2397 exons in a nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2398 Ensembl protein ID Protein ID (Ensembl)|Ensembl ID (protein) Unique identifier for a protein from the Ensembl database. FALSE http://edamontology.org/data_2610|http://edamontology.org/data_2907 beta12orEarlier data_2398 Unique identifier for a protein from the Ensembl database. Protein ID (Ensembl)|Ensembl ID (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2399 Gene transcriptional features report transcription of DNA into RNA including the regulation of transcription. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2399 transcription of DNA into RNA including the regulation of transcription. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_3134 1.8 http://edamontology.org/data_2400 Toxin annotation An informative report on a specific toxin. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2400 http://edamontology.org/data_0962 An informative report on a specific toxin. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2401 Protein report (membrane protein) An informative report on a membrane protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2401 http://edamontology.org/data_1277 An informative report on a membrane protein. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2402 Protein-drug interaction report An informative report on tentative or known protein-drug interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2402 An informative report on tentative or known protein-drug interaction(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1566 1.12 http://edamontology.org/data_2522 Map data "Data concerning a map of molecular sequence(s).|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2522 http://edamontology.org/data_2019|http://edamontology.org/data_1274 Data concerning a map of molecular sequence(s). http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2523 Phylogenetic data "Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2523 "Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2524 Protein data "Data concerning one or more protein molecules.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2524 http://edamontology.org/data_0896 Data concerning one or more protein molecules. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2525 Nucleic acid data "Data concerning one or more nucleic acid molecules.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2525 http://edamontology.org/data_2084 Data concerning one or more nucleic acid molecules. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2526 Text data Scientific text data|Article data "Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.|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." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2526 "Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal." Scientific text data|Article data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2527 Parameter Typically a simple numerical or string value that controls the operation of a tool. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2527 Typically a simple numerical or string value that controls the operation of a tool. http://purl.obolibrary.org/obo/edam#obsolete 1.16 http://edamontology.org/data_2528 Molecular data "Data concerning a specific type of molecule.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2528 http://edamontology.org/data_2087 Data concerning a specific type of molecule. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2529 Molecule report An informative report on a specific molecule. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2529 http://edamontology.org/data_2084|http://edamontology.org/data_0896 An informative report on a specific molecule. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2530 Organism report Organism annotation An informative report on a specific organism. FALSE http://edamontology.org/data_2048 beta12orEarlier data_2530 An informative report on a specific organism. Organism annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2531 Experiment report Experiment metadata|Experiment annotation "Annotation on a wet lab experiment, such as experimental conditions." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2531 "Annotation on a wet lab experiment, such as experimental conditions." Experiment metadata|Experiment annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2533 Nucleic acid features report (mutation) DNA mutation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2533 DNA mutation. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2534 Sequence attribute Sequence parameter "An attribute of a molecular sequence, possibly in reference to some other sequence." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2534 "An attribute of a molecular sequence, possibly in reference to some other sequence." Sequence parameter http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2535 Sequence tag profile Sequencing-based expression profile|Sequence tag profile (with gene assignment) "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.|This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.|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." FALSE http://edamontology.org/data_0928 beta12orEarlier data_2535 "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." Sequencing-based expression profile Sequence tag profile (with gene assignment) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2536 Mass spectrometry data Data concerning a mass spectrometry measurement. FALSE http://edamontology.org/data_3108 beta12orEarlier data_2536 Data concerning a mass spectrometry measurement. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2537 Protein structure raw data "Raw data from experimental methods for determining protein structure.|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." FALSE http://edamontology.org/data_3108 beta12orEarlier data_2537 Raw data from experimental methods for determining protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2538 Mutation identifier An identifier of a mutation. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2538 An identifier of a mutation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2539 Alignment data "Data concerning an alignment of two or more molecular sequences, structures or derived data.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2539 http://edamontology.org/data_2083|http://edamontology.org/data_1916 "Data concerning an alignment of two or more molecular sequences, structures or derived data." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2540 Data index data "Data concerning an index of data.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2540 http://edamontology.org/data_0955 Data concerning an index of data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2563 Amino acid name (single letter) "Single letter amino acid identifier, e.g. G." FALSE http://edamontology.org/data_1006 beta12orEarlier data_2563 "Single letter amino acid identifier, e.g. G." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2564 Amino acid name (three letter) "Three letter amino acid identifier, e.g. GLY." FALSE http://edamontology.org/data_1006 beta12orEarlier data_2564 "Three letter amino acid identifier, e.g. GLY." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2565 Amino acid name (full name) "Full name of an amino acid, e.g. Glycine." FALSE http://edamontology.org/data_1006 beta12orEarlier data_2565 "Full name of an amino acid, e.g. Glycine." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2576 Toxin identifier Identifier of a toxin. FALSE http://edamontology.org/data_1086 beta12orEarlier data_2576 Identifier of a toxin. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2578 ArachnoServer ID Unique identifier of a toxin from the ArachnoServer database. FALSE http://edamontology.org/data_2897 beta12orEarlier data_2578 Unique identifier of a toxin from the ArachnoServer database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2579 Expressed gene list A simple summary of expressed genes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2579 http://edamontology.org/data_2872 A simple summary of expressed genes. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2580 BindingDB Monomer ID Unique identifier of a monomer from the BindingDB database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_2580 Unique identifier of a monomer from the BindingDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2581 GO concept name The name of a concept from the GO ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2581 http://edamontology.org/data_2339 The name of a concept from the GO ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2582 GO concept ID (biological process) An identifier of a 'biological process' concept from the the Gene Ontology. FALSE http://edamontology.org/data_1176 beta12orEarlier data_2582 An identifier of a 'biological process' concept from the the Gene Ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]{7}|GO:[0-9]{7} http://edamontology.org/data_2583 GO concept ID (molecular function) An identifier of a 'molecular function' concept from the the Gene Ontology. FALSE http://edamontology.org/data_1176 beta12orEarlier data_2583 An identifier of a 'molecular function' concept from the the Gene Ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]{7}|GO:[0-9]{7} http://edamontology.org/data_2584 GO concept name (cellular component) The name of a concept for a cellular component from the GO ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2584 http://edamontology.org/data_2339 The name of a concept for a cellular component from the GO ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2586 Northern blot image An image arising from a Northern Blot experiment. FALSE http://edamontology.org/data_3424 beta12orEarlier data_2586 An image arising from a Northern Blot experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2587 Blot ID Unique identifier of a blot from a Northern Blot. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2587 Unique identifier of a blot from a Northern Blot. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2588 BlotBase blot ID Unique identifier of a blot from a Northern Blot from the BlotBase database. FALSE http://edamontology.org/data_2587 beta12orEarlier data_2588 Unique identifier of a blot from a Northern Blot from the BlotBase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2589 Hierarchy Hierarchy annotation "Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2589 "Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation." Hierarchy annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2590 Hierarchy identifier Identifier of an entry from a database of biological hierarchies. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2590 http://edamontology.org/data_2891 Identifier of an entry from a database of biological hierarchies. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2591 Brite hierarchy ID Identifier of an entry from the Brite database of biological hierarchies. FALSE http://edamontology.org/data_2891 beta12orEarlier data_2591 Identifier of an entry from the Brite database of biological hierarchies. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2592 Cancer type A type (represented as a string) of cancer. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2592 http://edamontology.org/data_2099 A type (represented as a string) of cancer. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2593 BRENDA organism ID A unique identifier for an organism used in the BRENDA database. FALSE http://edamontology.org/data_2908 beta12orEarlier data_2593 A unique identifier for an organism used in the BRENDA database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2594 UniGene taxon UniGene organism abbreviation The name of a taxon using the controlled vocabulary of the UniGene database. FALSE http://edamontology.org/data_1868 beta12orEarlier data_2594 The name of a taxon using the controlled vocabulary of the UniGene database. UniGene organism abbreviation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2595 UTRdb taxon The name of a taxon using the controlled vocabulary of the UTRdb database. FALSE http://edamontology.org/data_1868 beta12orEarlier data_2595 The name of a taxon using the controlled vocabulary of the UTRdb database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2596 Catalogue ID Catalogue identifier An identifier of a catalogue of biological resources. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2596 An identifier of a catalogue of biological resources. Catalogue identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2597 CABRI catalogue name The name of a catalogue of biological resources from the CABRI database. FALSE http://edamontology.org/data_2596|http://edamontology.org/data_2099 beta12orEarlier data_2597 The name of a catalogue of biological resources from the CABRI database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2598 Secondary structure alignment metadata An informative report on protein secondary structure alignment-derived data or metadata. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2598 http://edamontology.org/data_0867 An informative report on protein secondary structure alignment-derived data or metadata. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2599 Molecule interaction report "An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." FALSE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2599 http://edamontology.org/data_0906 "An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." http://edamontology.org/data_2600 Pathway or network Network|Pathway Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). FALSE http://edamontology.org/data_0006 beta12orEarlier data_2600 Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). Network|Pathway http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2601 Small molecule data "Data concerning one or more small molecules.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2601 http://edamontology.org/data_0962 Data concerning one or more small molecules. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2602 Genotype and phenotype data "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2602 http://edamontology.org/data_0920 "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2603 Gene expression data Non-coding RNA quantification data|Transcriptome profile|Gene product quantification data|mRNA quantification data|Non-coding RNA profile|mRNA profile|Transcriptome quantification data|RNA quantification data|Microarray data|RNA-seq data|Gene product profile|Gene transcription quantification data|Gene transcription profile|RNA profile|Proteome profile|Protein profile|Protein quantification data|Proteome quantification data "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2603 "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification." Non-coding RNA quantification data|Transcriptome profile|Gene product quantification data|mRNA quantification data|Non-coding RNA profile|mRNA profile|Transcriptome quantification data|RNA quantification data|Microarray data|RNA-seq data|Gene product profile|Gene transcription quantification data|Gene transcription profile|RNA profile Proteome profile|Protein profile|Protein quantification data|Proteome quantification data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2605 Compound ID (KEGG) KEGG compound ID|KEGG compound identifier Unique identifier of a chemical compound from the KEGG database. FALSE http://edamontology.org/data_1154|http://edamontology.org/data_2894 beta12orEarlier data_2605 Unique identifier of a chemical compound from the KEGG database. KEGG compound ID|KEGG compound identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data C[0-9]+ http://edamontology.org/data_2606 RFAM name Name (not necessarily stable) an entry (RNA family) from the RFAM database. FALSE http://edamontology.org/data_2355|http://edamontology.org/data_2099 beta12orEarlier data_2606 Name (not necessarily stable) an entry (RNA family) from the RFAM database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2608 Reaction ID (KEGG) Identifier of a biological reaction from the KEGG reactions database. FALSE http://edamontology.org/data_1154|http://edamontology.org/data_2108 beta12orEarlier data_2608 Identifier of a biological reaction from the KEGG reactions database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data R[0-9]+ http://edamontology.org/data_2609 Drug ID (KEGG) Unique identifier of a drug from the KEGG Drug database. FALSE http://edamontology.org/data_2895|http://edamontology.org/data_1154 beta12orEarlier data_2609 Unique identifier of a drug from the KEGG Drug database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data D[0-9]+ http://edamontology.org/data_2610 Ensembl ID Ensembl IDs "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." Ensembl IDs http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data ENS[A-Z]*[FPTG][0-9]{11} http://edamontology.org/data_2611 ICD identifier An identifier of a disease from the International Classification of Diseases (ICD) database. FALSE http://edamontology.org/data_1150 beta12orEarlier data_2611 An identifier of a disease from the International Classification of Diseases (ICD) database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [A-Z][0-9]+(.[-[0-9]+])? http://edamontology.org/data_2612 Sequence cluster ID (CluSTr) CluSTr ID|CluSTr cluster ID Unique identifier of a sequence cluster from the CluSTr database. FALSE http://edamontology.org/data_1112 beta12orEarlier data_2612 Unique identifier of a sequence cluster from the CluSTr database. CluSTr ID|CluSTr cluster ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(.[0-9])?" http://edamontology.org/data_2613 KEGG Glycan ID Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). FALSE http://edamontology.org/data_2900|http://edamontology.org/data_1154 beta12orEarlier data_2613 Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data G[0-9]+ http://edamontology.org/data_2614 TCDB ID TC number A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.|OBO file for regular expression. FALSE http://edamontology.org/data_2910 beta12orEarlier data_2614 A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. TC number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ http://edamontology.org/data_2615 MINT ID Unique identifier of an entry from the MINT database of protein-protein interactions. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2615 Unique identifier of an entry from the MINT database of protein-protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "MINT-[0-9]{1,5}" http://edamontology.org/data_2616 DIP ID Unique identifier of an entry from the DIP database of protein-protein interactions. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2616 Unique identifier of an entry from the DIP database of protein-protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data DIP[:\-][0-9]{3}[EN] http://edamontology.org/data_2617 Signaling Gateway protein ID Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2617 Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data A[0-9]{6} http://edamontology.org/data_2618 Protein modification ID Identifier of a protein modification catalogued in a database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2618 Identifier of a protein modification catalogued in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2619 RESID ID Identifier of a protein modification catalogued in the RESID database. FALSE http://edamontology.org/data_2618 beta12orEarlier data_2619 Identifier of a protein modification catalogued in the RESID database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data AA[0-9]{4} http://edamontology.org/data_2620 RGD ID Identifier of an entry from the RGD database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2620 Identifier of an entry from the RGD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[0-9]{4,7}" http://edamontology.org/data_2621 TAIR accession (protein) Identifier of a protein sequence from the TAIR database. FALSE http://edamontology.org/data_1096|http://edamontology.org/data_2387 beta12orEarlier data_2621 Identifier of a protein sequence from the TAIR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data AASequence:[0-9]{10} http://edamontology.org/data_2622 Compound ID (HMDB) HMDB ID Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). FALSE http://edamontology.org/data_2894 beta12orEarlier data_2622 Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). HMDB ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data HMDB[0-9]{5} http://edamontology.org/data_2625 LIPID MAPS ID LM ID Identifier of an entry from the LIPID MAPS database. FALSE http://edamontology.org/data_2905 beta12orEarlier data_2625 Identifier of an entry from the LIPID MAPS database. LM ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? http://edamontology.org/data_2626 PeptideAtlas ID Identifier of a peptide from the PeptideAtlas peptide databases. FALSE http://edamontology.org/data_2906 beta12orEarlier data_2626 PDBML:pdbx_PDB_strand_id Identifier of a peptide from the PeptideAtlas peptide databases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PAp[0-9]{8} http://edamontology.org/data_2627 Molecular interaction ID Identifier of a report of molecular interactions from a database (typically). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2627 Identifier of a report of molecular interactions from a database (typically). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1074 1.7 http://edamontology.org/data_2628 BioGRID interaction ID A unique identifier of an interaction from the BioGRID database. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2628 A unique identifier of an interaction from the BioGRID database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2629 Enzyme ID (MEROPS) MEROPS ID Unique identifier of a peptidase enzyme from the MEROPS database. FALSE http://edamontology.org/data_2321 beta12orEarlier data_2629 Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data S[0-9]{2}.[0-9]{3} http://edamontology.org/data_2630 Mobile genetic element ID An identifier of a mobile genetic element. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2630 An identifier of a mobile genetic element. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2631 ACLAME ID An identifier of a mobile genetic element from the Aclame database. FALSE http://edamontology.org/data_2630 beta12orEarlier data_2631 An identifier of a mobile genetic element from the Aclame database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data mge:[0-9]+ http://edamontology.org/data_2632 SGD ID Identifier of an entry from the Saccharomyces genome database (SGD). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2632 Identifier of an entry from the Saccharomyces genome database (SGD). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PWY[a-zA-Z_0-9]{2}-[0-9]{3} http://edamontology.org/data_2633 Book ID Unique identifier of a book. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2633 Unique identifier of a book. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2634 ISBN The International Standard Book Number (ISBN) is for identifying printed books. FALSE http://edamontology.org/data_2633 beta12orEarlier data_2634 The International Standard Book Number (ISBN) is for identifying printed books. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" http://edamontology.org/data_2635 Compound ID (3DMET) 3DMET ID Identifier of a metabolite from the 3DMET database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_2635 Identifier of a metabolite from the 3DMET database. 3DMET ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data B[0-9]{5} http://edamontology.org/data_2636 MatrixDB interaction ID A unique identifier of an interaction from the MatrixDB database. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2636 A unique identifier of an interaction from the MatrixDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data ([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_.*) http://edamontology.org/data_2637 cPath ID "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.|These identifiers are unique within the cPath database, however, they are not stable between releases." FALSE http://edamontology.org/data_2365|http://edamontology.org/data_2109 beta12orEarlier data_2637 "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2638 PubChem bioassay ID Identifier of an assay from the PubChem database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2639 beta12orEarlier data_2638 Identifier of an assay from the PubChem database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2639 PubChem ID PubChem identifier Identifier of an entry from the PubChem database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2639 Identifier of an entry from the PubChem database. PubChem identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2641 Reaction ID (MACie) MACie entry number Identifier of an enzyme reaction mechanism from the MACie database. FALSE http://edamontology.org/data_2108 beta12orEarlier data_2641 Identifier of an enzyme reaction mechanism from the MACie database. MACie entry number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data M[0-9]{4} http://edamontology.org/data_2642 Gene ID (miRBase) miRNA name|miRNA ID|miRNA identifier Identifier for a gene from the miRBase database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2642 Identifier for a gene from the miRBase database. miRNA name|miRNA ID|miRNA identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data MI[0-9]{7} http://edamontology.org/data_2643 Gene ID (ZFIN) Identifier for a gene from the Zebrafish information network genome (ZFIN) database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2643 Identifier for a gene from the Zebrafish information network genome (ZFIN) database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data ZDB-GENE\-[0-9]+\-[0-9]+ http://edamontology.org/data_2644 Reaction ID (Rhea) Identifier of an enzyme-catalysed reaction from the Rhea database. FALSE http://edamontology.org/data_2108 beta12orEarlier data_2644 Identifier of an enzyme-catalysed reaction from the Rhea database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]{5} http://edamontology.org/data_2645 Pathway ID (Unipathway) upaid Identifier of a biological pathway from the Unipathway database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_2645 Identifier of a biological pathway from the Unipathway database. upaid http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data UPA[0-9]{5} http://edamontology.org/data_2646 Compound ID (ChEMBL) ChEMBL ID Identifier of a small molecular from the ChEMBL database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_2646 Identifier of a small molecular from the ChEMBL database. ChEMBL ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2647 LGICdb identifier Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2647 Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9]+ http://edamontology.org/data_2648 Reaction kinetics ID (SABIO-RK) Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. FALSE http://edamontology.org/data_2309 beta12orEarlier data_2648 Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2649 PharmGKB ID Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 beta12orEarlier data_2649 Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PA[0-9]+ http://edamontology.org/data_2650 Pathway ID (PharmGKB) Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). FALSE http://edamontology.org/data_2365|http://edamontology.org/data_2649 beta12orEarlier data_2650 Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PA[0-9]+ http://edamontology.org/data_2651 Disease ID (PharmGKB) Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). FALSE http://edamontology.org/data_2649|http://edamontology.org/data_1150 beta12orEarlier data_2651 Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PA[0-9]+ http://edamontology.org/data_2652 Drug ID (PharmGKB) Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). FALSE http://edamontology.org/data_2895|http://edamontology.org/data_2649 beta12orEarlier data_2652 Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PA[0-9]+ http://edamontology.org/data_2653 Drug ID (TTD) Identifier of a drug from the Therapeutic Target Database (TTD). FALSE http://edamontology.org/data_2895 beta12orEarlier data_2653 Identifier of a drug from the Therapeutic Target Database (TTD). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data DAP[0-9]+ http://edamontology.org/data_2654 Target ID (TTD) Identifier of a target protein from the Therapeutic Target Database (TTD). FALSE http://edamontology.org/data_2907 beta12orEarlier data_2654 Identifier of a target protein from the Therapeutic Target Database (TTD). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data TTDS[0-9]+ http://edamontology.org/data_2655 Cell type identifier A unique identifier of a type or group of cells. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2655 A unique identifier of a type or group of cells. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2656 NeuronDB ID A unique identifier of a neuron from the NeuronDB database. FALSE http://edamontology.org/data_2893 beta12orEarlier data_2656 A unique identifier of a neuron from the NeuronDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2657 NeuroMorpho ID A unique identifier of a neuron from the NeuroMorpho database. FALSE http://edamontology.org/data_2893 beta12orEarlier data_2657 A unique identifier of a neuron from the NeuroMorpho database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9]+ http://edamontology.org/data_2658 Compound ID (ChemIDplus) ChemIDplus ID Identifier of a chemical from the ChemIDplus database. FALSE http://edamontology.org/data_2894 beta12orEarlier data_2658 Identifier of a chemical from the ChemIDplus database. ChemIDplus ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2659 Pathway ID (SMPDB) Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). FALSE http://edamontology.org/data_2365 beta12orEarlier data_2659 Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data SMP[0-9]{5} http://edamontology.org/data_2660 BioNumbers ID Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. FALSE http://edamontology.org/data_2091 beta12orEarlier data_2660 Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2662 T3DB ID Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. FALSE http://edamontology.org/data_2897 beta12orEarlier data_2662 Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data T3D[0-9]+ http://edamontology.org/data_2663 Carbohydrate identifier Identifier of a carbohydrate. FALSE http://edamontology.org/data_1086 beta12orEarlier data_2663 Identifier of a carbohydrate. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2664 GlycomeDB ID Identifier of an entry from the GlycomeDB database. FALSE http://edamontology.org/data_2900 beta12orEarlier data_2664 Identifier of an entry from the GlycomeDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2665 LipidBank ID Identifier of an entry from the LipidBank database. FALSE http://edamontology.org/data_2905 beta12orEarlier data_2665 Identifier of an entry from the LipidBank database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [a-zA-Z_0-9]+[0-9]+ http://edamontology.org/data_2666 CDD ID Identifier of a conserved domain from the Conserved Domain Database. FALSE http://edamontology.org/data_1038 beta12orEarlier data_2666 Identifier of a conserved domain from the Conserved Domain Database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data cd[0-9]{5} http://edamontology.org/data_2667 MMDB ID MMDB accession An identifier of an entry from the MMDB database. FALSE http://edamontology.org/data_1070 beta12orEarlier data_2667 An identifier of an entry from the MMDB database. MMDB accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[0-9]{1,5}" http://edamontology.org/data_2668 iRefIndex ID Unique identifier of an entry from the iRefIndex database of protein-protein interactions. FALSE http://edamontology.org/data_1074 beta12orEarlier data_2668 Unique identifier of an entry from the iRefIndex database of protein-protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2669 ModelDB ID Unique identifier of an entry from the ModelDB database. FALSE http://edamontology.org/data_2891 beta12orEarlier data_2669 Unique identifier of an entry from the ModelDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2670 Pathway ID (DQCS) Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). FALSE http://edamontology.org/data_2365 beta12orEarlier data_2670 Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2671 Ensembl ID (Homo sapiens) "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2671 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENS([EGTP])[0-9]{11} http://edamontology.org/data_2672 Ensembl ID ('Bos taurus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2672 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSBTA([EGTP])[0-9]{11} http://edamontology.org/data_2673 Ensembl ID ('Canis familiaris') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2673 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSCAF([EGTP])[0-9]{11} http://edamontology.org/data_2674 Ensembl ID ('Cavia porcellus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2674 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSCPO([EGTP])[0-9]{11} http://edamontology.org/data_2675 Ensembl ID ('Ciona intestinalis') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2675 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSCIN([EGTP])[0-9]{11} http://edamontology.org/data_2676 Ensembl ID ('Ciona savignyi') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2676 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSCSAV([EGTP])[0-9]{11} http://edamontology.org/data_2677 Ensembl ID ('Danio rerio') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2677 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSDAR([EGTP])[0-9]{11} http://edamontology.org/data_2678 Ensembl ID ('Dasypus novemcinctus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2678 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSDNO([EGTP])[0-9]{11} http://edamontology.org/data_2679 Ensembl ID ('Echinops telfairi') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2679 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSETE([EGTP])[0-9]{11} http://edamontology.org/data_2680 Ensembl ID ('Erinaceus europaeus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2680 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSEEU([EGTP])[0-9]{11} http://edamontology.org/data_2681 Ensembl ID ('Felis catus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2681 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSFCA([EGTP])[0-9]{11} http://edamontology.org/data_2682 Ensembl ID ('Gallus gallus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2682 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSGAL([EGTP])[0-9]{11} http://edamontology.org/data_2683 Ensembl ID ('Gasterosteus aculeatus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2683 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSGAC([EGTP])[0-9]{11} http://edamontology.org/data_2684 Ensembl ID ('Homo sapiens') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2684 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSHUM([EGTP])[0-9]{11} http://edamontology.org/data_2685 Ensembl ID ('Loxodonta africana') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2685 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSLAF([EGTP])[0-9]{11} http://edamontology.org/data_2686 Ensembl ID ('Macaca mulatta') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2686 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSMMU([EGTP])[0-9]{11} http://edamontology.org/data_2687 Ensembl ID ('Monodelphis domestica') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2687 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSMOD([EGTP])[0-9]{11} http://edamontology.org/data_2688 Ensembl ID ('Mus musculus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2688 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSMUS([EGTP])[0-9]{11} http://edamontology.org/data_2689 Ensembl ID ('Myotis lucifugus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2689 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSMLU([EGTP])[0-9]{11} http://edamontology.org/data_2690 "Ensembl ID (""Ornithorhynchus anatinus\"")" "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2690 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSOAN([EGTP])[0-9]{11} http://edamontology.org/data_2691 Ensembl ID ('Oryctolagus cuniculus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2691 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSOCU([EGTP])[0-9]{11} http://edamontology.org/data_2692 Ensembl ID ('Oryzias latipes') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2692 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSORL([EGTP])[0-9]{11} http://edamontology.org/data_2693 Ensembl ID ('Otolemur garnettii') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2693 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSSAR([EGTP])[0-9]{11} http://edamontology.org/data_2694 Ensembl ID ('Pan troglodytes') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2694 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSPTR([EGTP])[0-9]{11} http://edamontology.org/data_2695 Ensembl ID ('Rattus norvegicus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2695 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSRNO([EGTP])[0-9]{11} http://edamontology.org/data_2696 Ensembl ID ('Spermophilus tridecemlineatus') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2696 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSSTO([EGTP])[0-9]{11} http://edamontology.org/data_2697 Ensembl ID ('Takifugu rubripes') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2697 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSFRU([EGTP])[0-9]{11} http://edamontology.org/data_2698 Ensembl ID ('Tupaia belangeri') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2698 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSTBE([EGTP])[0-9]{11} http://edamontology.org/data_2699 Ensembl ID ('Xenopus tropicalis') "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2699 http://edamontology.org/data_2610 "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier ENSXET([EGTP])[0-9]{11} http://edamontology.org/data_2700 CATH identifier Identifier of a protein domain (or other node) from the CATH database. FALSE http://edamontology.org/data_1038 beta12orEarlier data_2700 Identifier of a protein domain (or other node) from the CATH database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2701 CATH node ID (family) A code number identifying a family from the CATH database. FALSE http://edamontology.org/data_1043 beta12orEarlier 2.10.10.10 data_2701 A code number identifying a family from the CATH database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2702 Enzyme ID (CAZy) CAZy ID Identifier of an enzyme from the CAZy enzymes database. FALSE http://edamontology.org/data_2321 beta12orEarlier data_2702 Identifier of an enzyme from the CAZy enzymes database. CAZy ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2704 Clone ID (IMAGE) I.M.A.G.E. cloneID|IMAGE cloneID A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). FALSE http://edamontology.org/data_1855 beta12orEarlier data_2704 A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). I.M.A.G.E. cloneID|IMAGE cloneID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2705 GO concept ID (cellular component) GO concept identifier (cellular compartment) An identifier of a 'cellular component' concept from the Gene Ontology. FALSE http://edamontology.org/data_1176 beta12orEarlier data_2705 An identifier of a 'cellular component' concept from the Gene Ontology. GO concept identifier (cellular compartment) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]{7}|GO:[0-9]{7} http://edamontology.org/data_2706 Chromosome name (BioCyc) Name of a chromosome as used in the BioCyc database. FALSE http://edamontology.org/data_0987 beta12orEarlier data_2706 Name of a chromosome as used in the BioCyc database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2709 CleanEx entry name An identifier of a gene expression profile from the CleanEx database. FALSE http://edamontology.org/data_1080 beta12orEarlier data_2709 An identifier of a gene expression profile from the CleanEx database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2710 CleanEx dataset code An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. FALSE http://edamontology.org/data_1078 beta12orEarlier data_2710 An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2711 Genome report An informative report of general information concerning a genome as a whole. FALSE http://edamontology.org/data_2530 beta12orEarlier data_2711 An informative report of general information concerning a genome as a whole. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2713 Protein ID (CORUM) CORUM complex ID Unique identifier for a protein complex from the CORUM database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2713 Unique identifier for a protein complex from the CORUM database. CORUM complex ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2714 CDD PSSM-ID Unique identifier of a position-specific scoring matrix from the CDD database. FALSE http://edamontology.org/data_1115 beta12orEarlier data_2714 Unique identifier of a position-specific scoring matrix from the CDD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2715 Protein ID (CuticleDB) CuticleDB ID Unique identifier for a protein from the CuticleDB database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2715 Unique identifier for a protein from the CuticleDB database. CuticleDB ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2716 DBD ID Identifier of a predicted transcription factor from the DBD database. FALSE http://edamontology.org/data_2911 beta12orEarlier data_2716 Identifier of a predicted transcription factor from the DBD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2717 Oligonucleotide probe annotation Oligonucleotide probe sets annotation "General annotation on an oligonucleotide probe, or a set of probes." FALSE http://edamontology.org/data_3115 beta12orEarlier data_2717 "General annotation on an oligonucleotide probe, or a set of probes." Oligonucleotide probe sets annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2718 Oligonucleotide ID Identifier of an oligonucleotide from a database. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_2119 beta12orEarlier data_2718 Identifier of an oligonucleotide from a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2719 dbProbe ID Identifier of an oligonucleotide probe from the dbProbe database. FALSE http://edamontology.org/data_2718 beta12orEarlier data_2719 Identifier of an oligonucleotide probe from the dbProbe database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2720 Dinucleotide property Physicochemical property data for one or more dinucleotides. FALSE http://edamontology.org/data_2088 beta12orEarlier data_2720 Physicochemical property data for one or more dinucleotides. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2721 DiProDB ID Identifier of an dinucleotide property from the DiProDB database. FALSE http://edamontology.org/data_2718 beta12orEarlier data_2721 Identifier of an dinucleotide property from the DiProDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2722 Protein features report (disordered structure) disordered structure in a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2722 disordered structure in a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_2723 Protein ID (DisProt) DisProt ID Unique identifier for a protein from the DisProt database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2723 Unique identifier for a protein from the DisProt database. DisProt ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2724 Embryo report Annotation on an embryo or concerning embryological development. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2724 http://edamontology.org/data_1713 Annotation on an embryo or concerning embryological development. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2725 Ensembl transcript ID Transcript ID (Ensembl) Unique identifier for a gene transcript from the Ensembl database. FALSE http://edamontology.org/data_2610|http://edamontology.org/data_2769 beta12orEarlier data_2725 Unique identifier for a gene transcript from the Ensembl database. Transcript ID (Ensembl) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2726 Inhibitor annotation An informative report on one or more small molecules that are enzyme inhibitors. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2726 http://edamontology.org/data_0962 An informative report on one or more small molecules that are enzyme inhibitors. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2727 Promoter ID An identifier of a promoter of a gene that is catalogued in a database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2727 Moby:GeneAccessionList An identifier of a promoter of a gene that is catalogued in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2728 EST accession Identifier of an EST sequence. FALSE http://edamontology.org/data_1855 beta12orEarlier data_2728 Identifier of an EST sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2729 COGEME EST ID Identifier of an EST sequence from the COGEME database. FALSE http://edamontology.org/data_2728 beta12orEarlier data_2729 Identifier of an EST sequence from the COGEME database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2730 COGEME unisequence ID Identifier of a unisequence from the COGEME database.|A unisequence is a single sequence assembled from ESTs. FALSE http://edamontology.org/data_2728 beta12orEarlier data_2730 Identifier of a unisequence from the COGEME database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2731 Protein family ID (GeneFarm) GeneFarm family ID Accession number of an entry (family) from the TIGRFam database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_2731 Accession number of an entry (family) from the TIGRFam database. GeneFarm family ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2732 Family name The name of a family of organism. FALSE http://edamontology.org/data_1868 beta12orEarlier data_2732 The name of a family of organism. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2733 Genus name (virus) The name of a genus of viruses. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2733 http://edamontology.org/data_1870 The name of a genus of viruses. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2734 Family name (virus) The name of a family of viruses. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2734 http://edamontology.org/data_2732 The name of a family of viruses. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2735 Database name (SwissRegulon) The name of a SwissRegulon database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2735 http://edamontology.org/data_0957 The name of a SwissRegulon database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2736 Sequence feature ID (SwissRegulon) "A feature identifier as used in the SwissRegulon database.|This can be name of a gene, the ID of a TFBS, or genomic coordinates in form ""chr:start..end""." FALSE http://edamontology.org/data_1015 beta12orEarlier data_2736 A feature identifier as used in the SwissRegulon database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2737 FIG ID "A unique identifier of gene in the NMPDR database.|A FIG ID consists of four parts: a prefix, genome id, locus type and id number." FALSE http://edamontology.org/data_2295 beta12orEarlier data_2737 A unique identifier of gene in the NMPDR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2738 Gene ID (Xenbase) A unique identifier of gene in the Xenbase database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2738 A unique identifier of gene in the Xenbase database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2739 Gene ID (Genolist) A unique identifier of gene in the Genolist database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2739 A unique identifier of gene in the Genolist database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2740 Gene name (Genolist) Genolist gene name Name of an entry (gene) from the Genolist genes database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2740 http://edamontology.org/data_1026 Name of an entry (gene) from the Genolist genes database. Genolist gene name http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/data_2741 ABS ID ABS identifier Identifier of an entry (promoter) from the ABS database. FALSE http://edamontology.org/data_2727 beta12orEarlier data_2741 Identifier of an entry (promoter) from the ABS database. ABS identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2742 AraC-XylS ID Identifier of a transcription factor from the AraC-XylS database. FALSE http://edamontology.org/data_2911 beta12orEarlier data_2742 Identifier of a transcription factor from the AraC-XylS database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2743 Gene name (HUGO) Name of an entry (gene) from the HUGO database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2743 http://edamontology.org/data_1026 Name of an entry (gene) from the HUGO database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2744 Locus ID (PseudoCAP) Identifier of a locus from the PseudoCAP database. FALSE http://edamontology.org/data_1893 beta12orEarlier data_2744 Identifier of a locus from the PseudoCAP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2745 Locus ID (UTR) Identifier of a locus from the UTR database. FALSE http://edamontology.org/data_1893 beta12orEarlier data_2745 Identifier of a locus from the UTR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2746 MonosaccharideDB ID Unique identifier of a monosaccharide from the MonosaccharideDB database. FALSE http://edamontology.org/data_2898 beta12orEarlier data_2746 Unique identifier of a monosaccharide from the MonosaccharideDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2747 Database name (CMD) The name of a subdivision of the Collagen Mutation Database (CMD) database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2747 http://edamontology.org/data_0957 The name of a subdivision of the Collagen Mutation Database (CMD) database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2748 Database name (Osteogenesis) The name of a subdivision of the Osteogenesis database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2748 http://edamontology.org/data_0957 The name of a subdivision of the Osteogenesis database. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2749 Genome identifier An identifier of a particular genome. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2749 An identifier of a particular genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2751 GenomeReviews ID An identifier of a particular genome. FALSE http://edamontology.org/data_2903 beta12orEarlier data_2751 An identifier of a particular genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2752 GlycoMap ID Identifier of an entry from the GlycosciencesDB database. FALSE http://edamontology.org/data_2900 beta12orEarlier data_2752 Identifier of an entry from the GlycosciencesDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2753 Carbohydrate conformational map A conformational energy map of the glycosidic linkages in a carbohydrate molecule. FALSE http://edamontology.org/data_3425 beta12orEarlier data_2753 A conformational energy map of the glycosidic linkages in a carbohydrate molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2754 Gene features report (intron) introns in a nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2754 introns in a nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2755 Transcription factor name The name of a transcription factor. FALSE http://edamontology.org/data_1009|http://edamontology.org/data_1077 beta12orEarlier data_2755 The name of a transcription factor. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2756 TCID Identifier of a membrane transport proteins from the transport classification database (TCDB). FALSE http://edamontology.org/data_2907 beta12orEarlier data_2756 Identifier of a membrane transport proteins from the transport classification database (TCDB). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2757 Pfam domain name Name of a domain from the Pfam database. FALSE http://edamontology.org/data_1131 beta12orEarlier data_2757 Name of a domain from the Pfam database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data PF[0-9]{5} http://edamontology.org/data_2758 Pfam clan ID Accession number of a Pfam clan. FALSE http://edamontology.org/data_2910 beta12orEarlier data_2758 Accession number of a Pfam clan. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data CL[0-9]{4} http://edamontology.org/data_2759 Gene ID (VectorBase) VectorBase ID Identifier for a gene from the VectorBase database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2759 Identifier for a gene from the VectorBase database. VectorBase ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2761 UTRSite ID Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. FALSE http://edamontology.org/data_1114 beta12orEarlier data_2761 Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2762 Sequence signature report Sequence profile report|Sequence motif report "An informative report about 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." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2762 "An informative report about 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." Sequence profile report|Sequence motif report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2763 Locus annotation Locus report An informative report on a particular locus. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2763 http://edamontology.org/data_0916 An informative report on a particular locus. Locus report http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2764 Protein name (UniProt) Official name of a protein as used in the UniProt database. FALSE http://edamontology.org/data_1009 beta12orEarlier data_2764 Official name of a protein as used in the UniProt database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2765 Term ID list One or more terms from one or more controlled vocabularies which are annotations on an entity.|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. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2765 http://edamontology.org/data_2872 One or more terms from one or more controlled vocabularies which are annotations on an entity. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2766 HAMAP ID Name of a protein family from the HAMAP database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_2766 Name of a protein family from the HAMAP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2767 Identifier with metadata "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2767 http://edamontology.org/data_0842 "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/data_2768 Gene symbol annotation Annotation about a gene symbol. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2768 http://edamontology.org/data_2048 Annotation about a gene symbol. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2769 Transcript ID Identifier of a RNA transcript. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_2119 beta12orEarlier data_2769 Identifier of a RNA transcript. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2770 HIT ID Identifier of an RNA transcript from the H-InvDB database. FALSE http://edamontology.org/data_2769 beta12orEarlier data_2770 Identifier of an RNA transcript from the H-InvDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2771 HIX ID A unique identifier of gene cluster in the H-InvDB database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2771 A unique identifier of gene cluster in the H-InvDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2772 HPA antibody id Identifier of a antibody from the HPA database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2772 Identifier of a antibody from the HPA database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2773 IMGT/HLA ID Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2773 Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2774 Gene ID (JCVI) A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). FALSE http://edamontology.org/data_2295 beta12orEarlier data_2774 A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2775 Kinase name The name of a kinase protein. FALSE http://edamontology.org/data_1009 beta12orEarlier data_2775 The name of a kinase protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2776 ConsensusPathDB entity ID Identifier of a physical entity from the ConsensusPathDB database. FALSE http://edamontology.org/data_2917|http://edamontology.org/data_2091 beta12orEarlier data_2776 Identifier of a physical entity from the ConsensusPathDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2777 ConsensusPathDB entity name Name of a physical entity from the ConsensusPathDB database. FALSE http://edamontology.org/data_2917|http://edamontology.org/data_2099 beta12orEarlier data_2777 Name of a physical entity from the ConsensusPathDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2778 CCAP strain number The number of a strain of algae and protozoa from the CCAP database. FALSE http://edamontology.org/data_2912 beta12orEarlier data_2778 The number of a strain of algae and protozoa from the CCAP database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2779 Stock number An identifier of stock from a catalogue of biological resources. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_2779 An identifier of stock from a catalogue of biological resources. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2780 Stock number (TAIR) A stock number from The Arabidopsis information resource (TAIR). FALSE http://edamontology.org/data_2779 beta12orEarlier data_2780 A stock number from The Arabidopsis information resource (TAIR). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2781 REDIdb ID Identifier of an entry from the RNA editing database (REDIdb). FALSE http://edamontology.org/data_1097 beta12orEarlier data_2781 Identifier of an entry from the RNA editing database (REDIdb). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2782 SMART domain name Name of a domain from the SMART database. FALSE http://edamontology.org/data_1131 beta12orEarlier data_2782 Name of a domain from the SMART database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2783 Protein family ID (PANTHER) Panther family ID Accession number of an entry (family) from the PANTHER database. FALSE http://edamontology.org/data_2910 beta12orEarlier data_2783 Accession number of an entry (family) from the PANTHER database. Panther family ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2784 RNAVirusDB ID A unique identifier for a virus from the RNAVirusDB database.|Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. FALSE http://edamontology.org/data_2785 beta12orEarlier data_2784 A unique identifier for a virus from the RNAVirusDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2785 Virus ID An accession of annotation on a (group of) viruses (catalogued in a database). FALSE http://edamontology.org/data_2908|http://edamontology.org/data_2913 beta12orEarlier data_2785 An accession of annotation on a (group of) viruses (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2786 NCBI Genome Project ID An identifier of a genome project assigned by NCBI. FALSE http://edamontology.org/data_2903 beta12orEarlier data_2786 An identifier of a genome project assigned by NCBI. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2787 NCBI genome accession A unique identifier of a whole genome assigned by the NCBI. FALSE http://edamontology.org/data_2903 beta12orEarlier data_2787 A unique identifier of a whole genome assigned by the NCBI. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2788 Sequence profile data "Data concerning, extracted from, or derived from the analysis of 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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2788 "Data concerning, extracted from, or derived from the analysis of 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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0860 1.8 http://edamontology.org/data_2789 Protein ID (TopDB) TopDB ID Unique identifier for a membrane protein from the TopDB database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2789 Unique identifier for a membrane protein from the TopDB database. TopDB ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2790 Gel ID Gel identifier Identifier of a two-dimensional (protein) gel. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2790 Identifier of a two-dimensional (protein) gel. Gel identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2791 Reference map name (SWISS-2DPAGE) Name of a reference map gel from the SWISS-2DPAGE database. FALSE http://edamontology.org/data_2790|http://edamontology.org/data_2099 beta12orEarlier data_2791 Name of a reference map gel from the SWISS-2DPAGE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2792 Protein ID (PeroxiBase) PeroxiBase ID Unique identifier for a peroxidase protein from the PeroxiBase database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2792 Unique identifier for a peroxidase protein from the PeroxiBase database. PeroxiBase ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2793 SISYPHUS ID Identifier of an entry from the SISYPHUS database of tertiary structure alignments. FALSE http://edamontology.org/data_1072 beta12orEarlier data_2793 Identifier of an entry from the SISYPHUS database of tertiary structure alignments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2794 ORF ID Accession of an open reading frame (catalogued in a database). FALSE http://edamontology.org/data_2795|http://edamontology.org/data_1893 beta12orEarlier data_2794 Accession of an open reading frame (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2795 ORF identifier An identifier of an open reading frame. FALSE http://edamontology.org/data_0976 beta12orEarlier data_2795 An identifier of an open reading frame. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2796 Linucs ID Identifier of an entry from the GlycosciencesDB database. FALSE http://edamontology.org/data_2900 beta12orEarlier data_2796 Identifier of an entry from the GlycosciencesDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2797 Protein ID (LGICdb) LGICdb ID Unique identifier for a ligand-gated ion channel protein from the LGICdb database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2797 Unique identifier for a ligand-gated ion channel protein from the LGICdb database. LGICdb ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2798 MaizeDB ID Identifier of an EST sequence from the MaizeDB database. FALSE http://edamontology.org/data_2728 beta12orEarlier data_2798 Identifier of an EST sequence from the MaizeDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2799 Gene ID (MfunGD) A unique identifier of gene in the MfunGD database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2799 A unique identifier of gene in the MfunGD database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2800 Orpha number An identifier of a disease from the Orpha database. FALSE http://edamontology.org/data_1150 beta12orEarlier data_2800 An identifier of a disease from the Orpha database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2802 Protein ID (EcID) Unique identifier for a protein from the EcID database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2802 Unique identifier for a protein from the EcID database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2803 Clone ID (RefSeq) A unique identifier of a cDNA molecule catalogued in the RefSeq database. FALSE http://edamontology.org/data_1855|http://edamontology.org/data_1098 beta12orEarlier data_2803 A unique identifier of a cDNA molecule catalogued in the RefSeq database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2804 Protein ID (ConoServer) Unique identifier for a cone snail toxin protein from the ConoServer database. FALSE http://edamontology.org/data_2907 beta12orEarlier data_2804 Unique identifier for a cone snail toxin protein from the ConoServer database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2805 GeneSNP ID Identifier of a GeneSNP database entry. FALSE http://edamontology.org/data_2294 beta12orEarlier data_2805 Identifier of a GeneSNP database entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2812 Lipid identifier Identifier of a lipid. FALSE http://edamontology.org/data_0982 beta12orEarlier data_2812 Identifier of a lipid. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2831 Databank A flat-file (textual) data archive. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2831 A flat-file (textual) data archive. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0957 beta12orEarlier http://edamontology.org/data_2832 Web portal A web site providing data (web pages) on a common theme to a HTTP client. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2832 A web site providing data (web pages) on a common theme to a HTTP client. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0958 beta12orEarlier http://edamontology.org/data_2835 Gene ID (VBASE2) VBASE2 ID Identifier for a gene from the VBASE2 database. FALSE http://edamontology.org/data_2295 beta12orEarlier data_2835 Identifier for a gene from the VBASE2 database. VBASE2 ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2836 DPVweb ID DPVweb virus ID A unique identifier for a virus from the DPVweb database. FALSE http://edamontology.org/data_2785 beta12orEarlier data_2836 A unique identifier for a virus from the DPVweb database. DPVweb virus ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2837 Pathway ID (BioSystems) Identifier of a pathway from the BioSystems pathway database. FALSE http://edamontology.org/data_2365 beta12orEarlier data_2837 Identifier of a pathway from the BioSystems pathway database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [0-9]+ http://edamontology.org/data_2838 Experimental data (proteomics) Data concerning a proteomics experiment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2838 http://edamontology.org/data_2531 Data concerning a proteomics experiment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2849 Abstract An abstract of a scientific article. FALSE http://edamontology.org/data_2526 beta12orEarlier data_2849 An abstract of a scientific article. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2850 Lipid structure 3D coordinate and associated data for a lipid structure. FALSE http://edamontology.org/data_0883 beta12orEarlier data_2850 3D coordinate and associated data for a lipid structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2851 Drug structure 3D coordinate and associated data for the (3D) structure of a drug. FALSE http://edamontology.org/data_1463 beta12orEarlier data_2851 3D coordinate and associated data for the (3D) structure of a drug. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2852 Toxin structure 3D coordinate and associated data for the (3D) structure of a toxin. FALSE http://edamontology.org/data_1463 beta12orEarlier data_2852 3D coordinate and associated data for the (3D) structure of a toxin. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2854 Position-specific scoring matrix PSSM "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." FALSE http://edamontology.org/data_2082|http://edamontology.org/data_1354 beta12orEarlier data_2854 "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." PSSM http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2855 Distance matrix "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." FALSE http://edamontology.org/data_2082 beta12orEarlier data_2855 "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2856 Structural distance matrix Distances (values representing similarity) between a group of molecular structures. FALSE http://edamontology.org/data_2855 beta12orEarlier data_2856 Distances (values representing similarity) between a group of molecular structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2857 Article metadata Bibliographic data concerning scientific article(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2857 http://edamontology.org/data_2526 Bibliographic data concerning scientific article(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2858 Ontology concept "A concept from a biological ontology.|This includes any fields from the concept definition such as concept name, definition, comments and so on." FALSE http://edamontology.org/data_2353 beta12orEarlier data_2858 A concept from a biological ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2865 Codon usage bias A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. FALSE http://edamontology.org/data_0914 beta12orEarlier data_2865 A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2866 Northern blot report Northern Blot experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2866 Northern Blot experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_2867 Nucleic acid features report (VNTR) variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2867 variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2868 Nucleic acid features report (microsatellite) microsatellite polymorphism in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2868 http://edamontology.org/data_2868 microsatellite polymorphism in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2869 Nucleic acid features report (RFLP) restriction fragment length polymorphisms (RFLP) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2869 restriction fragment length polymorphisms (RFLP) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_2870 Radiation hybrid map RH map A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.|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. FALSE http://edamontology.org/data_1280 beta12orEarlier data_2870 A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. RH map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2872 ID list "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." FALSE http://edamontology.org/data_2093 beta12orEarlier data_2872 "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2873 Phylogenetic gene frequencies data Gene frequencies data that may be read during phylogenetic tree calculation. FALSE http://edamontology.org/data_1426 beta12orEarlier data_2873 Gene frequencies data that may be read during phylogenetic tree calculation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2874 Sequence set (polymorphic) "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2874 http://edamontology.org/data_1234 "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2875 DRCAT resource An entry (resource) from the DRCAT bioinformatics resource catalogue. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2875 http://edamontology.org/data_1883 An entry (resource) from the DRCAT bioinformatics resource catalogue. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2877 Protein complex "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." FALSE http://edamontology.org/data_1460 beta12orEarlier data_2877 "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2878 Protein structural motif 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. FALSE http://edamontology.org/data_1460 beta12orEarlier data_2878 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2879 Lipid report Annotation on or information derived from one or more specific lipid 3D structure(s). FALSE http://edamontology.org/data_2085 beta12orEarlier data_2879 Annotation on or information derived from one or more specific lipid 3D structure(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2880 Secondary structure image Image of one or more molecular secondary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2880 http://edamontology.org/data_2992 Image of one or more molecular secondary structures. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/data_2881 Secondary structure report "An informative report on general information, properties or features of one or more molecular secondary structures." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2881 http://edamontology.org/data_2085 "An informative report on general information, properties or features of one or more molecular secondary structures." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2882 DNA features DNA sequence-specific feature annotation (not in a feature table). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2882 http://edamontology.org/data_1276 DNA sequence-specific feature annotation (not in a feature table). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_2883 RNA features report Features concerning RNA or regions of DNA that encode an RNA molecule. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2883 http://edamontology.org/data_0916 Features concerning RNA or regions of DNA that encode an RNA molecule. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2884 Plot Biological data that has been plotted as a graph of some type. FALSE http://edamontology.org/data_0006 beta12orEarlier data_2884 Biological data that has been plotted as a graph of some type. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2885 Nucleic acid features report (polymorphism) DNA polymorphism. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2885 DNA polymorphism. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 http://edamontology.org/data_2886 Protein sequence record Sequence record (protein) A protein sequence and associated metadata. FALSE http://edamontology.org/data_0849|http://edamontology.org/data_2976 beta12orEarlier data_2886 A protein sequence and associated metadata. Sequence record (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2887 Nucleic acid sequence record Sequence record (nucleic acid)|Nucleotide sequence record|DNA sequence record|RNA sequence record A nucleic acid sequence and associated metadata. FALSE http://edamontology.org/data_2977|http://edamontology.org/data_0849 beta12orEarlier data_2887 A nucleic acid sequence and associated metadata. Sequence record (nucleic acid)|Nucleotide sequence record DNA sequence record|RNA sequence record http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2888 Protein sequence record (full) "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2888 "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2889 Nucleic acid sequence record (full) "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2889 "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0849 1.8 http://edamontology.org/data_2891 Biological model accession "Accession of a mathematical model, typically an entry from a database." FALSE http://edamontology.org/data_1085|http://edamontology.org/data_2091 beta12orEarlier data_2891 "Accession of a mathematical model, typically an entry from a database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2892 Cell type name The name of a type or group of cells. FALSE http://edamontology.org/data_2655|http://edamontology.org/data_2099 beta12orEarlier data_2892 The name of a type or group of cells. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2893 Cell type accession Cell type ID Accession of a type or group of cells (catalogued in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2655 beta12orEarlier data_2893 Accession of a type or group of cells (catalogued in a database). Cell type ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2894 Compound accession Chemical compound accession|Small molecule accession Accession of an entry from a database of chemicals. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_1086 beta12orEarlier data_2894 Accession of an entry from a database of chemicals. Chemical compound accession|Small molecule accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2895 Drug accession Accession of a drug. FALSE http://edamontology.org/data_0993|http://edamontology.org/data_2091 beta12orEarlier data_2895 Accession of a drug. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2896 Toxin name Name of a toxin. FALSE http://edamontology.org/data_2099|http://edamontology.org/data_2576 beta12orEarlier data_2896 Name of a toxin. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2897 Toxin accession Accession of a toxin (catalogued in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2576 beta12orEarlier data_2897 Accession of a toxin (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2898 Monosaccharide accession Accession of a monosaccharide (catalogued in a database). FALSE http://edamontology.org/data_0996|http://edamontology.org/data_2091 beta12orEarlier data_2898 Accession of a monosaccharide (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2899 Drug name Common name of a drug. FALSE http://edamontology.org/data_0990|http://edamontology.org/data_0993 beta12orEarlier data_2899 Common name of a drug. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2900 Carbohydrate accession Accession of an entry from a database of carbohydrates. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_2663 beta12orEarlier data_2900 Accession of an entry from a database of carbohydrates. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2901 Molecule accession Accession of a specific molecule (catalogued in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_0982 beta12orEarlier data_2901 Accession of a specific molecule (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2902 Data resource definition accession Accession of a data definition (catalogued in a database). FALSE http://edamontology.org/data_1084|http://edamontology.org/data_2091 beta12orEarlier data_2902 Accession of a data definition (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2903 Genome accession An accession of a particular genome (in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2749 beta12orEarlier data_2903 An accession of a particular genome (in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2904 Map accession An accession of a map of a molecular sequence (deposited in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2117 beta12orEarlier data_2904 An accession of a map of a molecular sequence (deposited in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2905 Lipid accession Accession of an entry from a database of lipids. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_2812 beta12orEarlier data_2905 Accession of an entry from a database of lipids. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2906 Peptide ID Accession of a peptide deposited in a database. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_0988 beta12orEarlier data_2906 Accession of a peptide deposited in a database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2907 Protein accession Protein accessions Accession of a protein deposited in a database. FALSE http://edamontology.org/data_2901|http://edamontology.org/data_0989 beta12orEarlier data_2907 Accession of a protein deposited in a database. Protein accessions http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2908 Organism accession An accession of annotation on a (group of) organisms (catalogued in a database). FALSE http://edamontology.org/data_1869|http://edamontology.org/data_2091 beta12orEarlier data_2908 An accession of annotation on a (group of) organisms (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2909 Organism name The name of an organism (or group of organisms). FALSE http://edamontology.org/data_1869|http://edamontology.org/data_2099 beta12orEarlier data_2909 Moby:Organism_Name|Moby:OrganismsLongName|Moby:FirstEpithet|Moby:BriefOccurrenceRecord|Moby:InfraspecificEpithet|Moby:OccurrenceRecord|Moby:OrganismsShortName The name of an organism (or group of organisms). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2910 Protein family accession Accession of a protein family (that is deposited in a database). FALSE http://edamontology.org/data_2091|http://edamontology.org/data_1075 beta12orEarlier data_2910 Accession of a protein family (that is deposited in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2911 Transcription factor accession Accession of an entry from a database of transcription factors or binding sites. FALSE http://edamontology.org/data_1077|http://edamontology.org/data_2091|http://edamontology.org/data_2907 beta12orEarlier data_2911 Accession of an entry from a database of transcription factors or binding sites. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2912 Strain accession "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." FALSE http://edamontology.org/data_2908|http://edamontology.org/data_2379 beta12orEarlier data_2912 "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2913 Virus identifier An accession of annotation on a (group of) viruses (catalogued in a database). FALSE http://edamontology.org/data_1869 beta12orEarlier data_2913 An accession of annotation on a (group of) viruses (catalogued in a database). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2914 Sequence features metadata Metadata on sequence features. FALSE http://edamontology.org/data_0006 beta12orEarlier data_2914 Metadata on sequence features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2915 Gramene identifier Identifier of a Gramene database entry. FALSE http://edamontology.org/data_1096 beta12orEarlier data_2915 Identifier of a Gramene database entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2916 DDBJ accession DDBJ identifier|DDBJ accession number|DDBJ ID An identifier of an entry from the DDBJ sequence database. FALSE http://edamontology.org/data_1103 beta12orEarlier data_2916 An identifier of an entry from the DDBJ sequence database. DDBJ identifier|DDBJ accession number|DDBJ ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2917 ConsensusPathDB identifier An identifier of an entity from the ConsensusPathDB database. FALSE http://edamontology.org/data_2109 beta12orEarlier data_2917 An identifier of an entity from the ConsensusPathDB database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2925 Sequence data "Data concerning, extracted from, or derived from the analysis of molecular sequence(s). |This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2925 http://edamontology.org/data_2534 "Data concerning, extracted from, or derived from the analysis of molecular sequence(s). " http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/data_2927 Codon usage "Data concerning codon usage.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2927 http://edamontology.org/data_0914 Data concerning codon usage. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2954 Article report Data derived from the analysis of a scientific text such as a full text article from a scientific journal. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2954 http://edamontology.org/data_0972|http://edamontology.org/data_3779 Data derived from the analysis of a scientific text such as a full text article from a scientific journal. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2955 Sequence report Sequence-derived report "An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties." FALSE http://edamontology.org/data_2048 beta12orEarlier data_2955 "An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties." Sequence-derived report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2956 Protein secondary structure report An informative report about the properties or features of one or more protein secondary structures. FALSE http://edamontology.org/data_1537 beta12orEarlier data_2956 An informative report about the properties or features of one or more protein secondary structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2957 Hopp and Woods plot A Hopp and Woods plot of predicted antigenicity of a peptide or protein. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_1534 beta12orEarlier data_2957 A Hopp and Woods plot of predicted antigenicity of a peptide or protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2958 Nucleic acid melting curve A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).|Shows the proportion of nucleic acid which are double-stranded versus temperature. FALSE http://edamontology.org/data_2884|http://edamontology.org/data_1583 beta12orEarlier data_2958 A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2959 Nucleic acid probability profile A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).|Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature FALSE http://edamontology.org/data_1583 beta12orEarlier data_2959 A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2960 Nucleic acid temperature profile Melting map A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).|Plots melting temperature versus base position. FALSE http://edamontology.org/data_1583 beta12orEarlier data_2960 A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Melting map http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2961 Gene regulatory network report A report typically including a map (diagram) of a gene regulatory network. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2961 A report typically including a map (diagram) of a gene regulatory network. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2984 1.8 http://edamontology.org/data_2965 2D PAGE gel report An informative report on a two-dimensional (2D PAGE) gel. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2965 An informative report on a two-dimensional (2D PAGE) gel. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_2966 Oligonucleotide probe sets annotation "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2966 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2717 1.14 http://edamontology.org/data_2967 Microarray image An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2967 http://edamontology.org/data_2968 An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2968 Image Image data "Biological or biomedical data has been rendered into an image, typically for display on screen." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2968 "Biological or biomedical data has been rendered into an image, typically for display on screen." Image data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2969 Sequence image "Image of a molecular sequence, possibly with sequence features or properties shown." FALSE http://edamontology.org/data_2968|http://edamontology.org/data_2955 beta12orEarlier data_2969 "Image of a molecular sequence, possibly with sequence features or properties shown." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2970 Protein hydropathy data Protein hydropathy report A report on protein properties concerning hydropathy. FALSE http://edamontology.org/data_0897 beta12orEarlier data_2970 A report on protein properties concerning hydropathy. Protein hydropathy report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2971 Workflow data Data concerning a computational workflow. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2971 http://edamontology.org/data_0949 Data concerning a computational workflow. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2972 Workflow A computational workflow. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2972 http://edamontology.org/data_0949 A computational workflow. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2973 Secondary structure data Data concerning molecular secondary structure data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2973 http://edamontology.org/data_2085 Data concerning molecular secondary structure data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2974 Protein sequence (raw) Raw sequence (protein)|Raw protein sequence A raw protein sequence (string of characters). FALSE http://edamontology.org/data_0848|http://edamontology.org/data_2976 beta12orEarlier data_2974 A raw protein sequence (string of characters). Raw sequence (protein)|Raw protein sequence http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2975 Nucleic acid sequence (raw) Nucleotide sequence (raw)|Raw sequence (nucleic acid)|Nucleic acid raw sequence A raw nucleic acid sequence. FALSE http://edamontology.org/data_2977|http://edamontology.org/data_0848 beta12orEarlier data_2975 A raw nucleic acid sequence. Nucleotide sequence (raw)|Raw sequence (nucleic acid)|Nucleic acid raw sequence http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2976 Protein sequence Protein sequences "One or more protein sequences, possibly with associated annotation." FALSE http://edamontology.org/data_2044 beta12orEarlier data_2976 "One or more protein sequences, possibly with associated annotation." Protein sequences http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2977 Nucleic acid sequence Nucleic acid sequences|Nucleotide sequences|Nucleotide sequence|DNA sequence "One or more nucleic acid sequences, possibly with associated annotation." FALSE http://edamontology.org/data_2044 beta12orEarlier data_2977 "One or more nucleic acid sequences, possibly with associated annotation." Nucleic acid sequences|Nucleotide sequences|Nucleotide sequence DNA sequence http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2978 Reaction data Reaction annotation|Enzyme kinetics annotation "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_2978 "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." Reaction annotation|Enzyme kinetics annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2979 Peptide property Peptide data Data concerning small peptides. FALSE http://edamontology.org/data_2087 beta12orEarlier data_2979 Data concerning small peptides. Peptide data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2980 Protein classification "An informative report concerning the classification of protein sequences or structures.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2980 http://edamontology.org/data_0907 An informative report concerning the classification of protein sequences or structures. http://edamontology.org/data_2981 Sequence motif data "Data concerning specific or conserved pattern in molecular sequences.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2981 Data concerning specific or conserved pattern in molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0860 1.8 http://edamontology.org/data_2982 Sequence profile data "Data concerning models representing a (typically multiple) sequence alignment.|This is a broad data type and is used a placeholder for other, more specific types." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2982 http://edamontology.org/data_1354 Data concerning models representing a (typically multiple) sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2983 Pathway or network data Data concerning a specific biological pathway or network. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2983 http://edamontology.org/data_2984|http://edamontology.org/data_2600 Data concerning a specific biological pathway or network. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/data_2984 Pathway or network report "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." FALSE http://edamontology.org/data_3753 beta12orEarlier data_2984 "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2985 Nucleic acid thermodynamic data Nucleic acid property (thermodynamic or kinetic)|Nucleic acid thermodynamic property A thermodynamic or kinetic property of a nucleic acid molecule. FALSE http://edamontology.org/data_0912 beta12orEarlier data_2985 A thermodynamic or kinetic property of a nucleic acid molecule. Nucleic acid property (thermodynamic or kinetic)|Nucleic acid thermodynamic property http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2986 Nucleic acid classification "Data concerning the classification of nucleic acid sequences or structures.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2986 http://edamontology.org/data_3148 Data concerning the classification of nucleic acid sequences or structures. http://edamontology.org/data_2987 Classification report "A report on a classification of molecular sequences, structures or other entities.|This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2987 http://edamontology.org/data_2048 "A report on a classification of molecular sequences, structures or other entities." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_2989 Protein features report (key folding sites) key residues involved in protein folding. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_2989 key residues involved in protein folding. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_2991 Protein geometry report Torsion angle data "Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc." FALSE http://edamontology.org/data_1537 beta12orEarlier data_2991 "Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc." Torsion angle data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2992 Protein structure image Structure image (protein) An image of protein structure. FALSE http://edamontology.org/data_1710|http://edamontology.org/data_3153 beta12orEarlier data_2992 An image of protein structure. Structure image (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_2994 Phylogenetic character weights Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. FALSE http://edamontology.org/data_2523 beta12orEarlier data_2994 Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3002 Annotation track Genome-browser track|Genome annotation track|Genomic track|Genome track|Sequence annotation track "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." FALSE http://edamontology.org/data_1255 beta12orEarlier data_3002 "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." Genome-browser track|Genome annotation track|Genomic track|Genome track|Sequence annotation track http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3021 UniProt accession UniProtKB accession|UniProt entry accession|UniProt accession number|UniProtKB accession number|TrEMBL entry accession|Swiss-Prot entry accession Accession number of a UniProt (protein sequence) database entry. FALSE http://edamontology.org/data_1096 beta12orEarlier P43353|Q7M1G0|Q9C199|A5A6J6 data_3021 Accession number of a UniProt (protein sequence) database entry. UniProtKB accession|UniProt entry accession|UniProt accession number|UniProtKB accession number TrEMBL entry accession|Swiss-Prot entry accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}" http://edamontology.org/data_3022 NCBI genetic code ID Identifier of a genetic code in the NCBI list of genetic codes. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier 16 data_3022 Identifier of a genetic code in the NCBI list of genetic codes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data [1-9][0-9]? http://edamontology.org/data_3025 Ontology concept identifier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. FALSE http://edamontology.org/data_0976 beta12orEarlier data_3025 Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3026 GO concept name (biological process) The name of a concept for a biological process from the GO ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_3026 http://edamontology.org/data_2339 The name of a concept for a biological process from the GO ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_3027 GO concept name (molecular function) The name of a concept for a molecular function from the GO ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_3027 http://edamontology.org/data_2339 The name of a concept for a molecular function from the GO ontology. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/data_3028 Taxonomy Taxonomic data "Data concerning the classification, identification and naming of organisms.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 beta12orEarlier data_3028 "Data concerning the classification, identification and naming of organisms." Taxonomic data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3029 Protein ID (EMBL/GenBank/DDBJ) "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.|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." FALSE http://edamontology.org/data_2907 beta13 data_3029 "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3031 Core data "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.|Core data entities typically have a format and may be identified by an accession number." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3031 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0006 1.5 http://edamontology.org/data_3034 Sequence feature identifier Name or other identifier of molecular sequence feature(s). FALSE http://edamontology.org/data_0976 beta13 data_3034 Name or other identifier of molecular sequence feature(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3035 Structure identifier "An identifier of a molecular tertiary structure, typically an entry from a structure database." FALSE http://edamontology.org/data_0976 beta13 data_3035 "An identifier of a molecular tertiary structure, typically an entry from a structure database." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3036 Matrix identifier "An identifier of an array of numerical values, such as a comparison matrix." FALSE http://edamontology.org/data_0976 beta13 data_3036 "An identifier of an array of numerical values, such as a comparison matrix." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3085 Protein sequence composition A report (typically a table) on character or word composition / frequency of protein sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3085 A report (typically a table) on character or word composition / frequency of protein sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1261 1.8 http://edamontology.org/data_3086 Nucleic acid sequence composition (report) A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3086 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1261 1.8 http://edamontology.org/data_3101 Protein domain classification node A node from a classification of protein structural domain(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3101 http://edamontology.org/data_2980 A node from a classification of protein structural domain(s). http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3102 CAS number CAS registry number "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." FALSE http://edamontology.org/data_2895 beta13 data_3102 "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." CAS registry number http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3103 ATC code "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)." FALSE http://edamontology.org/data_2895 beta13 data_3103 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3104 UNII Unique Ingredient Identifier "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." FALSE http://edamontology.org/data_1086 beta13 data_3104 "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." Unique Ingredient Identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3105 Geotemporal metadata Basic information concerning geographical location or time. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3105 Basic information concerning geographical location or time. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3106 System metadata "Metadata concerning the software, hardware or other aspects of a computer system." FALSE http://edamontology.org/data_2337 beta13 data_3106 "Metadata concerning the software, hardware or other aspects of a computer system." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3107 Sequence feature name "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3107 "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1022 1.15 http://edamontology.org/data_3108 Experimental measurement Experimental measurement data|Experimentally measured data|Measured data|Measurement|Measurement data|Raw experimental data|Measurement metadata "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.|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." FALSE http://edamontology.org/data_0006 beta13 data_3108 "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." Experimental measurement data|Experimentally measured data|Measured data|Measurement|Measurement data Raw experimental data|Measurement metadata http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3110 Raw microarray data Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.|Such data as found in Affymetrix CEL or GPR files. FALSE http://edamontology.org/data_3108|http://edamontology.org/data_3117 beta13 data_3110 Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3111 Processed microarray data Gene annotation (expression)|Gene expression report|Microarray probe set data Data generated from processing and analysis of probe set data from a microarray experiment.|Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. FALSE http://edamontology.org/data_3117 beta13 data_3111 Data generated from processing and analysis of probe set data from a microarray experiment. Gene annotation (expression)|Gene expression report|Microarray probe set data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3112 Gene expression matrix Normalised microarray data|Gene expression data matrix The final processed (normalised) data for a set of hybridisations in a microarray experiment.|This combines data from all hybridisations. FALSE http://edamontology.org/data_2603|http://edamontology.org/data_2082 beta13 data_3112 The final processed (normalised) data for a set of hybridisations in a microarray experiment. Normalised microarray data|Gene expression data matrix http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3113 Sample annotation "Annotation on a biological sample, for example experimental factors and their values.|This might include compound and dose in a dose response experiment." FALSE http://edamontology.org/data_2337 beta13 data_3113 "Annotation on a biological sample, for example experimental factors and their values." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3115 Microarray metadata "Annotation on the array itself used in a microarray experiment.|This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc." FALSE http://edamontology.org/data_2603 beta13 data_3115 Annotation on the array itself used in a microarray experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3116 Microarray protocol annotation Annotation on laboratory and/or data processing protocols used in an microarray experiment.|This might describe e.g. the normalisation methods used to process the raw data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3116 Annotation on laboratory and/or data processing protocols used in an microarray experiment. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3117 Microarray hybridisation data Data concerning the hybridisations measured during a microarray experiment. FALSE http://edamontology.org/data_2603 beta13 data_3117 Data concerning the hybridisations measured during a microarray experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3118 Protein features report (topological domains) topological domains such as cytoplasmic regions in a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3118 topological domains such as cytoplasmic regions in a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_3119 Sequence features (compositionally-biased regions) A report of regions in a molecular sequence that are biased to certain characters. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3119 http://edamontology.org/data_1261 A report of regions in a molecular sequence that are biased to certain characters. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3122 Nucleic acid features (difference and change) A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3122 A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.5 http://edamontology.org/data_3123 Nucleic acid features report (expression signal) regions within a nucleic acid sequence containing a signal that alters a biological function. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3123 regions within a nucleic acid sequence containing a signal that alters a biological function. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3125 Nucleic acid features report (binding) nucleic acids binding to some other molecule.|This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3125 nucleic acids binding to some other molecule. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3126 Nucleic acid repeats (report) repetitive elements within a nucleic acid sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3126 repetitive elements within a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3127 Nucleic acid features report (replication and recombination) DNA replication or recombination. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3127 DNA replication or recombination. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3128 Nucleic acid structure report Nucleic acid features (structure)|Stem loop (report)|d-loop (report)|Quadruplexes (report) A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. FALSE http://edamontology.org/data_2085|http://edamontology.org/data_2084 beta13 data_3128 A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. Nucleic acid features (structure) Stem loop (report)|d-loop (report)|Quadruplexes (report) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3129 Protein features report (repeats) short repetitive subsequences (repeat sequences) in a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3129 short repetitive subsequences (repeat sequences) in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1277 1.8 http://edamontology.org/data_3130 Sequence motif matches (protein) "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3130 "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0858 1.8 http://edamontology.org/data_3131 Sequence motif matches (nucleic acid) "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3131 "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_0858 1.8 http://edamontology.org/data_3132 Nucleic acid features (d-loop) A report on displacement loops in a mitochondrial DNA sequence.|A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3132 http://edamontology.org/data_3128 A report on displacement loops in a mitochondrial DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3133 Nucleic acid features (stem loop) A report on stem loops in a DNA sequence.|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. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3133 http://edamontology.org/data_3128 A report on stem loops in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3134 Gene transcript report Gene transcript annotation|Clone or EST (report)|Transcript (report)|mRNA features|Nucleic acid features (mRNA features)|mRNA (report) "An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. |This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR)." FALSE http://edamontology.org/data_0916 beta13 data_3134 "An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. " Gene transcript annotation|Clone or EST (report)|Transcript (report)|mRNA features|Nucleic acid features (mRNA features)|mRNA (report) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3135 Nucleic acid features report (signal or transit peptide) coding sequences for a signal or transit peptide. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3135 coding sequences for a signal or transit peptide. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3137 Non-coding RNA "features of non-coding or functional RNA molecules, including tRNA and rRNA." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3137 "features of non-coding or functional RNA molecules, including tRNA and rRNA." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3138 Transcriptional features (report) "Features concerning transcription of DNA into RNA including the regulation of transcription.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3138 http://edamontology.org/data_3134 Features concerning transcription of DNA into RNA including the regulation of transcription. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3139 Nucleic acid features report (STS) sequence tagged sites (STS) in nucleic acid sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3139 sequence tagged sites (STS) in nucleic acid sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1276 1.8 http://edamontology.org/data_3140 Nucleic acid features (immunoglobulin gene structure) "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3140 http://edamontology.org/data_0916 "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3141 SCOP class Information on a 'class' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3141 http://edamontology.org/data_2980 Information on a 'class' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3142 SCOP fold Information on a 'fold' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3142 http://edamontology.org/data_2980 Information on a 'fold' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3143 SCOP superfamily Information on a 'superfamily' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3143 http://edamontology.org/data_2980 Information on a 'superfamily' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3144 SCOP family Information on a 'family' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3144 http://edamontology.org/data_2980 Information on a 'family' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3145 SCOP protein Information on a 'protein' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3145 http://edamontology.org/data_2980 Information on a 'protein' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3146 SCOP species Information on a 'species' node from the SCOP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3146 http://edamontology.org/data_2980 Information on a 'species' node from the SCOP database. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3147 Mass spectrometry experiment mass spectrometry experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 data_3147 mass spectrometry experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3148 Gene family report Nucleic acid classification|Gene annotation (homology information)|Gene homology (report)|Gene annotation (homology)|Homology information|Gene family annotation "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, or any other classification of nucleic acid sequences or structures that reflects gene structure.|This includes reports on on gene homologues between species." FALSE http://edamontology.org/data_2084 beta13 data_3148 Nucleic acid classification "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, or any other classification of nucleic acid sequences or structures that reflects gene structure." Gene annotation (homology information)|Gene homology (report)|Gene annotation (homology)|Homology information|Gene family annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3153 Protein image An image of a protein. FALSE http://edamontology.org/data_2968 beta13 data_3153 An image of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3154 Protein alignment An alignment of protein sequences and/or structures. FALSE http://edamontology.org/data_1916 beta13 data_3154 An alignment of protein sequences and/or structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3165 NGS experiment "sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.0 data_3165 "sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3181 Sequence assembly report Assembly report "An informative report about a DNA sequence assembly.|This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc." FALSE http://edamontology.org/data_0867 1.1 data_3181 An informative report about a DNA sequence assembly. Assembly report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3210 Genome index An index of a genome sequence.|Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. FALSE http://edamontology.org/data_0955 1.1 data_3210 An index of a genome sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3231 GWAS report Report concerning genome-wide association study experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 data_3231 Report concerning genome-wide association study experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3236 Cytoband position "The position of a cytogenetic band in a genome.|Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on." FALSE http://edamontology.org/data_2012 1.2 data_3236 The position of a cytogenetic band in a genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3238 Cell type ontology ID CL ID Cell type ontology concept ID. FALSE http://edamontology.org/data_1087|http://edamontology.org/data_2893 1.2|beta12orEarlier data_3238 Cell type ontology concept ID. CL ID http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data CL_[0-9]{7} http://edamontology.org/data_3241 Kinetic model "Mathematical model of a network, that contains biochemical kinetics." FALSE http://edamontology.org/data_0950 1.2 data_3241 "Mathematical model of a network, that contains biochemical kinetics." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3264 COSMIC ID cosmic ID|COSMIC identifier|cosmic id|cosmic identifier Identifier of a COSMIC database entry. FALSE http://edamontology.org/data_2294 1.3 data_3264 Identifier of a COSMIC database entry. cosmic ID|COSMIC identifier|cosmic id|cosmic identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3265 HGMD ID hgmd id|HGMD identifier|hgmd ID|hgmd identifier Identifier of a HGMD database entry. FALSE http://edamontology.org/data_2294 beta12orEarlier data_3265 Identifier of a HGMD database entry. hgmd id|HGMD identifier|hgmd ID|hgmd identifier http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3266 Sequence assembly ID Sequence assembly version Unique identifier of sequence assembly. FALSE http://edamontology.org/data_1064 1.3 data_3266 Unique identifier of sequence assembly. Sequence assembly version http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3268 Sequence feature type "A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.3 data_3268 http://edamontology.org/data_0842 "A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory." http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3269 Gene homology (report) An informative report on gene homologues between species. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier data_3269 http://edamontology.org/data_3148 An informative report on gene homologues between species. http://purl.obolibrary.org/obo/edam#obsolete 1.5 http://edamontology.org/data_3270 Ensembl gene tree ID Ensembl ID (gene tree) Unique identifier for a gene tree from the Ensembl database. FALSE http://edamontology.org/data_2610|http://edamontology.org/data_1068 1.3 ENSGT00390000003602 data_3270 Unique identifier for a gene tree from the Ensembl database. Ensembl ID (gene tree) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3271 Gene tree A phylogenetic tree that is an estimate of the character's phylogeny. FALSE http://edamontology.org/data_0872 1.3 data_3271 A phylogenetic tree that is an estimate of the character's phylogeny. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3272 Species tree A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. FALSE http://edamontology.org/data_0872 1.3 data_3272 A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3273 Sample ID Sample accession Name or other identifier of an entry from a biosample database. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 1.3 data_3273 Name or other identifier of an entry from a biosample database. Sample accession http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3274 MGI accession Identifier of an object from the MGI database. FALSE http://edamontology.org/data_2091|http://edamontology.org/data_2109 1.3 data_3274 Identifier of an object from the MGI database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3275 Phenotype name Phenotypes|Phenotype Name of a phenotype. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2099 1.3 data_3275 Name of a phenotype. Phenotypes|Phenotype http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3354 Transition matrix HMM transition matrix "A HMM transition matrix contains the probabilities of switching from one HMM state to another.|Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa." FALSE http://edamontology.org/data_2082 1.4 data_3354 A HMM transition matrix contains the probabilities of switching from one HMM state to another. HMM transition matrix http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3355 Emission matrix HMM emission matrix "A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.|Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state." FALSE http://edamontology.org/data_2082 1.4 data_3355 "A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM." HMM emission matrix http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3356 Hidden Markov model A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.4 data_3356 A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_1364 1.15 http://edamontology.org/data_3358 Format identifier An identifier of a data format. FALSE http://edamontology.org/data_0976 1.4 data_3358 An identifier of a data format. http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3424 Raw image Raw biological or biomedical image generated by some experimental technique. FALSE http://edamontology.org/data_2968 beta12orEarlier|1.5 data_3424 Raw biological or biomedical image generated by some experimental technique. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3425 Carbohydrate property Carbohydrate data "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates." FALSE http://edamontology.org/data_2087 1.5 data_3425 "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates." Carbohydrate data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3426 Proteomics experiment report Report concerning proteomics experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.5 data_3426 Report concerning proteomics experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3427 RNAi report RNAi experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.5 data_3427 RNAi experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3428 Simulation experiment report "biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.5 data_3428 "biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/data_2531 1.8 http://edamontology.org/data_3442 MRI image "Nuclear magnetic resonance imaging image |Magnetic resonance tomography image |Magnetic resonance imaging image |MRT image|NMRI image" "An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body." FALSE http://edamontology.org/data_3424 1.7 data_3442 "An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body." "Nuclear magnetic resonance imaging image |Magnetic resonance tomography image |Magnetic resonance imaging image |MRT image|NMRI image" http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3449 Cell migration track image An image from a cell migration track assay. FALSE http://edamontology.org/data_2968 1.7 data_3449 An image from a cell migration track assay. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3451 Rate of association kon Rate of association of a protein with another protein or some other molecule. FALSE http://edamontology.org/data_0897 1.7 data_3451 Rate of association of a protein with another protein or some other molecule. kon http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3479 Gene order Multiple gene identifiers in a specific order.|Such data are often used for genome rearrangement tools and phylogenetic tree labeling. FALSE http://edamontology.org/data_2082 1.7 data_3479 Multiple gene identifiers in a specific order. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3483 Spectrum Spectra The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. FALSE http://edamontology.org/data_0006 1.7 data_3483 The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. Spectra http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3488 NMR spectrum NMR spectra Spectral information for a molecule from a nuclear magnetic resonance experiment. FALSE http://edamontology.org/data_3483 1.7 data_3488 Spectral information for a molecule from a nuclear magnetic resonance experiment. NMR spectra http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/data_3490 Chemical structure sketch Small molecule sketch A sketch of a small molecule made with some specialised drawing package.|Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. FALSE http://edamontology.org/data_1712 1.8 data_3490 A sketch of a small molecule made with some specialised drawing package. Small molecule sketch http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3492 Nucleic acid signature An informative report about a specific or conserved nucleic acid sequence pattern. FALSE http://edamontology.org/data_2762 1.8 data_3492 An informative report about a specific or conserved nucleic acid sequence pattern. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3494 DNA sequence DNA sequences A DNA sequence. FALSE http://edamontology.org/data_2977 1.8 data_3494 A DNA sequence. DNA sequences http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3495 RNA sequence RNA sequences FALSE http://edamontology.org/data_2977 1.8 data_3495 RNA sequences http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3496 RNA sequence (raw) RNA raw sequence|Raw sequence (RNA) A raw RNA sequence. FALSE http://edamontology.org/data_3495|http://edamontology.org/data_2975 1.8 data_3496 A raw RNA sequence. RNA raw sequence|Raw sequence (RNA) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3497 DNA sequence (raw) DNA raw sequence|Raw sequence (DNA) A raw DNA sequence. FALSE http://edamontology.org/data_3494|http://edamontology.org/data_2975 1.8 data_3497 A raw DNA sequence. DNA raw sequence|Raw sequence (DNA) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3498 Sequence variations Gene sequence variations Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.|Variations are stored along with a reference genome. FALSE http://edamontology.org/data_0006 1.8 data_3498 Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. Gene sequence variations http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3505 Bibliography A list of publications such as scientic papers or books. FALSE http://edamontology.org/data_2526 1.8 data_3505 A list of publications such as scientic papers or books. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3509 Ontology mapping A mapping of supplied textual terms or phrases to ontology concepts (URIs). FALSE http://edamontology.org/data_2093 beta12orEarlier data_3509 A mapping of supplied textual terms or phrases to ontology concepts (URIs). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3546 Image metadata Image-associated data|Image-related data "Any data concerning a specific biological or biomedical image.|This can include basic provenance and technical information about the image, scientific annotation and so on." FALSE http://edamontology.org/data_2048 1.9 data_3546 Any data concerning a specific biological or biomedical image. Image-associated data|Image-related data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3558 Clinical trial report Clinical trial information A report concerning a clinical trial. FALSE http://edamontology.org/data_2048 1.9 data_3558 A report concerning a clinical trial. Clinical trial information http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3567 Reference sample report Biosample report A report about a biosample. FALSE http://edamontology.org/data_2048 1.10 data_3567 A report about a biosample. Biosample report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3568 Gene Expression Atlas Experiment ID Accession number of an entry from the Gene Expression Atlas. FALSE http://edamontology.org/data_1078 1.10 data_3568 Accession number of an entry from the Gene Expression Atlas. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3667 Disease identifier Identifier of an entry from a database of disease. FALSE http://edamontology.org/data_0976|http://edamontology.org/data_2091 beta12orEarlier data_3667 Identifier of an entry from a database of disease. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3668 Disease name The name of some disease. FALSE http://edamontology.org/data_3667|http://edamontology.org/data_2099 1.12 data_3668 The name of some disease. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3669 Training material OER|Open educational resource Some material that is used for educational (training) purposes. FALSE http://edamontology.org/data_0006 1.12 data_3669 Some material that is used for educational (training) purposes. OER|Open educational resource http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3670 Online course On-line course|Massive open online course|MOOC A training course available for use on the Web. FALSE http://edamontology.org/data_3669 1.12 data_3670 A training course available for use on the Web. On-line course Massive open online course|MOOC http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3671 Text Free text|Textual search query|Plain text "Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query." FALSE http://edamontology.org/data_2526 1.12 data_3671 "Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query." Free text Textual search query|Plain text http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3707 Biodiversity report Biodiversity information|OTU table A report about biodiversity data. FALSE http://edamontology.org/data_3736|http://edamontology.org/data_2048 1.9 data_3707 A report about biodiversity data. Biodiversity information OTU table http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3716 Biosafety report Biosafety information A report about biosafety data. FALSE http://edamontology.org/data_2048 1.14 data_3716 A report about biosafety data. Biosafety information http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3717 Isolation report Geographic location|Isolation source A report about any kind of isolation of biological material. FALSE http://edamontology.org/data_2048 1.14 data_3717 A report about any kind of isolation of biological material. Geographic location|Isolation source http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3718 Pathogenicity report Pathogenicity Information about the ability of an organism to cause disease in a corresponding host. FALSE http://edamontology.org/data_3716 1.14 data_3718 Information about the ability of an organism to cause disease in a corresponding host. Pathogenicity http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3719 Biosafety classification Biosafety level Information about the biosafety classification of an organism according to corresponding law. FALSE http://edamontology.org/data_3716 1.14 data_3719 Information about the biosafety classification of an organism according to corresponding law. Biosafety level http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3720 Geographic location A report about localisation of the isolaton of biological material e.g. country or coordinates. FALSE http://edamontology.org/data_3717 1.14 data_3720 A report about localisation of the isolaton of biological material e.g. country or coordinates. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3721 Isolation source "A report about any kind of isolation source of biological material e.g. blood, water, soil." FALSE http://edamontology.org/data_3717 1.14 data_3721 "A report about any kind of isolation source of biological material e.g. blood, water, soil." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3722 Physiology parameter "Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum." FALSE http://edamontology.org/data_3108 1.14 data_3722 "Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3723 Morphology parameter "Experimentally determined parameter of the morphology of an organism, e.g. size & shape." FALSE http://edamontology.org/data_3108 1.14 data_3723 "Experimentally determined parameter of the morphology of an organism, e.g. size & shape." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3724 Cultivation parameter Cultivation conditions|Salinity|Nitrogen source|Culture media composition|pH value|Carbon source|Temperature Experimental determined parameter for the cultivation of an organism. FALSE http://edamontology.org/data_3108 1.14 data_3724 Experimental determined parameter for the cultivation of an organism. Cultivation conditions Salinity|Nitrogen source|Culture media composition|pH value|Carbon source|Temperature http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3732 Sequencing metadata name "Data concerning a sequencing experiment, that may be specified as an input to some tool." FALSE http://edamontology.org/data_2099 1.15 data_3732 "Data concerning a sequencing experiment, that may be specified as an input to some tool." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3733 Flow cell identifier "An identifier of a flow cell of a sequencing machine.|A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 ""lanes"" which allows 8 experiments in a single analysis." FALSE http://edamontology.org/data_3732 1.15 data_3733 An identifier of a flow cell of a sequencing machine. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3734 Lane identifier "An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced." FALSE http://edamontology.org/data_3732 1.15 data_3734 "An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3735 Run number "A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. " FALSE http://edamontology.org/data_3732 1.15 data_3735 "A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3736 Ecological data "Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment.|This is a broad data type and is used a placeholder for other, more specific types." FALSE http://edamontology.org/data_0006 1.15 data_3736 Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3737 Alpha diversity data α-diversity The mean species diversity in sites or habitats at a local scale. FALSE http://edamontology.org/data_3707 1.15 data_3737 The mean species diversity in sites or habitats at a local scale. α-diversity http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3738 Beta diversity data True beta diversity|β-diversity The ratio between regional and local species diversity. FALSE http://edamontology.org/data_3707 1.15 data_3738 The ratio between regional and local species diversity. True beta diversity|β-diversity http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3739 Gamma diversity data γ-diversity The total species diversity in a landscape. FALSE http://edamontology.org/data_3707 1.15 data_3739 The total species diversity in a landscape. γ-diversity http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3743 Ordination plot "A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart." FALSE http://edamontology.org/data_2884|http://edamontology.org/data_0897 1.15 data_3743 "A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3753 Over-representation report Enrichment report|Functional enrichment report "An informative report containing a ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data." FALSE http://edamontology.org/data_2048 1.16 data_3753 "An informative report containing a ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data." Enrichment report Functional enrichment report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3754 GO-term enrichment report GO-term report|Gene ontology term enrichment report|Gene ontology enrichment report|Gene ontology concept over-representation report "An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins." FALSE http://edamontology.org/data_3753 1.16 data_3754 GO-term report "An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins." Gene ontology term enrichment report|Gene ontology enrichment report|Gene ontology concept over-representation report http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3756 Localisation score PTM localisation|False localisation rate|PTM score Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. FALSE http://edamontology.org/data_1772 1.16 data_3756 Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. PTM localisation|False localisation rate|PTM score http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3757 Unimod ID Identifier of a protein modification catalogued in the Unimod database. FALSE http://edamontology.org/data_2618 1.16 data_3757 Identifier of a protein modification catalogued in the Unimod database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3759 ProteomeXchange ID Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. FALSE http://edamontology.org/data_1078 1.16 data_3759 Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3768 Clustered gene expression profiles Groupings of gene expression profiles according to a clustering algorithm. FALSE http://edamontology.org/data_2603 1.16 data_3768 Groupings of gene expression profiles according to a clustering algorithm. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3769 BRENDA ontology concept ID An identifier of a concept from the BRENDA ontology. FALSE http://edamontology.org/data_1087 1.16 data_3769 An identifier of a concept from the BRENDA ontology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#identifiers|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3779 Annotated text "A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations." FALSE http://edamontology.org/data_2526|http://edamontology.org/data_3671 1.16 data_3779 "A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/data_3786 Query script "A structured query, in form of a script, that defines a database search task." FALSE http://edamontology.org/data_0006 1.16 data_3786 "A structured query, in form of a script, that defines a database search task." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/format_1196 SMILES Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. FALSE http://edamontology.org/format_2035|http://edamontology.org/format_2330 beta12orEarlier http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html|http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification format_1196 http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html|http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1197 InChI Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. FALSE http://edamontology.org/format_2035|http://edamontology.org/format_2330 beta12orEarlier format_1197 Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1198 mf "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.|The general MF query format consists of a series of valid atomic symbols, with an optional number or range." FALSE http://edamontology.org/format_2035|http://edamontology.org/format_2330 beta12orEarlier format_1198 "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1199 InChIKey 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.|An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification. FALSE http://edamontology.org/format_2035|http://edamontology.org/format_2330 beta12orEarlier format_1199 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1200 smarts "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." FALSE http://edamontology.org/format_1196 beta12orEarlier format_1200 "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1206 unambiguous pure Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. FALSE http://edamontology.org/format_2094|http://edamontology.org/format_2096 beta12orEarlier format_1206 Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1207 nucleotide "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.|Non-sequence characters may be used for example for gaps." FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_1207 "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1208 protein "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.|Non-sequence characters may be used for gaps and translation stop." FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_1208 "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1209 consensus Alphabet for the consensus of two or more molecular sequences. FALSE http://edamontology.org/format_2097|http://edamontology.org/format_2095 beta12orEarlier format_1209 Alphabet for the consensus of two or more molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1210 pure nucleotide Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. FALSE http://edamontology.org/format_2094|http://edamontology.org/format_1207 beta12orEarlier format_1210 Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1211 unambiguous pure nucleotide Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . FALSE http://edamontology.org/format_1206|http://edamontology.org/format_1207 beta12orEarlier format_1211 Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1212 dna "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." FALSE http://edamontology.org/format_1207 beta12orEarlier format_1212 "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1213 rna "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." FALSE http://edamontology.org/format_1207 beta12orEarlier format_1213 "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1214 unambiguous pure dna Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. FALSE http://edamontology.org/format_1206|http://edamontology.org/format_1212 beta12orEarlier format_1214 Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1215 pure dna Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. FALSE http://edamontology.org/format_1212|http://edamontology.org/format_1210 beta12orEarlier format_1215 Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1216 unambiguous pure rna sequence Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. FALSE http://edamontology.org/format_1213|http://edamontology.org/format_1206 beta12orEarlier format_1216 Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1217 pure rna Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. FALSE http://edamontology.org/format_1213|http://edamontology.org/format_1210 beta12orEarlier format_1217 Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1218 unambiguous pure protein Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. FALSE http://edamontology.org/format_1208|http://edamontology.org/format_1206 beta12orEarlier format_1218 Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1219 pure protein Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. FALSE http://edamontology.org/format_1208|http://edamontology.org/format_2094 beta12orEarlier format_1219 Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1228 UniGene entry format "Format of an entry from UniGene.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1228 http://edamontology.org/format_2331 Format of an entry from UniGene. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1247 COG sequence cluster format Format of an entry from the COG database of clusters of (related) protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1247 http://edamontology.org/format_2331 Format of an entry from the COG database of clusters of (related) protein sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1248 EMBL feature location Feature location Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. FALSE http://edamontology.org/format_2078|http://edamontology.org/format_2330 beta12orEarlier format_1248 Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. Feature location http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1295 quicktandem Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). FALSE http://edamontology.org/format_2155|http://edamontology.org/format_2330 beta12orEarlier format_1295 Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1296 Sanger inverted repeats Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). FALSE http://edamontology.org/format_2155|http://edamontology.org/format_2330 beta12orEarlier format_1296 Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1297 EMBOSS repeat Report format for tandem repeats in a sequence (an EMBOSS report format). FALSE http://edamontology.org/format_2155|http://edamontology.org/format_2330 beta12orEarlier format_1297 Report format for tandem repeats in a sequence (an EMBOSS report format). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1316 est2genome format Format of a report on exon-intron structure generated by EMBOSS est2genome. FALSE http://edamontology.org/format_2031|http://edamontology.org/format_2330 beta12orEarlier format_1316 Format of a report on exon-intron structure generated by EMBOSS est2genome. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1318 restrict format Report format for restriction enzyme recognition sites used by EMBOSS restrict program. FALSE http://edamontology.org/format_2158|http://edamontology.org/format_2330 beta12orEarlier format_1318 Report format for restriction enzyme recognition sites used by EMBOSS restrict program. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1319 restover format Report format for restriction enzyme recognition sites used by EMBOSS restover program. FALSE http://edamontology.org/format_2158|http://edamontology.org/format_2330 beta12orEarlier format_1319 Report format for restriction enzyme recognition sites used by EMBOSS restover program. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1320 REBASE restriction sites Report format for restriction enzyme recognition sites used by REBASE database. FALSE http://edamontology.org/format_2158|http://edamontology.org/format_2330 beta12orEarlier format_1320 Report format for restriction enzyme recognition sites used by REBASE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1332 FASTA search results format "Format of results of a sequence database search using FASTA.|This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)" FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1332 Format of results of a sequence database search using FASTA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1333 BLAST results "Format of results of a sequence database search using some variant of BLAST.|This includes score data, alignment data and summary table." FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1333 Format of results of a sequence database search using some variant of BLAST. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1334 mspcrunch Format of results of a sequence database search using some variant of MSPCrunch. FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1334 Format of results of a sequence database search using some variant of MSPCrunch. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1335 Smith-Waterman format Format of results of a sequence database search using some variant of Smith Waterman. FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1335 Format of results of a sequence database search using some variant of Smith Waterman. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1336 dhf Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.|The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1336 Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1337 lhf Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.|The hits are putative ligand-binding sequences and are found from a search of a sequence database. FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1337 Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1341 InterPro hits format Results format for searches of the InterPro database. FALSE http://edamontology.org/format_2066|http://edamontology.org/format_2330 beta12orEarlier format_1341 Results format for searches of the InterPro database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1342 InterPro protein view report format Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.|The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. FALSE http://edamontology.org/format_1341 beta12orEarlier format_1342 Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1343 InterPro match table format "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.|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." FALSE http://edamontology.org/format_1341 beta12orEarlier format_1343 Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1349 HMMER Dirichlet prior Dirichlet distribution HMMER format. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2074 beta12orEarlier format_1349 Dirichlet distribution HMMER format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1350 MEME Dirichlet prior Dirichlet distribution MEME format. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2074 beta12orEarlier format_1350 Dirichlet distribution MEME format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1351 HMMER emission and transition Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. FALSE http://edamontology.org/format_2075|http://edamontology.org/format_2330 beta12orEarlier format_1351 Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1356 prosite-pattern Format of a regular expression pattern from the Prosite database. FALSE http://edamontology.org/format_2068|http://edamontology.org/format_2330 beta12orEarlier format_1356 Format of a regular expression pattern from the Prosite database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1357 EMBOSS sequence pattern Format of an EMBOSS sequence pattern. FALSE http://edamontology.org/format_2068|http://edamontology.org/format_2330 beta12orEarlier format_1357 Format of an EMBOSS sequence pattern. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1360 meme-motif A motif in the format generated by the MEME program. FALSE http://edamontology.org/format_2068|http://edamontology.org/format_2330 beta12orEarlier format_1360 A motif in the format generated by the MEME program. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1366 prosite-profile Sequence profile (sequence classifier) format used in the PROSITE database. FALSE http://edamontology.org/format_2069|http://edamontology.org/format_2330 beta12orEarlier format_1366 Sequence profile (sequence classifier) format used in the PROSITE database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1367 JASPAR format A profile (sequence classifier) in the format used in the JASPAR database. FALSE http://edamontology.org/format_2069|http://edamontology.org/format_2330 beta12orEarlier format_1367 A profile (sequence classifier) in the format used in the JASPAR database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1369 MEME background Markov model Format of the model of random sequences used by MEME. FALSE http://edamontology.org/format_2072|http://edamontology.org/format_2330 beta12orEarlier format_1369 Format of the model of random sequences used by MEME. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1370 HMMER format Format of a hidden Markov model representation used by the HMMER package. FALSE http://edamontology.org/format_2072|http://edamontology.org/format_2330 beta12orEarlier format_1370 Format of a hidden Markov model representation used by the HMMER package. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1391 HMMER-aln FASTA-style format for multiple sequences aligned by HMMER package to an HMM. FALSE http://edamontology.org/format_2200|http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1391 FASTA-style format for multiple sequences aligned by HMMER package to an HMM. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1392 DIALIGN format Format of multiple sequences aligned by DIALIGN package. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1392 Format of multiple sequences aligned by DIALIGN package. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1393 daf "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.|The format is clustal-like and includes annotation of domain family classification information." FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1393 "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1419 Sequence-MEME profile alignment Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. FALSE http://edamontology.org/format_2014|http://edamontology.org/format_2330 beta12orEarlier format_1419 Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1421 HMMER profile alignment (sequences versus HMMs) Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. FALSE http://edamontology.org/format_2014|http://edamontology.org/format_2330 beta12orEarlier format_1421 Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1422 HMMER profile alignment (HMM versus sequences) Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. FALSE http://edamontology.org/format_2014|http://edamontology.org/format_2330 beta12orEarlier format_1422 Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1423 Phylip distance matrix "Format of PHYLIP phylogenetic distance matrix data.|Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float)." FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2067 beta12orEarlier format_1423 Format of PHYLIP phylogenetic distance matrix data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1424 ClustalW dendrogram Dendrogram (tree file) format generated by ClustalW. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1424 Dendrogram (tree file) format generated by ClustalW. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1425 Phylip tree raw Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1425 Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1430 Phylip continuous quantitative characters PHYLIP file format for continuous quantitative character data. FALSE http://edamontology.org/format_2037|http://edamontology.org/format_2330 beta12orEarlier format_1430 PHYLIP file format for continuous quantitative character data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1431 Phylogenetic property values format Format of phylogenetic property data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1431 http://edamontology.org/format_2036 Format of phylogenetic property data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1432 Phylip character frequencies format PHYLIP file format for phylogenetics character frequency data. FALSE http://edamontology.org/format_2037|http://edamontology.org/format_2330 beta12orEarlier format_1432 PHYLIP file format for phylogenetics character frequency data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1433 Phylip discrete states format Format of PHYLIP discrete states data. FALSE http://edamontology.org/format_2038|http://edamontology.org/format_2330 beta12orEarlier format_1433 Format of PHYLIP discrete states data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1434 Phylip cliques format Format of PHYLIP cliques data. FALSE http://edamontology.org/format_2039|http://edamontology.org/format_2330 beta12orEarlier format_1434 Format of PHYLIP cliques data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1435 Phylip tree format Phylogenetic tree data format used by the PHYLIP program. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1435 Phylogenetic tree data format used by the PHYLIP program. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1436 TreeBASE format The format of an entry from the TreeBASE database of phylogenetic data. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1436 The format of an entry from the TreeBASE database of phylogenetic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1437 TreeFam format The format of an entry from the TreeFam database of phylogenetic data. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1437 The format of an entry from the TreeFam database of phylogenetic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1445 Phylip tree distance format "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." FALSE http://edamontology.org/format_2049|http://edamontology.org/format_2330 beta12orEarlier format_1445 "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1454 dssp "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).|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." FALSE http://edamontology.org/format_2077|http://edamontology.org/format_2330 beta12orEarlier format_1454 Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1455 hssp Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). FALSE http://edamontology.org/format_2077|http://edamontology.org/format_2330 beta12orEarlier format_1455 Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1457 Dot-bracket format Vienna RNA secondary structure format|Vienna RNA format "Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server." FALSE http://edamontology.org/format_2076|http://edamontology.org/format_2330 beta12orEarlier format_1457 "Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server." Vienna RNA secondary structure format|Vienna RNA format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1458 Vienna local RNA secondary structure format "Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server." FALSE http://edamontology.org/format_1457|http://edamontology.org/format_2330 beta12orEarlier format_1458 "Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1475 PDB database entry format PDB entry format Format of an entry (or part of an entry) from the PDB database. FALSE http://edamontology.org/format_2033 beta12orEarlier format_1475 Format of an entry (or part of an entry) from the PDB database. PDB entry format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1476 PDB PDB format Entry format of PDB database in PDB format. FALSE http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1476 Entry format of PDB database in PDB format. PDB format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1477 mmCIF mmcif Entry format of PDB database in mmCIF format. FALSE http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1477 Entry format of PDB database in mmCIF format. mmcif http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1478 PDBML Entry format of PDB database in PDBML (XML) format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_1475 beta12orEarlier format_1478 Entry format of PDB database in PDBML (XML) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1500 Domainatrix 3D-1D scoring matrix format Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1500 Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_2064 beta12orEarlier http://edamontology.org/format_1504 aaindex Amino acid index format used by the AAindex database. FALSE http://edamontology.org/format_2017|http://edamontology.org/format_2330 beta12orEarlier format_1504 Amino acid index format used by the AAindex database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1511 IntEnz enzyme report format "Format of an entry from IntEnz (The Integrated Relational Enzyme Database).|IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1511 http://edamontology.org/format_2331 Format of an entry from IntEnz (The Integrated Relational Enzyme Database). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1512 BRENDA enzyme report format Format of an entry from the BRENDA enzyme database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1512 http://edamontology.org/format_2331 Format of an entry from the BRENDA enzyme database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1513 KEGG REACTION enzyme report format Format of an entry from the KEGG REACTION database of biochemical reactions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1513 http://edamontology.org/format_2331 Format of an entry from the KEGG REACTION database of biochemical reactions. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1514 KEGG ENZYME enzyme report format Format of an entry from the KEGG ENZYME database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1514 http://edamontology.org/format_2331 Format of an entry from the KEGG ENZYME database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1515 REBASE proto enzyme report format Format of an entry from the proto section of the REBASE enzyme database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1515 http://edamontology.org/format_2331 Format of an entry from the proto section of the REBASE enzyme database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1516 REBASE withrefm enzyme report format Format of an entry from the withrefm section of the REBASE enzyme database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1516 http://edamontology.org/format_2331 Format of an entry from the withrefm section of the REBASE enzyme database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1551 Pcons report format Format of output of the Pcons Model Quality Assessment Program (MQAP).|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. FALSE http://edamontology.org/format_2065|http://edamontology.org/format_2330 beta12orEarlier format_1551 Format of output of the Pcons Model Quality Assessment Program (MQAP). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1552 ProQ report format Format of output of the ProQ protein model quality predictor.|ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. FALSE http://edamontology.org/format_2065|http://edamontology.org/format_2330 beta12orEarlier format_1552 Format of output of the ProQ protein model quality predictor. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1563 SMART domain assignment report format "Format of SMART domain assignment data.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1563 http://edamontology.org/format_2331 Format of SMART domain assignment data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1568 BIND entry format Entry format for the BIND database of protein interaction. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1568 http://edamontology.org/format_2331 Entry format for the BIND database of protein interaction. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1569 IntAct entry format Entry format for the IntAct database of protein interaction. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1569 http://edamontology.org/format_2331 Entry format for the IntAct database of protein interaction. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1570 InterPro entry format "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1570 http://edamontology.org/format_2331 Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1571 InterPro entry abstract format Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.|References are included and a functional inference is made where possible. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1571 http://edamontology.org/format_2331 Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1572 Gene3D entry format Entry format for the Gene3D protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1572 http://edamontology.org/format_2331 Entry format for the Gene3D protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1573 PIRSF entry format Entry format for the PIRSF protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1573 http://edamontology.org/format_2331 Entry format for the PIRSF protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1574 PRINTS entry format Entry format for the PRINTS protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1574 http://edamontology.org/format_2331 Entry format for the PRINTS protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1575 Panther Families and HMMs entry format Entry format for the Panther library of protein families and subfamilies. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1575 http://edamontology.org/format_2331 Entry format for the Panther library of protein families and subfamilies. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1576 Pfam entry format Entry format for the Pfam protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1576 http://edamontology.org/format_2331 Entry format for the Pfam protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1577 SMART entry format Entry format for the SMART protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1577 http://edamontology.org/format_2331 Entry format for the SMART protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1578 Superfamily entry format Entry format for the Superfamily protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1578 http://edamontology.org/format_2331 Entry format for the Superfamily protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1579 TIGRFam entry format Entry format for the TIGRFam protein secondary database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1579 http://edamontology.org/format_2331 Entry format for the TIGRFam protein secondary database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1580 ProDom entry format Entry format for the ProDom protein domain classification database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1580 http://edamontology.org/format_2331 Entry format for the ProDom protein domain classification database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1581 FSSP entry format Entry format for the FSSP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1581 http://edamontology.org/format_2331 Entry format for the FSSP database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1582 findkm "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)." FALSE http://edamontology.org/format_2027|http://edamontology.org/format_2330 beta12orEarlier format_1582 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1603 Ensembl gene report format Entry format of Ensembl genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1603 http://edamontology.org/format_2331 Entry format of Ensembl genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1604 DictyBase gene report format Entry format of DictyBase genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1604 http://edamontology.org/format_2331 Entry format of DictyBase genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1605 CGD gene report format Entry format of Candida Genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1605 http://edamontology.org/format_2331 Entry format of Candida Genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1606 DragonDB gene report format Entry format of DragonDB genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1606 http://edamontology.org/format_2331 Entry format of DragonDB genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1607 EcoCyc gene report format Entry format of EcoCyc genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1607 http://edamontology.org/format_2331 Entry format of EcoCyc genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1608 FlyBase gene report format Entry format of FlyBase genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1608 http://edamontology.org/format_2331 Entry format of FlyBase genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1609 Gramene gene report format Entry format of Gramene genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1609 http://edamontology.org/format_2331 Entry format of Gramene genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1610 KEGG GENES gene report format Entry format of KEGG GENES genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1610 http://edamontology.org/format_2331 Entry format of KEGG GENES genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1611 MaizeGDB gene report format Entry format of the Maize genetics and genomics database (MaizeGDB). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1611 http://edamontology.org/format_2331 Entry format of the Maize genetics and genomics database (MaizeGDB). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1612 MGD gene report format Entry format of the Mouse Genome Database (MGD). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1612 http://edamontology.org/format_2331 Entry format of the Mouse Genome Database (MGD). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1613 RGD gene report format Entry format of the Rat Genome Database (RGD). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1613 http://edamontology.org/format_2331 Entry format of the Rat Genome Database (RGD). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1614 SGD gene report format Entry format of the Saccharomyces Genome Database (SGD). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1614 http://edamontology.org/format_2331 Entry format of the Saccharomyces Genome Database (SGD). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1615 GeneDB gene report format Entry format of the Sanger GeneDB genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1615 http://edamontology.org/format_2331 Entry format of the Sanger GeneDB genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1616 TAIR gene report format Entry format of The Arabidopsis Information Resource (TAIR) genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1616 http://edamontology.org/format_2331 Entry format of The Arabidopsis Information Resource (TAIR) genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1617 WormBase gene report format Entry format of the WormBase genomes database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1617 http://edamontology.org/format_2331 Entry format of the WormBase genomes database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1618 ZFIN gene report format Entry format of the Zebrafish Information Network (ZFIN) genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1618 http://edamontology.org/format_2331 Entry format of the Zebrafish Information Network (ZFIN) genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1619 TIGR gene report format Entry format of the TIGR genome database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1619 http://edamontology.org/format_2331 Entry format of the TIGR genome database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1620 dbSNP polymorphism report format Entry format for the dbSNP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1620 http://edamontology.org/format_2331 Entry format for the dbSNP database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1623 OMIM entry format Format of an entry from the OMIM database of genotypes and phenotypes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1623 http://edamontology.org/format_2331 Format of an entry from the OMIM database of genotypes and phenotypes. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1624 HGVbase entry format Format of a record from the HGVbase database of genotypes and phenotypes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1624 http://edamontology.org/format_2331 Format of a record from the HGVbase database of genotypes and phenotypes. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1625 HIVDB entry format Format of a record from the HIVDB database of genotypes and phenotypes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1625 http://edamontology.org/format_2331 Format of a record from the HIVDB database of genotypes and phenotypes. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1626 KEGG DISEASE entry format Format of an entry from the KEGG DISEASE database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1626 http://edamontology.org/format_2331 Format of an entry from the KEGG DISEASE database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1627 Primer3 primer Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. FALSE http://edamontology.org/format_2061|http://edamontology.org/format_2330 beta12orEarlier format_1627 Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1628 ABI A format of raw sequence read data from an Applied Biosystems sequencing machine. FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier format_1628 A format of raw sequence read data from an Applied Biosystems sequencing machine. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1629 mira Format of MIRA sequence trace information file. FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2330 beta12orEarlier format_1629 Format of MIRA sequence trace information file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1630 CAF "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2561 beta12orEarlier http://www.sanger.ac.uk/resources/software/caf/ format_1630 http://www.sanger.ac.uk/resources/software/caf/ "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1631 exp Sequence assembly project file EXP format. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2561 beta12orEarlier format_1631 Sequence assembly project file EXP format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1632 SCF "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier http://staden.sourceforge.net/manual/formats_unix_2.html format_1632 http://staden.sourceforge.net/manual/formats_unix_2.html "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1633 PHD PHD sequence trace format to store serialised chromatogram data (reads). FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2330 beta12orEarlier http://www.bioperl.org/wiki/PHD_sequence_format format_1633 http://www.bioperl.org/wiki/PHD_sequence_format PHD sequence trace format to store serialised chromatogram data (reads). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1637 dat Affymetrix image data file format Format of Affymetrix data file of raw image data. FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 beta12orEarlier format_1637 Format of Affymetrix data file of raw image data. Affymetrix image data file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1638 cel Affymetrix probe raw data format Format of Affymetrix data file of information about (raw) expression levels of the individual probes. FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 beta12orEarlier format_1638 Format of Affymetrix data file of information about (raw) expression levels of the individual probes. Affymetrix probe raw data format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1639 affymetrix "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2172 beta12orEarlier format_1639 "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1640 ArrayExpress entry format Entry format for the ArrayExpress microarrays database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1640 http://edamontology.org/format_2331 Entry format for the ArrayExpress microarrays database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1641 affymetrix-exp Affymetrix experimental conditions data file format Affymetrix data file format for information about experimental conditions and protocols. FALSE http://edamontology.org/format_2056|http://edamontology.org/format_2330 beta12orEarlier format_1641 Affymetrix data file format for information about experimental conditions and protocols. Affymetrix experimental conditions data file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1644 CHP Affymetrix probe normalised data format Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 beta12orEarlier format_1644 Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. Affymetrix probe normalised data format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1645 EMDB entry format Format of an entry from the Electron Microscopy DataBase (EMDB). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1645 http://edamontology.org/format_2331 Format of an entry from the Electron Microscopy DataBase (EMDB). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1647 KEGG PATHWAY entry format The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1647 http://edamontology.org/format_2331 The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1648 MetaCyc entry format The format of an entry from the MetaCyc metabolic pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1648 http://edamontology.org/format_2331 The format of an entry from the MetaCyc metabolic pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1649 HumanCyc entry format The format of a report from the HumanCyc metabolic pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1649 http://edamontology.org/format_2331 The format of a report from the HumanCyc metabolic pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1650 INOH entry format The format of an entry from the INOH signal transduction pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1650 http://edamontology.org/format_2331 The format of an entry from the INOH signal transduction pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1651 PATIKA entry format The format of an entry from the PATIKA biological pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1651 http://edamontology.org/format_2331 The format of an entry from the PATIKA biological pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1652 Reactome entry format The format of an entry from the reactome biological pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1652 http://edamontology.org/format_2331 The format of an entry from the reactome biological pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1653 aMAZE entry format The format of an entry from the aMAZE biological pathways and molecular interactions database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1653 http://edamontology.org/format_2331 The format of an entry from the aMAZE biological pathways and molecular interactions database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1654 CPDB entry format The format of an entry from the CPDB database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1654 http://edamontology.org/format_2331 The format of an entry from the CPDB database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1655 Panther Pathways entry format The format of an entry from the Panther Pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1655 http://edamontology.org/format_2331 The format of an entry from the Panther Pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1665 Taverna workflow format Format of Taverna workflows. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2032 beta12orEarlier format_1665 Format of Taverna workflows. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1666 BioModel mathematical model format "Format of mathematical models from the BioModel database.|Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1666 http://edamontology.org/format_2331 Format of mathematical models from the BioModel database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1697 KEGG LIGAND entry format The format of an entry from the KEGG LIGAND chemical database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1697 http://edamontology.org/format_2331 The format of an entry from the KEGG LIGAND chemical database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1698 KEGG COMPOUND entry format The format of an entry from the KEGG COMPOUND database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1698 http://edamontology.org/format_2331 The format of an entry from the KEGG COMPOUND database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1699 KEGG PLANT entry format The format of an entry from the KEGG PLANT database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1699 http://edamontology.org/format_2331 The format of an entry from the KEGG PLANT database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1700 KEGG GLYCAN entry format The format of an entry from the KEGG GLYCAN database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1700 http://edamontology.org/format_2331 The format of an entry from the KEGG GLYCAN database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1701 PubChem entry format The format of an entry from PubChem. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1701 http://edamontology.org/format_2331 The format of an entry from PubChem. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1702 ChemSpider entry format The format of an entry from a database of chemical structures and property predictions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1702 http://edamontology.org/format_2331 The format of an entry from a database of chemical structures and property predictions. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1703 ChEBI entry format The format of an entry from Chemical Entities of Biological Interest (ChEBI).|ChEBI includes an ontological classification defining relations between entities or classes of entities. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1703 http://edamontology.org/format_2331 The format of an entry from Chemical Entities of Biological Interest (ChEBI). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1704 MSDchem ligand dictionary entry format The format of an entry from the MSDchem ligand dictionary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1704 http://edamontology.org/format_2331 The format of an entry from the MSDchem ligand dictionary. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1705 HET group dictionary entry format The format of an entry from the HET group dictionary (HET groups from PDB files). FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2030 beta12orEarlier format_1705 The format of an entry from the HET group dictionary (HET groups from PDB files). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1706 KEGG DRUG entry format The format of an entry from the KEGG DRUG database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1706 http://edamontology.org/format_2331 The format of an entry from the KEGG DRUG database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1734 PubMed citation Format of bibliographic reference as used by the PubMed database. FALSE http://edamontology.org/format_2848|http://edamontology.org/format_2330 beta12orEarlier format_1734 Format of bibliographic reference as used by the PubMed database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1735 Medline Display Format Format for abstracts of scientific articles from the Medline database.|Bibliographic reference information including citation information is included FALSE http://edamontology.org/format_2848|http://edamontology.org/format_2330 beta12orEarlier format_1735 Format for abstracts of scientific articles from the Medline database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1736 CiteXplore-core "CiteXplore 'core' citation format including title, journal, authors and abstract." FALSE http://edamontology.org/format_2848|http://edamontology.org/format_2330 beta12orEarlier format_1736 "CiteXplore 'core' citation format including title, journal, authors and abstract." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1737 CiteXplore-all CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. FALSE http://edamontology.org/format_2848|http://edamontology.org/format_2330 beta12orEarlier format_1737 CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1739 pmc Article format of the PubMed Central database. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2020 beta12orEarlier format_1739 Article format of the PubMed Central database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1740 iHOP format The format of iHOP (Information Hyperlinked over Proteins) text-mining result. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2331|http://edamontology.org/format_2021 beta12orEarlier format_1740 The format of iHOP (Information Hyperlinked over Proteins) text-mining result. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1741 OSCAR format "OSCAR format of annotated chemical text.|OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3780|http://edamontology.org/format_2330 http://doi.org/10.1186/1758-2946-3-41 beta12orEarlier format_1741 OSCAR format of annotated chemical text. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1747 PDB atom record format Format of an ATOM record (describing data for an individual atom) from a PDB file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1747 http://edamontology.org/format_1476 Format of an ATOM record (describing data for an individual atom) from a PDB file. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/format_1760 CATH chain report format "Format of CATH domain classification information for a polypeptide chain.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1760 http://edamontology.org/format_2331 Format of CATH domain classification information for a polypeptide chain. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1761 CATH PDB report format "Format of CATH domain classification information for a protein PDB file.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1761 http://edamontology.org/format_2331 Format of CATH domain classification information for a protein PDB file. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1782 NCBI gene report format Entry (gene) format of the NCBI database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1782 http://edamontology.org/format_2331 Entry (gene) format of the NCBI database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1808 GeneIlluminator gene report format "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.|This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1808 http://edamontology.org/format_2331 Moby:GI_Gene "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1809 BacMap gene card format Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1809 http://edamontology.org/format_2331 Moby:BacMapGeneCard 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://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1810 ColiCard report format "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1810 http://edamontology.org/format_2331 "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1861 PlasMapper TextMap Map of a plasmid (circular DNA) in PlasMapper TextMap format. FALSE http://edamontology.org/format_2060|http://edamontology.org/format_2330 beta12orEarlier format_1861 Map of a plasmid (circular DNA) in PlasMapper TextMap format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1910 newick nh Phylogenetic tree Newick (text) format. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1910 Phylogenetic tree Newick (text) format. nh http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1911 TreeCon format Phylogenetic tree TreeCon (text) format. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1911 Phylogenetic tree TreeCon (text) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1912 Nexus format Phylogenetic tree Nexus (text) format. FALSE http://edamontology.org/format_2556|http://edamontology.org/format_2330 beta12orEarlier format_1912 Phylogenetic tree Nexus (text) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1915 Format Data model|Exchange format|Data format|File format "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.|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." FALSE http://www.w3.org/2002/07/owl#Thing beta12orEarlier format_1915 Data model "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere." Exchange format|Data format File format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_1918 Atomic data format Data format for an individual atom. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1918 http://edamontology.org/format_1475 Data format for an individual atom. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/format_1919 Sequence record format Data format for a molecular sequence record. FALSE http://edamontology.org/format_2350 beta12orEarlier format_1919 Data format for a molecular sequence record. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_1920 Sequence feature annotation format Data format for molecular sequence feature information. FALSE http://edamontology.org/format_2350 beta12orEarlier format_1920 Data format for molecular sequence feature information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_1921 Alignment format Data format for molecular sequence alignment information. FALSE http://edamontology.org/format_2350 beta12orEarlier format_1921 Data format for molecular sequence alignment information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_1923 acedb ACEDB sequence format. FALSE http://edamontology.org/format_2551 beta12orEarlier format_1923 ACEDB sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1924 clustal sequence format Clustalw output format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1924 http://edamontology.org/format_1982 Clustalw output format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1925 codata Codata entry format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1925 Codata entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1926 dbid Fasta format variant with database name before ID. FALSE http://edamontology.org/format_2200 beta12orEarlier format_1926 Fasta format variant with database name before ID. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1927 EMBL format EMBL|EMBL sequence format EMBL entry format. FALSE http://edamontology.org/format_2181|http://edamontology.org/format_2206 beta12orEarlier format_1927 EMBL entry format. EMBL|EMBL sequence format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1928 Staden experiment format Staden experiment file format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1928 Staden experiment file format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1929 FASTA FASTA sequence format|FASTA format FASTA format including NCBI-style IDs. FALSE http://edamontology.org/format_2200|http://edamontology.org/format_2554 beta12orEarlier format_1929 FASTA format including NCBI-style IDs. FASTA sequence format|FASTA format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1930 FASTQ FASTAQ|fq FASTQ short read format ignoring quality scores. FALSE http://edamontology.org/format_2182 beta12orEarlier format_1930 FASTQ short read format ignoring quality scores. FASTAQ|fq http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1931 FASTQ-illumina FASTQ Illumina 1.3 short read format. FALSE http://edamontology.org/format_2182 beta12orEarlier format_1931 FASTQ Illumina 1.3 short read format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1932 FASTQ-sanger FASTQ short read format with phred quality. FALSE http://edamontology.org/format_2182 beta12orEarlier format_1932 FASTQ short read format with phred quality. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1933 FASTQ-solexa FASTQ Solexa/Illumina 1.0 short read format. FALSE http://edamontology.org/format_2182 beta12orEarlier format_1933 FASTQ Solexa/Illumina 1.0 short read format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1934 fitch program Fitch program format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1934 Fitch program format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1935 GCG GCG SSF GCG sequence file format.| GCG SSF (single sequence file) file format. FALSE http://edamontology.org/format_3486|http://edamontology.org/format_2330 beta12orEarlier format_1935 GCG sequence file format. GCG SSF http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1936 GenBank format GenBank Genbank entry format. FALSE http://edamontology.org/format_2205|http://edamontology.org/format_2206 beta12orEarlier format_1936 Genbank entry format. GenBank http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1937 genpept Genpept protein entry format.|Currently identical to refseqp format FALSE http://edamontology.org/format_2205 beta12orEarlier format_1937 Genpept protein entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1938 GFF2-seq GFF feature file format with sequence in the header. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1974 beta12orEarlier format_1938 GFF feature file format with sequence in the header. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1939 GFF3-seq GFF3 feature file format with sequence. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1975 beta12orEarlier format_1939 GFF3 feature file format with sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1940 giFASTA format FASTA sequence format including NCBI-style GIs. FALSE http://edamontology.org/format_2200 beta12orEarlier format_1940 FASTA sequence format including NCBI-style GIs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1941 hennig86 Hennig86 output sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1941 Hennig86 output sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1942 ig Intelligenetics sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1942 Intelligenetics sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1943 igstrict Intelligenetics sequence format (strict version). FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1943 Intelligenetics sequence format (strict version). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1944 jackknifer Jackknifer interleaved and non-interleaved sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1944 Jackknifer interleaved and non-interleaved sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1945 mase format Mase program sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1945 Mase program sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1946 mega-seq Mega interleaved and non-interleaved sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1946 Mega interleaved and non-interleaved sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1947 GCG MSF MSF GCG MSF (multiple sequence file) file format. FALSE http://edamontology.org/format_3486 beta12orEarlier format_1947 GCG MSF (multiple sequence file) file format. MSF http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1948 nbrf/pir nbrf|pir NBRF/PIR entry sequence format. FALSE http://edamontology.org/format_2330 beta12orEarlier format_1948 NBRF/PIR entry sequence format. nbrf|pir http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1949 nexus-seq Nexus/paup interleaved sequence format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1949 Nexus/paup interleaved sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1950 pdbatom PDB sequence format (ATOM lines).|pdb format in EMBOSS. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1950 PDB sequence format (ATOM lines). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1951 pdbatomnuc PDB nucleotide sequence format (ATOM lines).|pdbnuc format in EMBOSS. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1951 PDB nucleotide sequence format (ATOM lines). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1952 pdbseqresnuc PDB nucleotide sequence format (SEQRES lines).|pdbnucseq format in EMBOSS. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1952 PDB nucleotide sequence format (SEQRES lines). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1953 pdbseqres PDB sequence format (SEQRES lines).|pdbseq format in EMBOSS. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_1475|http://edamontology.org/format_2330 beta12orEarlier format_1953 PDB sequence format (SEQRES lines). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1954 Pearson format Plain old FASTA sequence format (unspecified format for IDs). FALSE http://edamontology.org/format_2200 beta12orEarlier format_1954 Plain old FASTA sequence format (unspecified format for IDs). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1955 phylip sequence format Phylip interleaved sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1955 http://edamontology.org/format_1997 Phylip interleaved sequence format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1956 phylipnon sequence format Phylip non-interleaved sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1956 http://edamontology.org/format_1998 Phylip non-interleaved sequence format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1957 raw Raw sequence format with no non-sequence characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_1957 Raw sequence format with no non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1958 refseqp Refseq protein entry sequence format.|Currently identical to genpept format FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1958 Refseq protein entry sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1959 selex sequence format Selex sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1959 http://edamontology.org/format_2000 Selex sequence format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1960 Staden format Staden suite sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden|http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html format_1960 http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden|http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html Staden suite sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1961 Stockholm format Stockholm multiple sequence alignment format (used by Pfam and Rfam). FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier http://en.wikipedia.org/wiki/Stockholm_format format_1961 http://en.wikipedia.org/wiki/Stockholm_format Stockholm multiple sequence alignment format (used by Pfam and Rfam). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1962 strider format DNA strider output sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1962 DNA strider output sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1963 UniProtKB format SwissProt format|UniProt format UniProtKB entry sequence format. FALSE http://edamontology.org/format_2187 beta12orEarlier format_1963 UniProtKB entry sequence format. SwissProt format|UniProt format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1964 plain text format (unformatted) Plain text sequence format (essentially unformatted). FALSE http://edamontology.org/format_2330 beta12orEarlier format_1964 Plain text sequence format (essentially unformatted). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1965 treecon sequence format Treecon output sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1965 http://edamontology.org/format_2005 Treecon output sequence format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1966 ASN.1 sequence format NCBI ASN.1-based sequence format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1966 NCBI ASN.1-based sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1967 DAS format das sequence format DAS sequence (XML) format (any type). FALSE http://edamontology.org/format_2552|http://edamontology.org/format_2332 beta12orEarlier format_1967 DAS sequence (XML) format (any type). das sequence format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1968 dasdna DAS sequence (XML) format (nucleotide-only).|The use of this format is deprecated. FALSE http://edamontology.org/format_2552|http://edamontology.org/format_2332 beta12orEarlier format_1968 DAS sequence (XML) format (nucleotide-only). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1969 debug-seq EMBOSS debugging trace sequence format of full internal data content. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1969 EMBOSS debugging trace sequence format of full internal data content. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1970 jackknifernon Jackknifer output sequence non-interleaved format. FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1970 Jackknifer output sequence non-interleaved format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1971 meganon sequence format Mega non-interleaved output sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1971 http://edamontology.org/format_1992 Mega non-interleaved output sequence format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1972 NCBI format NCBI FASTA sequence format with NCBI-style IDs.|There are several variants of this. FALSE http://edamontology.org/format_2200 beta12orEarlier format_1972 NCBI FASTA sequence format with NCBI-style IDs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1973 nexusnon Nexus/paup non-interleaved sequence format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_1973 Nexus/paup non-interleaved sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1974 GFF2 General Feature Format (GFF) of sequence features. FALSE http://edamontology.org/format_2305 beta12orEarlier http://www.sanger.ac.uk/resources/software/gff/spec.html format_1974 http://www.sanger.ac.uk/resources/software/gff/spec.html General Feature Format (GFF) of sequence features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1975 GFF3 Generic Feature Format version 3 (GFF3) of sequence features. FALSE http://edamontology.org/format_2305 beta12orEarlier https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md format_1975 http://www.sequenceontology.org/ https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md Generic Feature Format version 3 (GFF3) of sequence features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1976 pir PIR feature format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1976 PIR feature format. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_1948 1.7 http://edamontology.org/format_1977 swiss feature Swiss-Prot feature format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1977 http://edamontology.org/format_1963 Swiss-Prot feature format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1978 DASGFF DASGFF feature|das feature DAS GFF (XML) feature format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2553 beta12orEarlier format_1978 DAS GFF (XML) feature format. DASGFF feature|das feature http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1979 debug-feat EMBOSS debugging trace feature format of full internal data content. FALSE http://edamontology.org/format_1920|http://edamontology.org/format_2330 beta12orEarlier format_1979 EMBOSS debugging trace feature format of full internal data content. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1980 EMBL feature EMBL feature format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1980 http://edamontology.org/format_1927 EMBL feature format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1981 GenBank feature Genbank feature format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1981 http://edamontology.org/format_1936 Genbank feature format. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1982 ClustalW format clustal ClustalW format for (aligned) sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1982 ClustalW format for (aligned) sequences. clustal http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1983 debug EMBOSS alignment format for debugging trace of full internal data content. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1983 EMBOSS alignment format for debugging trace of full internal data content. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1984 FASTA-aln Fasta format for (aligned) sequences. FALSE http://edamontology.org/format_2200|http://edamontology.org/format_2554 beta12orEarlier format_1984 Fasta format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1985 markx0 Pearson MARKX0 alignment format. FALSE http://edamontology.org/format_2922 beta12orEarlier format_1985 Pearson MARKX0 alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1986 markx1 Pearson MARKX1 alignment format. FALSE http://edamontology.org/format_2922 beta12orEarlier format_1986 Pearson MARKX1 alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1987 markx10 Pearson MARKX10 alignment format. FALSE http://edamontology.org/format_2922 beta12orEarlier format_1987 Pearson MARKX10 alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1988 markx2 Pearson MARKX2 alignment format. FALSE http://edamontology.org/format_2922 beta12orEarlier format_1988 Pearson MARKX2 alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1989 markx3 Pearson MARKX3 alignment format. FALSE http://edamontology.org/format_2922 beta12orEarlier format_1989 Pearson MARKX3 alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1990 match Alignment format for start and end of matches between sequence pairs. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1990 Alignment format for start and end of matches between sequence pairs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1991 mega Mega format for (typically aligned) sequences. FALSE http://edamontology.org/format_2923 beta12orEarlier format_1991 Mega format for (typically aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1992 meganon Mega non-interleaved format for (typically aligned) sequences. FALSE http://edamontology.org/format_2923 beta12orEarlier format_1992 Mega non-interleaved format for (typically aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1993 msf alignment format MSF format for (aligned) sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1993 http://edamontology.org/format_1947 MSF format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1994 nexus alignment format Nexus/paup format for (aligned) sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1994 http://edamontology.org/format_1949 Nexus/paup format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1995 nexusnon alignment format Nexus/paup non-interleaved format for (aligned) sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_1995 http://edamontology.org/format_1973 Nexus/paup non-interleaved format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_1996 pair EMBOSS simple sequence pair alignment format. FALSE http://edamontology.org/format_2554 beta12orEarlier format_1996 EMBOSS simple sequence pair alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1997 PHYLIP format ph|PHYLIP interleaved format|phy Phylip format for (aligned) sequences. FALSE http://edamontology.org/format_2924 beta12orEarlier http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format format_1997 Phylip format for (aligned) sequences. ph|PHYLIP interleaved format|phy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1998 phylipnon PHYLIP sequential format Phylip non-interleaved format for (aligned) sequences. FALSE http://edamontology.org/format_2924 beta12orEarlier http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format format_1998 Phylip non-interleaved format for (aligned) sequences. PHYLIP sequential format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_1999 scores format Alignment format for score values for pairs of sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_1999 Alignment format for score values for pairs of sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2000 selex SELEX format for (aligned) sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_2000 SELEX format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2001 EMBOSS simple format EMBOSS simple multiple alignment format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_2001 EMBOSS simple multiple alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2002 srs format Simple multiple sequence (alignment) format for SRS. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_2002 Simple multiple sequence (alignment) format for SRS. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2003 srspair Simple sequence pair (alignment) format for SRS. FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2330 beta12orEarlier format_2003 Simple sequence pair (alignment) format for SRS. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2004 T-Coffee format T-Coffee program alignment format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_2004 T-Coffee program alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2005 TreeCon-seq Treecon format for (aligned) sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_2005 Treecon format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2006 Phylogenetic tree format Data format for a phylogenetic tree. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2006 Data format for a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2013 Biological pathway or network format Data format for a biological pathway or network. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2013 Data format for a biological pathway or network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2014 Sequence-profile alignment format Data format for a sequence-profile alignment. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2014 Data format for a sequence-profile alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2015 Sequence-profile alignment (HMM) format Data format for a sequence-HMM profile alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2015 http://edamontology.org/format_2014 Data format for a sequence-HMM profile alignment. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2017 Amino acid index format Data format for an amino acid index. FALSE http://edamontology.org/format_3033 beta12orEarlier format_2017 Data format for an amino acid index. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2020 Article format Literature format Data format for a full-text scientific article. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2020 Data format for a full-text scientific article. Literature format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2021 Text mining report format Data format of a report from text mining. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2021 Data format of a report from text mining. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2027 Enzyme kinetics report format Data format for reports on enzyme kinetics. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2027 Data format for reports on enzyme kinetics. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2030 Small molecule report format Chemical compound annotation format Format of a report on a chemical compound. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2030 Format of a report on a chemical compound. Chemical compound annotation format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2031 Gene annotation format Gene features format "Format of a report on a particular locus, gene, gene system or groups of genes." FALSE http://edamontology.org/format_2350 beta12orEarlier format_2031 "Format of a report on a particular locus, gene, gene system or groups of genes." Gene features format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2032 Workflow format Format of a workflow. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2032 Format of a workflow. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2033 Tertiary structure format Data format for a molecular tertiary structure. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2033 Data format for a molecular tertiary structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2034 Biological model format Data format for a biological model. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2034 http://edamontology.org/format_2013 Data format for a biological model. http://purl.obolibrary.org/obo/edam#obsolete 1.2 http://edamontology.org/format_2035 Chemical formula format Text format of a chemical formula. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2035 Text format of a chemical formula. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2036 Phylogenetic character data format Format of raw (unplotted) phylogenetic data. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2036 Format of raw (unplotted) phylogenetic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2037 Phylogenetic continuous quantitative character format Format of phylogenetic continuous quantitative character data. FALSE http://edamontology.org/format_2036 beta12orEarlier format_2037 Format of phylogenetic continuous quantitative character data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2038 Phylogenetic discrete states format Format of phylogenetic discrete states data. FALSE http://edamontology.org/format_2036 beta12orEarlier format_2038 Format of phylogenetic discrete states data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2039 Phylogenetic tree report (cliques) format Format of phylogenetic cliques data. FALSE http://edamontology.org/format_2036 beta12orEarlier format_2039 Format of phylogenetic cliques data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2040 Phylogenetic tree report (invariants) format Format of phylogenetic invariants data. FALSE http://edamontology.org/format_2036 beta12orEarlier format_2040 Format of phylogenetic invariants data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2045 Electron microscopy model format Annotation format for electron microscopy models. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2045 http://edamontology.org/format_2350 Annotation format for electron microscopy models. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2049 Phylogenetic tree report (tree distances) format Format for phylogenetic tree distance data. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2049 Format for phylogenetic tree distance data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2051 Polymorphism report format Format for sequence polymorphism data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2051 http://edamontology.org/format_2921 Format for sequence polymorphism data. http://purl.obolibrary.org/obo/edam#obsolete 1.0 http://edamontology.org/format_2052 Protein family report format Format for reports on a protein family. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2052 Format for reports on a protein family. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2054 Protein interaction format Molecular interaction format Format for molecular interaction data. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2054 Molecular interaction format Format for molecular interaction data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2055 Sequence assembly format Format for sequence assembly data. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2055 Format for sequence assembly data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2056 Microarray experiment data format Format for information about a microarray experimental per se (not the data generated from that experiment). FALSE http://edamontology.org/format_3167 beta12orEarlier format_2056 Format for information about a microarray experimental per se (not the data generated from that experiment). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2057 Sequence trace format Format for sequence trace data (i.e. including base call information). FALSE http://edamontology.org/format_1919 beta12orEarlier format_2057 Format for sequence trace data (i.e. including base call information). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2058 Gene expression report format Gene expression data format "Format of a file of gene expression data, e.g. a gene expression matrix or profile." FALSE http://edamontology.org/format_2350 beta12orEarlier format_2058 "Format of a file of gene expression data, e.g. a gene expression matrix or profile." Gene expression data format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2059 Genotype and phenotype annotation format Format of a report on genotype / phenotype information. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2059 http://edamontology.org/format_2350 Format of a report on genotype / phenotype information. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2060 Map format Format of a map of (typically one) molecular sequence annotated with features. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2060 Format of a map of (typically one) molecular sequence annotated with features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2061 Nucleic acid features (primers) format Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2061 Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2062 Protein report format Format of a report of general information about a specific protein. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2062 Format of a report of general information about a specific protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2063 Protein report (enzyme) format Format of a report of general information about a specific enzyme. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2063 http://edamontology.org/format_2350 Format of a report of general information about a specific enzyme. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2064 3D-1D scoring matrix format Format of a matrix of 3D-1D scores (amino acid environment probabilities). FALSE http://edamontology.org/format_3033 beta12orEarlier format_2064 Format of a matrix of 3D-1D scores (amino acid environment probabilities). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2065 Protein structure report (quality evaluation) format Format of a report on the quality of a protein three-dimensional model. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2065 Format of a report on the quality of a protein three-dimensional model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2066 Database hits (sequence) format Format of a report on sequence hits and associated data from searching a sequence database. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2066 Format of a report on sequence hits and associated data from searching a sequence database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2067 Sequence distance matrix format Format of a matrix of genetic distances between molecular sequences. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2067 Format of a matrix of genetic distances between molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2068 Sequence motif format Format of a sequence motif. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2068 Format of a sequence motif. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2069 Sequence profile format Format of a sequence profile. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2069 Format of a sequence profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2072 Hidden Markov model format Format of a hidden Markov model. FALSE http://edamontology.org/format_2069 beta12orEarlier format_2072 Format of a hidden Markov model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2074 Dirichlet distribution format Data format of a dirichlet distribution. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2074 Data format of a dirichlet distribution. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2075 HMM emission and transition counts format Data format for the emission and transition counts of a hidden Markov model. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2075 Data format for the emission and transition counts of a hidden Markov model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2076 RNA secondary structure format Format for secondary structure (predicted or real) of an RNA molecule. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2076 Format for secondary structure (predicted or real) of an RNA molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2077 Protein secondary structure format Format for secondary structure (predicted or real) of a protein molecule. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2077 Format for secondary structure (predicted or real) of a protein molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2078 Sequence range format Format used to specify range(s) of sequence positions. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2078 Format used to specify range(s) of sequence positions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2094 pure Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_2094 Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2095 unpure Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_2095 Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2096 unambiguous sequence Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_2096 Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2097 ambiguous Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_2097 Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2155 Sequence features (repeats) format Format used for map of repeats in molecular (typically nucleotide) sequences. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2155 Format used for map of repeats in molecular (typically nucleotide) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2158 Nucleic acid features (restriction sites) format Format used for report on restriction enzyme recognition sites in nucleotide sequences. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2158 Format used for report on restriction enzyme recognition sites in nucleotide sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2159 Gene features (coding region) format Format used for report on coding regions in nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2159 Format used for report on coding regions in nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_2031 1.10 http://edamontology.org/format_2170 Sequence cluster format Format used for clusters of molecular sequences. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2170 Format used for clusters of molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2171 Sequence cluster format (protein) Format used for clusters of protein sequences. FALSE http://edamontology.org/format_2170 beta12orEarlier format_2171 Format used for clusters of protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2172 Sequence cluster format (nucleic acid) Format used for clusters of nucleotide sequences. FALSE http://edamontology.org/format_2170 beta12orEarlier format_2172 Format used for clusters of nucleotide sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2175 Gene cluster format Format used for clusters of genes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2175 http://edamontology.org/format_2172 Format used for clusters of genes. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/format_2181 EMBL-like (text) A text format resembling EMBL entry format.|This concept may be used for the many non-standard EMBL-like text formats. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2543 beta12orEarlier format_2181 A text format resembling EMBL entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2182 FASTQ-like format (text) A text format resembling FASTQ short read format.|This concept may be used for non-standard FASTQ short read-like formats. FALSE http://edamontology.org/format_2545|http://edamontology.org/format_2330 beta12orEarlier format_2182 A text format resembling FASTQ short read format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2183 EMBLXML XML format for EMBL entries. FALSE http://edamontology.org/format_2204 beta12orEarlier format_2183 XML format for EMBL entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2184 cdsxml XML format for EMBL entries. FALSE http://edamontology.org/format_2204 beta12orEarlier format_2184 XML format for EMBL entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2185 insdxml XML format for EMBL entries. FALSE http://edamontology.org/format_2204 beta12orEarlier format_2185 XML format for EMBL entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2186 geneseq Geneseq sequence format. FALSE http://edamontology.org/format_2181 beta12orEarlier format_2186 Geneseq sequence format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2187 UniProt-like (text) A text sequence format resembling uniprotkb entry format. FALSE http://edamontology.org/format_2547|http://edamontology.org/format_2330 beta12orEarlier format_2187 A text sequence format resembling uniprotkb entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2188 UniProt format UniProt entry sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2188 UniProt entry sequence format. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_1963 1.8 http://edamontology.org/format_2189 ipi ipi sequence format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2189 http://edamontology.org/format_1963 ipi sequence format. http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/format_2194 medline Abstract format used by MedLine database. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2020 beta12orEarlier format_2194 Abstract format used by MedLine database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2195 Ontology format Format used for ontologies. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2195 Format used for ontologies. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2196 OBO format A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. FALSE http://edamontology.org/format_2195 beta12orEarlier format_2196 A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2197 OWL format A serialisation format conforming to the Web Ontology Language (OWL) model. FALSE http://edamontology.org/format_2195|http://edamontology.org/format_2376 beta12orEarlier format_2197 A serialisation format conforming to the Web Ontology Language (OWL) model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2200 FASTA-like (text) A text format resembling FASTA format.|This concept may also be used for the many non-standard FASTA-like formats. FALSE http://edamontology.org/format_2546|http://edamontology.org/format_2330 beta12orEarlier format_2200 A text format resembling FASTA format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2202 Sequence record full format "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2202 "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_1919 1.8 http://edamontology.org/format_2203 Sequence record lite format "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2203 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_1919 1.8 http://edamontology.org/format_2204 EMBL format (XML) An XML format for EMBL entries.|This is a placeholder for other more specific concepts. It should not normally be used for annotation. FALSE http://edamontology.org/format_2558 beta12orEarlier format_2204 An XML format for EMBL entries. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2205 GenBank-like format (text) A text format resembling GenBank entry (plain text) format.|This concept may be used for the non-standard GenBank-like text formats. FALSE http://edamontology.org/format_2559|http://edamontology.org/format_2330 beta12orEarlier format_2205 A text format resembling GenBank entry (plain text) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2206 Sequence feature table format (text) Text format for a sequence feature table. FALSE http://edamontology.org/format_2548 beta12orEarlier format_2206 Text format for a sequence feature table. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2210 Strain data format Format of a report on organism strain data / cell line. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2210 Format of a report on organism strain data / cell line. http://purl.obolibrary.org/obo/edam#obsolete 1.0 http://edamontology.org/format_2211 CIP strain data format Format for a report of strain data as used for CIP database entries. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2211 http://edamontology.org/format_2331 Format for a report of strain data as used for CIP database entries. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2243 phylip property values PHYLIP file format for phylogenetic property data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2243 http://edamontology.org/format_2036 PHYLIP file format for phylogenetic property data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2303 STRING entry format (HTML) Entry format (HTML) for the STRING database of protein interaction. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2303 http://edamontology.org/format_2331 Entry format (HTML) for the STRING database of protein interaction. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2304 STRING entry format (XML) Entry format (XML) for the STRING database of protein interaction. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2054 beta12orEarlier format_2304 Entry format (XML) for the STRING database of protein interaction. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2305 GFF GFF feature format (of indeterminate version). FALSE http://edamontology.org/format_2206|http://edamontology.org/format_2330 beta12orEarlier format_2305 GFF feature format (of indeterminate version). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2306 GTF "Gene Transfer Format (GTF), a restricted version of GFF." FALSE http://edamontology.org/format_2305 beta12orEarlier http://mblab.wustl.edu/GTF22.html format_2306 http://mblab.wustl.edu/GTF22.html|http://genome.ucsc.edu/FAQ/FAQformat#format4 "Gene Transfer Format (GTF), a restricted version of GFF." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2310 FASTA-HTML FASTA format wrapped in HTML elements. FALSE http://edamontology.org/format_2331|http://edamontology.org/format_2546 beta12orEarlier format_2310 FASTA format wrapped in HTML elements. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2311 EMBL-HTML EMBL entry format wrapped in HTML elements. FALSE http://edamontology.org/format_2331|http://edamontology.org/format_2543 beta12orEarlier format_2311 EMBL entry format wrapped in HTML elements. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2322 BioCyc enzyme report format Format of an entry from the BioCyc enzyme database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2322 http://edamontology.org/format_2331 Format of an entry from the BioCyc enzyme database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2323 ENZYME enzyme report format Format of an entry from the Enzyme nomenclature database (ENZYME). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2323 http://edamontology.org/format_2331 Format of an entry from the Enzyme nomenclature database (ENZYME). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2328 PseudoCAP gene report format Format of a report on a gene from the PseudoCAP database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2328 http://edamontology.org/format_2331 Format of a report on a gene from the PseudoCAP database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2329 GeneCards gene report format Format of a report on a gene from the GeneCards database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2329 http://edamontology.org/format_2331 Format of a report on a gene from the GeneCards database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2330 Textual format Plain text format|txt "Textual format.|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)." FALSE http://edamontology.org/format_1915 beta12orEarlier format_2330 Textual format. Plain text format|txt http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2331 HTML Hypertext Markup Language HTML format. FALSE http://edamontology.org/format_1915 beta12orEarlier format_2331 HTML format. Hypertext Markup Language http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2332 XML eXtensible Markup Language "eXtensible Markup Language (XML) format.|Data in XML format can be serialised into text, or binary format." FALSE http://edamontology.org/format_1915 beta12orEarlier xml format_2332 http://www.iana.org/assignments/media-types/application/xml|http://filext.com/file-extension/XML eXtensible Markup Language (XML) format. eXtensible Markup Language http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/application/xml http://edamontology.org/format_2333 Binary format "Binary format.|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." FALSE http://edamontology.org/format_1915 beta12orEarlier format_2333 Binary format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2334 URI format Typical textual representation of a URI. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2334 http://edamontology.org/data_1047 Typical textual representation of a URI. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/format_2341 NCI-Nature pathway entry format The format of an entry from the NCI-Nature pathways database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2341 http://edamontology.org/format_2331 The format of an entry from the NCI-Nature pathways database. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2350 Format (by type of data) Format (typed) "A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented.|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." FALSE http://edamontology.org/format_1915 beta12orEarlier format_2350 A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented. Format (typed) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2352 BioXSD (XML) BioXSD|BioJSON|BioYAML|BioXSD|GTrack|BioXSD format|BioXSD|BioXSD/GTrack|BioXSD data model|BioXSD XML format|BioXSD+XML|BioXSD in XML|BioXSD XML|BioXSD in XML format "BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming." FALSE http://edamontology.org/format_1919|http://edamontology.org/format_2332|http://edamontology.org/format_2555|http://edamontology.org/format_2571|http://edamontology.org/format_1920 http://doi.org/10.7490/f1000research.1113048.1|http://doi.org/10.1093/bioinformatics/btq391|http://doi.org/10.1186/1471-2105-12-494 beta12orEarlier http://bioxsd.org|http://bioxsd.org/BioXSD-1.1.xsd http://bioxsd.org/exampleFeatureRecords.html|http://bioxsd.org/accession.xml|http://bioxsd.org/sequenceRecord.xml|http://bioxsd.org/sequenceRecord.xml+json+yaml.xml format_2352 "Any ontology allowed, none mandatory. Preferrably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology." "'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'." BioXSD|BioJSON|BioYAML|BioXSD|GTrack|BioXSD format|BioXSD|BioXSD/GTrack|BioXSD data model http://bioxsd.org|http://bioxsd.org/BioXSD-1.1.xsd "BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming." BioXSD XML format|BioXSD+XML|BioXSD in XML|BioXSD XML|BioXSD in XML format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2376 RDF format Resource Description Framework format|Resource Description Framework|RDF A serialisation format conforming to the Resource Description Framework (RDF) model. FALSE http://edamontology.org/format_3748|http://edamontology.org/format_2195|http://edamontology.org/format_1915 beta12orEarlier format_2376 https://en.wikipedia.org/wiki/Resource_Description_Framework A serialisation format conforming to the Resource Description Framework (RDF) model. Resource Description Framework format Resource Description Framework|RDF http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2532 GenBank-HTML Genbank entry format wrapped in HTML elements. FALSE http://edamontology.org/format_2331|http://edamontology.org/format_2559 beta12orEarlier format_2532 Genbank entry format wrapped in HTML elements. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2542 Protein features (domains) format Format of a report on protein features (domain composition). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2542 http://edamontology.org/format_2350 Format of a report on protein features (domain composition). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2543 EMBL-like format A format resembling EMBL entry (plain text) format.|This concept may be used for the many non-standard EMBL-like formats. FALSE http://edamontology.org/format_1919 beta12orEarlier format_2543 A format resembling EMBL entry (plain text) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2545 FASTQ-like format A format resembling FASTQ short read format.|This concept may be used for non-standard FASTQ short read-like formats. FALSE http://edamontology.org/format_2057 beta12orEarlier format_2545 A format resembling FASTQ short read format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2546 FASTA-like A format resembling FASTA format.|This concept may be used for the many non-standard FASTA-like formats. FALSE http://edamontology.org/format_1919 beta12orEarlier format_2546 A format resembling FASTA format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2547 uniprotkb-like format A sequence format resembling uniprotkb entry format. FALSE http://edamontology.org/format_1919|http://edamontology.org/format_2548 beta12orEarlier format_2547 A sequence format resembling uniprotkb entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2548 Sequence feature table format Format for a sequence feature table. FALSE http://edamontology.org/format_1920 beta12orEarlier format_2548 Format for a sequence feature table. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2549 OBO OBO ontology text format. FALSE http://edamontology.org/format_2196|http://edamontology.org/format_2330 beta12orEarlier format_2549 OBO ontology text format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2550 OBO-XML OBO ontology XML format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2196 beta12orEarlier format_2550 OBO ontology XML format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2551 Sequence record format (text) Data format for a molecular sequence record. FALSE http://edamontology.org/format_1919 beta12orEarlier format_2551 Data format for a molecular sequence record. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2552 Sequence record format (XML) Data format for a molecular sequence record. FALSE http://edamontology.org/format_1919 beta12orEarlier format_2552 Data format for a molecular sequence record. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2553 Sequence feature table format (XML) XML format for a sequence feature table. FALSE http://edamontology.org/format_2548 beta12orEarlier format_2553 XML format for a sequence feature table. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2554 Alignment format (text) Text format for molecular sequence alignment information. FALSE http://edamontology.org/format_1921 beta12orEarlier format_2554 Text format for molecular sequence alignment information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2555 Alignment format (XML) XML format for molecular sequence alignment information. FALSE http://edamontology.org/format_1921 beta12orEarlier format_2555 XML format for molecular sequence alignment information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2556 Phylogenetic tree format (text) Text format for a phylogenetic tree. FALSE http://edamontology.org/format_2006 beta12orEarlier format_2556 Text format for a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2557 Phylogenetic tree format (XML) XML format for a phylogenetic tree. FALSE http://edamontology.org/format_2006 beta12orEarlier format_2557 XML format for a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2558 EMBL-like (XML) An XML format resembling EMBL entry format.|This concept may be used for the any non-standard EMBL-like XML formats. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2543 beta12orEarlier format_2558 An XML format resembling EMBL entry format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2559 GenBank-like format A format resembling GenBank entry (plain text) format.|This concept may be used for the non-standard GenBank-like formats. FALSE http://edamontology.org/format_1919 beta12orEarlier format_2559 A format resembling GenBank entry (plain text) format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2560 STRING entry format Entry format for the STRING database of protein interaction. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2560 http://edamontology.org/format_2331 Entry format for the STRING database of protein interaction. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/format_2561 Sequence assembly format (text) Text format for sequence assembly data. FALSE http://edamontology.org/format_2055 beta12orEarlier format_2561 Text format for sequence assembly data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2562 Amino acid identifier format Text format (representation) of amino acid residues. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier format_2562 http://edamontology.org/data_0994 Text format (representation) of amino acid residues. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/format_2566 completely unambiguous Alphabet for a molecular sequence without any unknown positions or ambiguity characters. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2330 beta12orEarlier format_2566 Alphabet for a molecular sequence without any unknown positions or ambiguity characters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2567 completely unambiguous pure "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." FALSE http://edamontology.org/format_2566|http://edamontology.org/format_2094 beta12orEarlier format_2567 "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2568 completely unambiguous pure nucleotide "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." FALSE http://edamontology.org/format_2567|http://edamontology.org/format_1207 beta12orEarlier format_2568 "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2569 completely unambiguous pure dna "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." FALSE http://edamontology.org/format_2567|http://edamontology.org/format_1212 beta12orEarlier format_2569 "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2570 completely unambiguous pure rna sequence "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." FALSE http://edamontology.org/format_2567|http://edamontology.org/format_1213 beta12orEarlier format_2570 "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2571 Raw sequence format Format of a raw molecular sequence (i.e. the alphabet used). FALSE http://edamontology.org/format_2350 beta12orEarlier format_2571 Format of a raw molecular sequence (i.e. the alphabet used). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2572 BAM "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." FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier http://samtools.sourceforge.net/SAM-1.3.pdf format_2572 http://samtools.sourceforge.net/SAM-1.3.pdf "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2573 SAM "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.|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." FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2057|http://edamontology.org/format_2330 beta12orEarlier http://samtools.sourceforge.net/SAM-1.3.pdf format_2573 http://samtools.sourceforge.net/SAM-1.3.pdf 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2585 SBML "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2013 beta12orEarlier http://sbml.org format_2585 http://sbml.org "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2607 completely unambiguous pure protein "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." FALSE http://edamontology.org/format_2567|http://edamontology.org/format_1208 beta12orEarlier format_2607 "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2848 Bibliographic reference format Format of a bibliographic reference. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2848 Format of a bibliographic reference. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2919 Sequence annotation track format Format of a sequence annotation track. FALSE http://edamontology.org/format_1920 beta12orEarlier format_2919 Format of a sequence annotation track. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2920 Alignment format (pair only) Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. FALSE http://edamontology.org/format_1921 beta12orEarlier format_2920 Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2921 Sequence variation annotation format Format of sequence variation annotation. FALSE http://edamontology.org/format_2350 beta12orEarlier format_2921 Format of sequence variation annotation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_2922 markx0 variant Some variant of Pearson MARKX alignment format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2330 beta12orEarlier format_2922 Some variant of Pearson MARKX alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2923 mega variant Some variant of Mega format for (typically aligned) sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_2923 Some variant of Mega format for (typically aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_2924 Phylip format variant Some variant of Phylip format for (aligned) sequences. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier format_2924 Some variant of Phylip format for (aligned) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3000 AB1 "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.|AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF)." FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier format_3000 AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3001 ACE "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." FALSE http://edamontology.org/format_2055|http://edamontology.org/format_2330 beta12orEarlier http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt format_3001 http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3003 BED "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.|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)." FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format1 format_3003 http://genome.ucsc.edu/FAQ/FAQformat#format1 "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3004 bigBed "bigBed format for large sequence annotation tracks, similar to textual BED format." FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2333 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format1.5 format_3004 http://genome.ucsc.edu/FAQ/FAQformat#format1.5 "bigBed format for large sequence annotation tracks, similar to textual BED format." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3005 WIG 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. FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/goldenPath/help/wiggle.html format_3005 http://genome.ucsc.edu/goldenPath/help/wiggle.html 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3006 bigWig bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2333 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format6.1 format_3006 http://genome.ucsc.edu/FAQ/FAQformat#format6.1 bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3007 PSL "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format2 format_3007 http://genome.ucsc.edu/FAQ/FAQformat#format2 "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3008 MAF "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.|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." FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format5 format_3008 http://genome.ucsc.edu/FAQ/FAQformat#format5 "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3009 2bit 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2333 beta12orEarlier http://jcomeau.freeshell.org/www/genome/2bitformat.html format_3009 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD|http://jcomeau.freeshell.org/www/genome/2bitformat.html 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3010 .nib .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. FALSE http://edamontology.org/format_2571|http://edamontology.org/format_2333 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format8 format_3010 http://genome.ucsc.edu/FAQ/FAQformat#format8 .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3011 genePred genePred table format for gene prediction tracks.|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. FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format9 format_3011 http://genome.ucsc.edu/FAQ/FAQformat#format9 genePred table format for gene prediction tracks. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3012 pgSnp "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/FAQ/FAQformat#format10 format_3012 http://genome.ucsc.edu/FAQ/FAQformat#format10 "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3013 axt "axt format of alignments, typically produced from BLASTZ." FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2330 beta12orEarlier http://genome.ucsc.edu/goldenPath/help/axt.html format_3013 http://genome.ucsc.edu/goldenPath/help/axt.html "axt format of alignments, typically produced from BLASTZ." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3014 LAV LAV format of alignments generated by BLASTZ and LASTZ. FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2330 beta12orEarlier http://www.bx.psu.edu/miller_lab/dist/lav_format.html format_3014 http://www.bx.psu.edu/miller_lab/dist/lav_format.html LAV format of alignments generated by BLASTZ and LASTZ. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3015 Pileup 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). FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2330 beta12orEarlier http://samtools.sourceforge.net/pileup.shtml format_3015 http://samtools.sourceforge.net/pileup.shtml 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3016 VCF "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." FALSE http://edamontology.org/format_2921|http://edamontology.org/format_2330 beta12orEarlier http://vcftools.sourceforge.net/specs.html format_3016 http://vcftools.sourceforge.net/specs.html "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3017 SRF Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier http://srf.sourceforge.net/ format_3017 http://srf.sourceforge.net/ Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3018 ZTR ZTR format for storing chromatogram data from DNA sequencing instruments. FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 beta12orEarlier http://staden.sourceforge.net/manual/formats_unix_12.html format_3018 http://staden.sourceforge.net/manual/formats_unix_12.html ZTR format for storing chromatogram data from DNA sequencing instruments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3019 GVF Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. FALSE http://edamontology.org/format_2921|http://edamontology.org/format_1975 beta12orEarlier http://sequenceontology.org/gvf.html format_3019 http://sequenceontology.org/gvf.html Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3020 BCF "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." FALSE http://edamontology.org/format_2921|http://edamontology.org/format_2333 beta12orEarlier format_3020 http://samtools.sourceforge.net/mpileup.shtml "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3033 Matrix format Format of a matrix (array) of numerical values. FALSE http://edamontology.org/format_2350 beta13 format_3033 Format of a matrix (array) of numerical values. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3097 Protein domain classification format Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). FALSE http://edamontology.org/format_2350 beta13 format_3097 Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3098 Raw SCOP domain classification format Format of raw SCOP domain classification data files.|These are the parsable data files provided by SCOP. FALSE http://edamontology.org/format_3097 beta13 format_3098 Format of raw SCOP domain classification data files. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3099 Raw CATH domain classification format Format of raw CATH domain classification data files.|These are the parsable data files provided by CATH. FALSE http://edamontology.org/format_3097 beta13 format_3099 Format of raw CATH domain classification data files. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3100 CATH domain report format "Format of summary of domain classification information for a CATH domain.|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." FALSE http://edamontology.org/format_3097 beta13 format_3100 Format of summary of domain classification information for a CATH domain. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3155 SBRML "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." FALSE http://edamontology.org/format_3166|http://edamontology.org/format_2332 1.0 http://www.comp-sys-bio.org/tiki-index.php?page=SBRML format_3155 http://www.comp-sys-bio.org/tiki-index.php?page=SBRML "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3156 BioPAX "BioPAX is an exchange format for pathway data, with its data model defined in OWL." FALSE http://edamontology.org/format_2013 1.0 http://www.biopax.org format_3156 http://www.biopax.org "BioPAX is an exchange format for pathway data, with its data model defined in OWL." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3157 EBI Application Result XML EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2066|http://edamontology.org/format_2920 1.0 http://www.ebi.ac.uk/schema/ApplicationResult.xsd format_3157 http://www.ebi.ac.uk/schema/ApplicationResult.xsd EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3158 PSI MI XML (MIF) MIF "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2054 1.0 http://www.psidev.info/mif format_3158 http://www.psidev.info/mif "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." MIF http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3159 phyloXML "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2557 1.0 http://www.phyloxml.org format_3159 http://www.phyloxml.org "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3160 NeXML NeXML is a standardised XML format for rich phyloinformatic data. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2557 1.0 http://www.nexml.org format_3160 http://www.nexml.org NeXML is a standardised XML format for rich phyloinformatic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3161 MAGE-ML "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2058 1.0 http://www.mged.org/Workgroups/MAGE/mage-ml.html format_3161 http://www.mged.org/Workgroups/MAGE/mage-ml.html "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3162 MAGE-TAB "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 1.0 http://www.mged.org/mage-tab format_3162 http://www.mged.org/mage-tab "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3163 GCDML "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3167 1.0 http://gcdml.gensc.org format_3163 http://gcdml.gensc.org "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3164 GTrack GTrack ecosystem of formats|GTrack|BTrack|GSuite GTrack|BioXSD|GTrack GTrack|GTrack|GSuite|BTrack GTrack|BioXSD/GTrack GTrack|GTrack format "GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation (""machine understandability"")." FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2206|http://edamontology.org/format_2330 http://doi.org/10.1186/1471-2105-12-494 1.0 http://www.gtrack.no|https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.txt|https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.html https://hyperbrowser.uio.no/hb/u/hb-superuser/h/gtrack-examples-from-the-specification format_3164 "'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes." GTrack ecosystem of formats http://www.gtrack.no|https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.txt|https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.html "GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation (""machine understandability"")." GTrack|BTrack|GSuite GTrack|BioXSD|GTrack GTrack|GTrack|GSuite|BTrack GTrack|BioXSD/GTrack GTrack|GTrack format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3166 Biological pathway or network report format Data format for a report of information derived from a biological pathway or network. FALSE http://edamontology.org/format_2350 beta12orEarlier format_3166 Data format for a report of information derived from a biological pathway or network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3167 Experiment annotation format Data format for annotation on a laboratory experiment. FALSE http://edamontology.org/format_2350 beta12orEarlier format_3167 Data format for annotation on a laboratory experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3235 Cytoband format Cytoband format for chromosome cytobands.|Reflects a UCSC Browser DB table. FALSE http://edamontology.org/format_2078|http://edamontology.org/format_2330 1.2 http://www.broadinstitute.org/software/igv/Cytoband format_3235 http://www.broadinstitute.org/software/igv/Cytoband Cytoband format for chromosome cytobands. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3239 CopasiML "CopasiML, the native format of COPASI." FALSE http://edamontology.org/format_3166|http://edamontology.org/format_2332|http://edamontology.org/format_2013 1.2 http://www.copasi.org/tiki-index.php?page_ref_id=128 format_3239 http://www.copasi.org/tiki-index.php?page_ref_id=128 "CopasiML, the native format of COPASI." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3240 CellML "CellML, the format for mathematical models of biological and other networks." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2013 1.2 http://www.cellml.org format_3240 http://www.cellml.org|http://www.iana.org/assignments/media-types/application/cellml+xml "CellML, the format for mathematical models of biological and other networks." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/application/cellml+xml http://edamontology.org/format_3242 PSI MI TAB (MITAB) "Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI." FALSE http://edamontology.org/format_2054|http://edamontology.org/format_2330 1.2 ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README format_3242 ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README "Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3243 PSI-PAR "Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema." FALSE http://edamontology.org/format_3158 1.2 http://www.psidev.info/psi-par format_3243 http://www.psidev.info/psi-par "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3244 mzML "mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.|mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.2 http://psidev.info/mzml format_3244 http://psidev.info/mzml "mzML format for raw spectrometer output data, standardised by HUPO PSI MSS." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3245 Mass spectrometry data format "Format for mass pectra and derived data, include peptide sequences etc." FALSE http://edamontology.org/format_2350 1.2 format_3245 "Format for mass pectra and derived data, include peptide sequences etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3246 TraML "TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.2 http://psidev.info/traml format_3246 http://psidev.info/traml "TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3247 mzIdentML "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." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.2 http://psidev.info/mzidentml format_3247 http://psidev.info/mzidentml "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3248 mzQuantML "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." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.2 http://psidev.info/mzquantml format_3248 http://psidev.info/mzquantml "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3249 GelML "GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3167 1.2 http://psidev.info/gelml format_3249 http://psidev.info/gelml "GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3250 spML "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." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3167 1.2 http://psidev.info format_3250 http://psidev.info "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3252 OWL Functional Syntax A human-readable encoding for the Web Ontology Language (OWL). FALSE http://edamontology.org/format_2197|http://edamontology.org/format_2330 1.2 format_3252 A human-readable encoding for the Web Ontology Language (OWL). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3253 Manchester OWL Syntax A syntax for writing OWL class expressions.|This format was influenced by the OWL Abstract Syntax and the DL style syntax. FALSE http://edamontology.org/format_2197|http://edamontology.org/format_2330 1.2 format_3253 A syntax for writing OWL class expressions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3254 KRSS2 Syntax "A superset of the ""Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort"".|This format is used in Protege 4." FALSE http://edamontology.org/format_2195|http://edamontology.org/format_2330 1.2 format_3254 "A superset of the ""Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort""." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3255 Turtle The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs.|The SPARQL Query Language incorporates a very similar syntax. FALSE http://edamontology.org/format_2376|http://edamontology.org/format_2330 1.2 format_3255 The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3256 N-Triples "A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.|N-Triples should not be confused with Notation 3 which is a superset of Turtle." FALSE http://edamontology.org/format_2376|http://edamontology.org/format_2330 1.2 format_3256 "A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3257 Notation3 N3 "A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind." FALSE http://edamontology.org/format_2376|http://edamontology.org/format_2330 format_3257 "A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind." N3 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3261 RDF/XML "Resource Description Framework (RDF) XML format.|RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2376 1.2 format_3261 Resource Description Framework (RDF) XML format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3262 OWL/XML OWL OWL ontology XML serialisation format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2197 1.2 format_3262 OWL ontology XML serialisation format. OWL http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3281 A2M The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. FALSE http://edamontology.org/format_2200|http://edamontology.org/format_2554 1.3 http://compbio.soe.ucsc.edu/a2m-desc.html format_3281 http://compbio.soe.ucsc.edu/a2m-desc.html The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3284 SFF Standard flowgram format Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. FALSE http://edamontology.org/format_2057|http://edamontology.org/format_2333 1.3 http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff format_3284 http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. Standard flowgram format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3285 MAP Plink MAP The MAP file describes SNPs and is used by the Plink package. FALSE http://edamontology.org/format_3288 1.3 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped format_3285 The MAP file describes SNPs and is used by the Plink package. Plink MAP http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3286 PED Plink PED The PED file describes individuals and genetic data and is used by the Plink package. FALSE http://edamontology.org/format_3288 1.3 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped format_3286 The PED file describes individuals and genetic data and is used by the Plink package. Plink PED http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3287 Individual genetic data format Data format for a metadata on an individual and their genetic data. FALSE http://edamontology.org/format_2350 1.3 format_3287 Data format for a metadata on an individual and their genetic data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3288 PED/MAP Plink PED/MAP The PED/MAP file describes data used by the Plink package. FALSE http://edamontology.org/format_3287|http://edamontology.org/format_2330 1.3 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped format_3288 The PED/MAP file describes data used by the Plink package. Plink PED/MAP http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3309 CT Connect format|Connectivity Table file format File format of a CT (Connectivity Table) file from the RNAstructure package. FALSE http://edamontology.org/format_2076|http://edamontology.org/format_2330 beta12orEarlier http://rna.urmc.rochester.edu/Text/File_Formats.html|http://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html format_3309 File format of a CT (Connectivity Table) file from the RNAstructure package. Connect format|Connectivity Table file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3310 SS XRNA old input style format. FALSE http://edamontology.org/format_2076|http://edamontology.org/format_2330 beta12orEarlier http://rna.ucsc.edu/rnacenter/xrna/xrna_faq.html format_3310 XRNA old input style format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3311 RNAML RNA Markup Language. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2076|http://edamontology.org/format_1921 beta12orEarlier http://www-lbit.iro.umontreal.ca/rnaml/ format_3311 RNA Markup Language. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3312 GDE Format for the Genetic Data Environment (GDE). FALSE http://edamontology.org/format_2551|http://edamontology.org/format_2330 beta12orEarlier http://home.cc.umanitoba.ca/~psgendb/birchhomedir/local/pkg/gde/doc/GDE2.2_manual.pdf format_3312 Format for the Genetic Data Environment (GDE). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3313 BLC Block file format "A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge." FALSE http://edamontology.org/format_2554 1.3 http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000 format_3313 "A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge." Block file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3326 Data index format FALSE http://edamontology.org/format_2350|http://edamontology.org/format_2333 1.3 format_3326 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3327 BAI BAM indexing format FALSE http://edamontology.org/format_3326 1.3 http://samtools.sourceforge.net/SAMv1.pdf format_3327 BAM indexing format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3328 HMMER2 HMMER profile HMM file for HMMER versions 2.x FALSE http://edamontology.org/format_1370 1.3 ftp://selab.janelia.org/pub/software/hmmer/2.4i/Userguide.pdf format_3328 HMMER profile HMM file for HMMER versions 2.x http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3329 HMMER3 HMMER profile HMM file for HMMER versions 3.x FALSE http://edamontology.org/format_1370 1.3 ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf format_3329 HMMER profile HMM file for HMMER versions 3.x http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3330 PO EMBOSS simple sequence pair alignment format. FALSE http://edamontology.org/format_2554 1.3 http://sourceforge.net/projects/poamsa/files/latest/download?source=files format_3330 EMBOSS simple sequence pair alignment format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3331 BLAST XML results format XML format as produced by the NCBI Blast package FALSE http://edamontology.org/format_1333|http://edamontology.org/format_2332 1.3 format_3331 XML format as produced by the NCBI Blast package http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3462 CRAM Reference-based compression of alignment format FALSE http://edamontology.org/format_2920|http://edamontology.org/format_2333 1.7 http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf format_3462 http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf Reference-based compression of alignment format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3464 JSON JavaScript Object Notation "JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs." FALSE http://edamontology.org/format_1915|http://edamontology.org/format_3750 1.7 json format_3464 http://filext.com/file-extension/JSON|https://en.wikipedia.org/wiki/JSON|http://www.iana.org/assignments/media-types/application/json "JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs." JavaScript Object Notation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/application/json http://edamontology.org/format_3466 EPS Encapsulated PostScript format FALSE http://edamontology.org/format_3696 1.7 format_3466 Encapsulated PostScript format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3467 GIF Graphics Interchange Format. FALSE http://edamontology.org/format_2333 1.7 format_3467 Graphics Interchange Format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3468 xls Microsoft Excel format Microsoft Excel spreadsheet format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3507 1.7 format_3468 Microsoft Excel spreadsheet format. Microsoft Excel format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3475 TSV Tab-separated values Tabular data represented as tab-separated values in a text file. FALSE http://edamontology.org/format_3751 1.7 tsv|tab format_3475 http://filext.com/file-extension/TSV|http://www.iana.org/assignments/media-types/text/tab-separated-values Tabular data represented as tab-separated values in a text file. Tab-separated values http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/text/tab-separated-values http://edamontology.org/format_3476 Gene expression data format "Format of a file of gene expression data, e.g. a gene expression matrix or profile." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.7 format_3476 "Format of a file of gene expression data, e.g. a gene expression matrix or profile." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/format_2058 1.10 http://edamontology.org/format_3477 Cytoscape input file format Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 1.7 format_3477 Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3484 ebwt Bowtie index format "Bowtie format for indexed reference genome for ""small"" genomes." FALSE http://edamontology.org/format_3326 1.7 https://github.com/BenLangmead/bowtie/blob/master/MANUAL format_3484 "Bowtie format for indexed reference genome for ""small"" genomes." Bowtie index format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3485 RSF GCG RSF "Rich sequence format.|RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual)." FALSE http://edamontology.org/format_3486 1.7 http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf format_3485 Rich sequence format. GCG RSF http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3486 GCG format variant Some format based on the GCG format. FALSE http://edamontology.org/format_2554|http://edamontology.org/format_2551|http://edamontology.org/format_2330 1.7 format_3486 Some format based on the GCG format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3487 BSML Bioinformatics Sequence Markup Language format. FALSE http://edamontology.org/format_2552|http://edamontology.org/format_2332 1.7 http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc format_3487 Bioinformatics Sequence Markup Language format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3491 ebwtl Bowtie long index format "Bowtie format for indexed reference genome for ""large"" genomes." FALSE http://edamontology.org/format_3326 1.7 https://github.com/BenLangmead/bowtie/blob/master/MANUAL format_3491 "Bowtie format for indexed reference genome for ""large"" genomes." Bowtie long index format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3499 Ensembl variation file format Ensembl standard format for variation data. FALSE http://edamontology.org/format_2921|http://edamontology.org/format_2330 1.8 format_3499 http://www.ensembl.org/info/website/upload/var.html Ensembl standard format for variation data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3506 docx Microsoft Word format|doc Microsoft Word format. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3507 1.8 format_3506 Microsoft Word format. Microsoft Word format|doc http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3507 Document format "Format of documents including word processor, spreadsheet and presentation." FALSE http://edamontology.org/format_2350 1.8 format_3507 "Format of documents including word processor, spreadsheet and presentation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3508 PDF Portable Document Format FALSE http://edamontology.org/format_3507|http://edamontology.org/format_2333 1.8 format_3508 Portable Document Format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3547 Image format Format used for images and image metadata. FALSE http://edamontology.org/format_2350 1.9 format_3547 Format used for images and image metadata. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3548 DICOM format "Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.9 http://dicom.nema.org/ format_3548 "Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3549 nii NIfTI-1 format "Medical image and metadata format of the Neuroimaging Informatics Technology Initiative. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.9 http://nifti.nimh.nih.gov/nifti-1 format_3549 "Medical image and metadata format of the Neuroimaging Informatics Technology Initiative. " NIfTI-1 format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3550 mhd Metalmage format Text-based tagged file format for medical images generated using the MetaImage software package. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_3547 1.9 http://www.itk.org/Wiki/ITK/MetaIO/Documentation format_3550 Text-based tagged file format for medical images generated using the MetaImage software package. Metalmage format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3551 nrrd Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. FALSE http://edamontology.org/format_2330|http://edamontology.org/format_3547 1.9 http://teem.sourceforge.net/nrrd/format.html format_3551 Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3554 R file format "File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. " FALSE http://edamontology.org/format_2330 1.9 format_3554 "File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3555 SPSS "File format used for scripts for the Statistical Package for the Social Sciences. " FALSE http://edamontology.org/format_2330 1.9 format_3555 "File format used for scripts for the Statistical Package for the Social Sciences. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3556 MHTML MIME HTML|HTML email message format|MHTML format|HTML email format|MHT|MIME HTML format|MHT format|MIME multipart message format|MIME multipart|MIME multipart format|MIME multipart message "MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. " FALSE http://edamontology.org/format_2331 1.9 https://tools.ietf.org/html/rfc2557 mhtml|mht|eml format_3556 "MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons incuded in EDAM as a specialisation of 'HTML'." http://www.iana.org/assignments/media-types/multipart/related|https://en.wikipedia.org/wiki/MHTML|https://tools.ietf.org/html/rfc2557 "MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. " MIME HTML|HTML email message format|MHTML format|HTML email format|MHT|MIME HTML format|MHT format MIME multipart message format|MIME multipart|MIME multipart format|MIME multipart message http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/multipart/related http://edamontology.org/format_3578 IDAT Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2333 1.10 format_3578 Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3579 JPG "Joint Picture Group file format for lossy graphics file. |Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.10 http://www.fileformat.info/format/jpeg/egff.htm format_3579 "Joint Picture Group file format for lossy graphics file. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3580 rcc "Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts." FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 1.10 format_3580 "Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3581 arff ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.|This file format is for machine learning. FALSE http://edamontology.org/format_2330 1.11 http://www.cs.waikato.ac.nz/ml/weka/arff.html format_3581 http://www.cs.waikato.ac.nz/ml/weka/arff.html ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3582 afg AFG is a single text-based file assembly format that holds read and consensus information together FALSE http://edamontology.org/format_2330|http://edamontology.org/format_2561 1.11 http://seqanswers.com/wiki/AFG format_3582 http://seqanswers.com/wiki/AFG AFG is a single text-based file assembly format that holds read and consensus information together http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3583 bedgraph The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data|Holds a tab-delimited chromosome /start /end / datavalue dataset. FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 1.11 http://genome.ucsc.edu/FAQ/FAQformat#format1.8 format_3583 http://genome.ucsc.edu/FAQ/FAQformat#format1.8 The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3584 bedstrict "Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. |Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. " FALSE http://edamontology.org/format_3003 1.11 http://genome.ucsc.edu/FAQ/FAQformat#format1 format_3584 http://genome.ucsc.edu/FAQ/FAQformat#format1 Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3585 bed6 "BED file format where each feature is described by chromosome, start, end, name, score, and strand.|Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6" FALSE http://edamontology.org/format_3584 1.11 http://bedtools.readthedocs.org/en/latest/content/general-usage.html format_3585 http://bedtools.readthedocs.org/en/latest/content/general-usage.html "BED file format where each feature is described by chromosome, start, end, name, score, and strand." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3586 bed12 A BED file where each feature is described by all twelve columns.|Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12 FALSE http://edamontology.org/format_3584 1.11 http://bedtools.readthedocs.org/en/latest/content/general-usage.html format_3586 http://bedtools.readthedocs.org/en/latest/content/general-usage.html A BED file where each feature is described by all twelve columns. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3587 chrominfo "Tabular format of chromosome names and sizes used by Galaxy.|Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. " FALSE http://edamontology.org/format_2330|http://edamontology.org/format_3003 1.11 http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&hgta_doSchemaDb=mm10&hgta_doSchemaTable=chromInfo format_3587 http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&hgta_doSchemaDb=mm10&hgta_doSchemaTable=chromInfo Tabular format of chromosome names and sizes used by Galaxy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3588 customtrack Custom Sequence annotation track format used by Galaxy.|Used for tracks/track views within galaxy. FALSE http://edamontology.org/format_2919|http://edamontology.org/format_2330 1.11 https://genome.ucsc.edu/goldenPath/help/customTrack.html format_3588 https://genome.ucsc.edu/goldenPath/help/customTrack.html Custom Sequence annotation track format used by Galaxy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3589 csfasta Color space FASTA format sequence variant.|FASTA format extended for color space information. FALSE http://edamontology.org/format_2200|http://edamontology.org/format_2554 1.3 http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html format_3589 http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html Color space FASTA format sequence variant. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3590 hdf5 h5 "HDF5 is a generic hierarchical data file format used to store and organize large amounts of data.|An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes." FALSE http://edamontology.org/format_2333 1.11 https://www.hdfgroup.org/HDF5/doc/H5.format.html format_3590 https://www.hdfgroup.org/HDF5/doc/H5.format.html HDF5 is a generic hierarchical data file format used to store and organize large amounts of data. h5 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3591 tiff "A versatile bitmap format.|The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/tiff/egff.htm format_3591 A versatile bitmap format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3592 bmp "Standard bitmap storage format in the Microsoft Windows environment.|Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/bmp/egff.htm format_3592 Standard bitmap storage format in the Microsoft Windows environment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3593 im "IM is a format used by LabEye and other applications based on the IFUNC image processing library.|IFUNC library reads and writes most uncompressed interchange versions of this format. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html format_3593 IM is a format used by LabEye and other applications based on the IFUNC image processing library. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3594 pcd "Photo CD format, which is the highest resolution format for images on a CD.|PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 https://www.coolutils.com/Formats/PCD format_3594 "Photo CD format, which is the highest resolution format for images on a CD." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3595 pcx "PCX is an image file format that uses a simple form of run-length encoding. It is lossless. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 https://www.coolutils.com/Formats/PCX format_3595 "PCX is an image file format that uses a simple form of run-length encoding. It is lossless. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3596 ppm "The PPM format is a lowest common denominator color image file format. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://netpbm.sourceforge.net/doc/ppm.html format_3596 "The PPM format is a lowest common denominator color image file format. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3597 psd PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved. FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/psd/egff.htm format_3597 PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3598 xbm X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. |The XBM format was replaced by XPM for X11 in 1989. FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/xbm/egff.htm format_3598 X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3599 xpm "X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. |Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/xpm/egff.htm format_3599 "X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3600 rgb "RGB file format is the native raster graphics file format for Silicon Graphics workstations. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.fileformat.info/format/jpeg/egff.htm format_3600 "RGB file format is the native raster graphics file format for Silicon Graphics workstations. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3601 pbm "The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. " FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://netpbm.sourceforge.net/doc/pbm.html format_3601 "The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3602 pgm "The PGM format is a lowest common denominator grayscale file format. |It is designed to be extremely easy to learn and write programs for." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://netpbm.sourceforge.net/doc/pgm.html format_3602 "The PGM format is a lowest common denominator grayscale file format. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3603 PNG png "PNG is a file format for image compression. |It iis expected to replace the Graphics Interchange Format (GIF)." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.w3.org/TR/PNG/ format_3603 "PNG is a file format for image compression. " png http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3604 SVG Scalable Vector Graphics|svg Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.| The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3547 1.11 http://www.w3.org/Graphics/SVG/ format_3604 Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. Scalable Vector Graphics|svg http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3605 rast Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems| The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 https://en.wikipedia.org/wiki/Sun_Raster format_3605 Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3606 Sequence quality report format (text) Textual report format for sequence quality for reports from sequencing machines. FALSE http://edamontology.org/format_2350|http://edamontology.org/format_2330 1.11 format_3606 Textual report format for sequence quality for reports from sequencing machines. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3607 qual FASTQ format subset for Phred sequencing quality score data only (no sequences).|Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities. FALSE http://edamontology.org/format_3606|http://edamontology.org/format_2182 1.11 http://en.wikipedia.org/wiki/Phred_quality_score format_3607 FASTQ format subset for Phred sequencing quality score data only (no sequences). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3608 qualsolexa FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.|Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected) FALSE http://edamontology.org/format_3607|http://edamontology.org/format_1933 1.11 format_3608 FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3609 qualillumina "FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.|Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 ""B"", is used also at the end of reads as a Read Segment Quality Control Indicator." FALSE http://edamontology.org/format_3607|http://edamontology.org/format_1931 1.11 http://en.wikipedia.org/wiki/Phred_quality_score format_3609 FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3610 qualsolid "FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.|For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format." FALSE http://edamontology.org/format_3607 1.11 http://en.wikipedia.org/wiki/Phred_quality_score format_3610 FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3611 qual454 FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. FALSE http://edamontology.org/format_3607 1.11 http://en.wikipedia.org/wiki/Phred_quality_score format_3611 FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3612 ENCODE peak format Human ENCODE peak format.|Format that covers both the broad peak format and narrow peak format from ENCODE. FALSE http://edamontology.org/format_3585 1.11 http://genome.ucsc.edu/FAQ/FAQformat#format13 format_3612 http://genome.ucsc.edu/FAQ/FAQformat#format13 Human ENCODE peak format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3613 ENCODE narrow peak format Human ENCODE narrow peak format.|Format that covers both the broad peak format and narrow peak format from ENCODE. FALSE http://edamontology.org/format_3612 1.11 http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html? format_3613 http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html? Human ENCODE narrow peak format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3614 ENCODE broad peak format Human ENCODE broad peak format. FALSE http://edamontology.org/format_3612 1.11 http://genome.ucsc.edu/FAQ/FAQformat#format12 format_3614 http://genome.ucsc.edu/FAQ/FAQformat#format12 Human ENCODE broad peak format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3615 bgzip "Blocked GNU Zip format.|BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format)." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.htslib.org/doc/tabix.html format_3615 Blocked GNU Zip format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3616 tabix TAB-delimited genome position file index format. FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.11 http://www.htslib.org/doc/tabix.html format_3616 http://www.htslib.org/doc/tabix.html TAB-delimited genome position file index format. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3617 Graph format Data format for graph data. FALSE http://edamontology.org/format_2350 1.11 format_3617 Data format for graph data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3618 xgmml XML-based format used to store graph descriptions within Galaxy. FALSE http://edamontology.org/format_3617 1.11 http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph format_3618 XML-based format used to store graph descriptions within Galaxy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3619 sif SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. FALSE http://edamontology.org/format_2013 1.11 http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph format_3619 SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3620 xlsx MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. FALSE http://edamontology.org/format_3507|http://edamontology.org/format_2333 1.11 format_3620 MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3621 SQLite format Data format used by the SQLite database. FALSE http://edamontology.org/format_2333 1.11 https://www.sqlite.org/fileformat2.html format_3621 Data format used by the SQLite database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3622 Gemini SQLite format Data format used by the SQLite database conformant to the Gemini schema. FALSE http://edamontology.org/format_2921|http://edamontology.org/format_3621 1.11 https://gemini.readthedocs.org/en/latest/content/quick_start.html format_3622 Data format used by the SQLite database conformant to the Gemini schema. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3623 Index format Format of a data index of some type. FALSE http://edamontology.org/format_2350|http://edamontology.org/format_2333 1.11 format_3623 Format of a data index of some type. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3624 snpeffdb "An index of a genome database, indexed for use by the snpeff tool." FALSE http://edamontology.org/format_3623 1.11 format_3624 "An index of a genome database, indexed for use by the snpeff tool." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3626 MAT .mat file format|MATLAB file format|MAT file format Binary format used by MATLAB files to store workspace variables. FALSE http://edamontology.org/format_3033 1.12 http://uk.mathworks.com/help/matlab/import_export/mat-file-versions.html format_3626 Binary format used by MATLAB files to store workspace variables. .mat file format|MATLAB file format|MAT file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3650 netCDF ANDI-MS Format used by netCDF software library for writing and reading chromatography-MS data files. FALSE http://edamontology.org/format_3245 1.12 http://www.astm.org/Standards/E1947.htm format_3650 Format used by netCDF software library for writing and reading chromatography-MS data files. ANDI-MS http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3651 MGF "Mascot Generic Format. Encodes multiple MS/MS spectra in a single file.|Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions." FALSE http://edamontology.org/format_3245 1.12 format_3651 Mascot Generic Format. Encodes multiple MS/MS spectra in a single file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3652 dta "Spectral data format file where each spectrum is written to a separate file.|Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum." FALSE http://edamontology.org/format_3245 1.12 format_3652 Spectral data format file where each spectrum is written to a separate file. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3653 pkl Spectral data file similar to dta.|Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to. FALSE http://edamontology.org/format_3245 1.12 format_3653 Spectral data file similar to dta. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3654 mzXML Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. FALSE http://edamontology.org/format_3245 1.12 https://dx.doi.org/10.1038%2Fnbt1031 format_3654 Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3655 pepXML "Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.12 http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd format_3655 "Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3657 GPML "Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2013 1.12 http://www.pathvisio.org/gpml/ format_3657 "Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3665 K-mer countgraph A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. FALSE http://edamontology.org/format_3617|http://edamontology.org/format_2333 1.12 http://khmer.readthedocs.org/en/v2.0/dev/binary-file-formats.html#countgraph oxlicg format_3665 http://khmer.readthedocs.org/en/v2.0/dev/binary-file-formats.html#countgraph|http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph http://edamontology.org/format_3681 mzTab mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results. FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2330 http://doi.org/10.1074/mcp.O113.036681 1.13 http://code.google.com/archive/p/mztab format_3681 http://code.google.com/archive/p/mztab mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3682 imzML "imzML is a data format for mass spectrometry imaging data. NB.: See comment.|Data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332|http://edamontology.org/format_2333 http://doi.org/10.1016/j.jprot.2012.07.026 1.13 http://www.imzml.org/index.php?option=com_content&view=article&id=188&Itemid=63 imzML|ibd format_3682 http://www.imzml.org/index.php?option=com_content&view=article&id=188&Itemid=63 imzML is a data format for mass spectrometry imaging data. NB.: See comment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3683 qcML "qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements.|The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332|http://edamontology.org/format_3167 1.13 http://code.google.com/archive/p/qcml format_3683 http://code.google.com/archive/p/qcml qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3684 PRIDE XML "PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332|http://edamontology.org/format_3167 1.13 http://www.ebi.ac.uk/pride/help/archive/submission/pridexml format_3684 http://www.ebi.ac.uk/pride/help/archive/submission/pridexml "PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3685 SED-ML "Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements." FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3167 http://doi.org/10.1186/1752-0509-5-198|http://doi.org/10.1007/978-3-540-88562-7_15 1.13 http://sed-ml.org format_3685 http://sed-ml.org "Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3686 COMBINE OMEX "Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology.|An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network)." FALSE http://edamontology.org/format_2013|http://edamontology.org/format_3167|http://edamontology.org/format_2333 http://doi.org/10.1186/s12859-014-0369-z 1.13 http://co.mbine.org/documents/archive format_3686 http://co.mbine.org/documents/archive Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3687 ISA-TAB ISA-Tab "The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from experiments employing a combination of technologies.|ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata)." FALSE http://edamontology.org/format_2058|http://edamontology.org/format_3167|http://edamontology.org/format_2330 1.13 http://www.isa-tools.org/format/specification format_3687 http://www.isa-tools.org/format/specification "The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from experiments employing a combination of technologies." ISA-Tab http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3688 SBtab SBtab is a tabular format for biochemical network models. FALSE http://edamontology.org/format_2013|http://edamontology.org/format_2330 http://arxiv.org/abs/1502.01463 1.13 http://sbtab.net format_3688 http://sbtab.net SBtab is a tabular format for biochemical network models. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3689 BCML Biological Connection Markup Language (BCML) is an XML format for biological pathways. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2013 1.13 http://compbiotoolbox.fmach.it/BCMLdocs format_3689 http://compbiotoolbox.fmach.it/BCMLdocs Biological Connection Markup Language (BCML) is an XML format for biological pathways. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3690 BDML Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. FALSE http://edamontology.org/format_2332 http://doi.org/10.1093/bioinformatics/btu767 1.13 http://ssbd.qbic.riken.jp/bdml format_3690 http://ssbd.qbic.riken.jp/bdml Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3691 BEL Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. FALSE http://edamontology.org/format_2330 1.13 http://www.openbel.org format_3691 http://www.openbel.org Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3692 SBGN-ML SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_2013 1.13 http://www.sbgn.org/LibSBGN#The_SBGN-ML_format format_3692 http://www.sbgn.org/LibSBGN#The_SBGN-ML_format SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3693 AGP "AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome)." FALSE http://edamontology.org/format_2055|http://edamontology.org/format_2330 1.13 http://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification format_3693 http://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification "AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3696 PS PostScript PostScript format FALSE http://edamontology.org/format_2330 1.13 format_3696 PostScript format PostScript http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3698 SRA format SRA| SRA archive format SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. FALSE http://edamontology.org/format_2333 1.13 http://www.ncbi.nlm.nih.gov/books/NBK242622/ format_3698 SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. SRA| SRA archive format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3699 VDB SRA native format VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. FALSE http://edamontology.org/format_2333 1.13 http://www.ncbi.nlm.nih.gov/books/NBK242622/ format_3699 VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. SRA native format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3700 Tabix index file format Index file format used by the samtools package to index TAB-delimited genome position files. FALSE http://edamontology.org/format_3326 1.3 http://samtools.github.io/hts-specs/tabix.pdf format_3700 Index file format used by the samtools package to index TAB-delimited genome position files. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3701 Sequin format "A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). " FALSE http://edamontology.org/format_2206 1.13 format_3701 "A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3702 MSF Magellan storage file format "Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software.|This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. " FALSE http://edamontology.org/format_3245 1.14 format_3702 Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. Magellan storage file format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3706 Biodiversity data format Data format for biodiversity data. FALSE http://edamontology.org/format_2350 1.14 format_3706 Data format for biodiversity data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3708 ABCD format ABCD Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). FALSE http://edamontology.org/format_3706 1.14 https://github.com/tdwg/abcd format_3708 Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). ABCD http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3709 GCT/Res format GCT format|Res format "Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample." FALSE http://edamontology.org/format_2058|http://edamontology.org/format_2330 1.14 format_3709 "Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample." GCT format|Res format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3710 WIFF format wiff Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex). FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2333 1.14 wiff format_3710 Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex). wiff http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3711 X!Tandem XML Output format used by X! series search engines that is based on the XML language BIOML. FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2333|http://edamontology.org/format_2330 1.14 http://www.thegpm.org/docs/X_series_output_form.pdf format_3711 Output format used by X! series search engines that is based on the XML language BIOML. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3712 Thermo RAW Proprietary file format for mass spectrometry data from Thermo Scientific.|Proprietary format for which documentation is not available. FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2333 1.14 format_3712 Proprietary file format for mass spectrometry data from Thermo Scientific. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3713 Mascot .dat file """Raw"" result file from Mascot database search." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2330 1.14 https://github.com/compomics/mascotdatfile format_3713 """Raw"" result file from Mascot database search." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3714 MaxQuant APL peaklist format MaxQuant APL Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2330 1.14 http://doi.org/10.1021/pr101065j format_3714 Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. MaxQuant APL http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3725 SBOL Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology.|SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs. FALSE http://edamontology.org/format_2332 1.14 http://sbolstandard.org/downloads/specification-data-model-2-0/ format_3725 Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3726 PMML PMML uses XML to represent mining models. The structure of the models is described by an XML Schema.| One or more mining models can be contained in a PMML document. FALSE http://edamontology.org/format_2332 1.14 http://dmg.org/pmml/v4-2-1/GeneralStructure.html format_3726 PMML uses XML to represent mining models. The structure of the models is described by an XML Schema. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3727 OME-TIFF "Image file format used by the Open Microscopy Environment (OME). |An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file’s first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions.|OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community." FALSE http://edamontology.org/format_2333|http://edamontology.org/format_3547 1.14 http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html format_3727 "Image file format used by the Open Microscopy Environment (OME). " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3728 LocARNA PP "The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record.|Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs." FALSE http://edamontology.org/format_2330 1.14 http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/ format_3728 "The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3729 dbGaP format "Input format used by the Database of Genotypes and Phenotypes (dbGaP).|The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype." FALSE http://edamontology.org/format_2330 1.14 http://www.ncbi.nlm.nih.gov/books/NBK154410/ format_3729 Input format used by the Database of Genotypes and Phenotypes (dbGaP). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3746 BIOM format BIological Observation Matrix format "The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables.|BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc." FALSE http://edamontology.org/format_3706|http://edamontology.org/format_2330 http://doi.org/10.1186/2047-217X-1-7 1.15 http://biom-format.org biom format_3746 The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables. BIological Observation Matrix format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3747 protXML "A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data.|No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML)." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.15 http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html format_3747 http://purl.obolibrary.org/obo/MS_1001422 "A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3748 Linked data format Linked Data format|Semantic Web format "A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries." FALSE http://edamontology.org/format_2350 https://www.w3.org/DesignIssues/LinkedData.html|http://doi.org/10.4018/jswis.2009081901 1.15 format_3748 https://en.wikipedia.org/wiki/Linked_data "A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries." Linked Data format Semantic Web format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3749 JSON-LD JavaScript Object Notation for Linked Data "JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON." FALSE http://edamontology.org/format_3464|http://edamontology.org/format_3748|http://edamontology.org/format_2376 1.15 http://www.w3.org/TR/json-ld jsonld format_3749 https://en.wikipedia.org/wiki/JSON-LD|http://www.iana.org/assignments/media-types/application/ld+json "JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON." JavaScript Object Notation for Linked Data http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/application/ld+json http://edamontology.org/format_3750 YAML YAML Ain't Markup Language "YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language.|YAML version 1.2 is a superset of JSON; prior versions were ""not strictly compatible"". |Data in YAML format can be serialised into text, or binary format." FALSE http://edamontology.org/format_1915 1.15 http://yaml.org yaml|yml format_3750 https://en.wikipedia.org/wiki/YAML|http://filext.com/file-extension/YML YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. YAML Ain't Markup Language http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3751 DSV Tabular format|Delimiter-separated values Tabular data represented as values in a text file delimited by some character. FALSE http://edamontology.org/format_2330 1.16 format_3751 Tabular format https://en.wikipedia.org/wiki/Delimiter-separated_values Tabular data represented as values in a text file delimited by some character. Delimiter-separated values http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3752 CSV Comma-separated values Tabular data represented as comma-separated values in a text file. FALSE http://edamontology.org/format_3751 1.16 csv format_3752 http://filext.com/file-extension/CSV|http://www.iana.org/assignments/media-types/text/csv Tabular data represented as comma-separated values in a text file. Comma-separated values http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/text/csv http://edamontology.org/format_3758 SEQUEST .out file """Raw"" result file from SEQUEST database search." FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2330 1.16 format_3758 """Raw"" result file from SEQUEST database search." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3764 idXML XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. FALSE http://edamontology.org/format_3245|http://edamontology.org/format_2332 1.16 http://open-ms.sourceforge.net/schemas/ format_3764 XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3765 KNIME datatable format Data table formatted such that it can be passed/streamed within the KNIME platform. FALSE http://edamontology.org/format_2032 1.16 format_3765 Data table formatted such that it can be passed/streamed within the KNIME platform. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3770 UniProtKB XML UniProt XML|UniProtKB XML format|UniProt XML format UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. FALSE http://edamontology.org/format_2552|http://edamontology.org/format_2332|http://edamontology.org/format_2547 1.16 http://www.uniprot.org/docs/uniprot.xsd format_3770 UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. UniProt XML|UniProtKB XML format|UniProt XML format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3771 UniProtKB RDF UniProtKB RDF format|UniProt RDF|UniProt RDF format|UniProtKB RDF/XML format|UniProt RDF/XML|UniProt RDF/XML format|UniProtKB RDF/XML UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). FALSE http://edamontology.org/format_2547|http://edamontology.org/format_2376 1.16 http://www.uniprot.org/format/uniprot_rdf format_3771 UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). UniProtKB RDF format|UniProt RDF|UniProt RDF format UniProtKB RDF/XML format|UniProt RDF/XML|UniProt RDF/XML format|UniProtKB RDF/XML http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3772 BioJSON (BioXSD) BioXSD JSON|BioXSD+JSON|BioJSON format (BioXSD)|BioXSD|GTrack BioJSON|BioJSON (BioXSD data model)|BioXSD in JSON format|BioXSD in JSON|BioXSD JSON format|BioXSD BioJSON format|BioXSD BioJSON|BioXSD/GTrack BioJSON|BioXSD|BioJSON|BioYAML BioJSON "BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming." FALSE http://edamontology.org/format_1919|http://edamontology.org/format_3464|http://edamontology.org/format_2571|http://edamontology.org/format_1921|http://edamontology.org/format_1920 http://doi.org/10.7490/f1000research.1113048.1 1.16 http://bioxsd.org http://bioxsd.org/sequenceRecord.json|http://bioxsd.org/sequenceRecord.xml+json+yaml.xml format_3772 "Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'." http://bioxsd.org "BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming." BioXSD JSON|BioXSD+JSON|BioJSON format (BioXSD)|BioXSD|GTrack BioJSON|BioJSON (BioXSD data model)|BioXSD in JSON format|BioXSD in JSON|BioXSD JSON format|BioXSD BioJSON format|BioXSD BioJSON|BioXSD/GTrack BioJSON|BioXSD|BioJSON|BioYAML BioJSON http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3773 BioYAML BioXSD BioYAML|BioXSD+YAML|BioYAML (BioXSD)|BioXSD|GTrack BioYAML|BioXSD|BioJSON|BioYAML BioYAML|BioYAML (BioXSD data model)|BioXSD BioYAML format|BioXSD/GTrack BioYAML|BioXSD YAML format|BioYAML format|BioYAML format (BioXSD)|BioXSD in YAML|BioXSD in YAML format|BioXSD YAML "BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming." FALSE http://edamontology.org/format_1919|http://edamontology.org/format_2571|http://edamontology.org/format_1921|http://edamontology.org/format_1920|http://edamontology.org/format_3750 http://doi.org/10.7490/f1000research.1113048.1 1.16 http://bioxsd.org http://bioxsd.org/sequenceRecord.yaml|http://bioxsd.org/sequenceRecord.xml+json+yaml.xml format_3773 "Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'." http://bioxsd.org "BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming." BioXSD BioYAML|BioXSD+YAML|BioYAML (BioXSD)|BioXSD|GTrack BioYAML|BioXSD|BioJSON|BioYAML BioYAML|BioYAML (BioXSD data model)|BioXSD BioYAML format|BioXSD/GTrack BioYAML|BioXSD YAML format|BioYAML format|BioYAML format (BioXSD)|BioXSD in YAML|BioXSD in YAML format|BioXSD YAML http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3774 BioJSON (Jalview) Jalview BioJSON format|JSON format (Jalview)|BioJSON format (Jalview)|JSON (Jalview)|Jalview JSON|Jalview JSON format|Jalview BioJSON "BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench." FALSE http://edamontology.org/format_3464|http://edamontology.org/format_1921|http://edamontology.org/format_1920 1.16 http://jalview.github.io/biojson format_3774 http://jalview.github.io/biojson "BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench." Jalview BioJSON format|JSON format (Jalview)|BioJSON format (Jalview)|JSON (Jalview)|Jalview JSON|Jalview JSON format|Jalview BioJSON http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3775 GSuite BioXSD/GTrack GSuite|GTrack|BTrack|GSuite GSuite|GSuite (GTrack ecosystem of formats)|BioXSD|GTrack GSuite|GTrack|GSuite|BTrack GSuite|GSuite format "GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata." FALSE http://edamontology.org/format_1920|http://edamontology.org/format_2330 http://doi.org/10.7490/f1000research.1112716.1|http://dx.doi.org/10.1101/067561 1.16 https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.txt|https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.html format_3775 "'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files." https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.txt|https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.html "GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata." BioXSD/GTrack GSuite|GTrack|BTrack|GSuite GSuite|GSuite (GTrack ecosystem of formats)|BioXSD|GTrack GSuite|GTrack|GSuite|BTrack GSuite|GSuite format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3776 BTrack GTrack|BTrack|GSuite BTrack|BTrack (GTrack ecosystem of formats)|BTrack format|GTrack|GSuite|BTrack BTrack|BioXSD/GTrack BTrack|BioXSD|GTrack BTrack "BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats." FALSE http://edamontology.org/format_1920|http://edamontology.org/format_2548|http://edamontology.org/format_2919|http://edamontology.org/format_2333 1.16 format_3776 "'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats." "BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats." GTrack|BTrack|GSuite BTrack|BTrack (GTrack ecosystem of formats)|BTrack format|GTrack|GSuite|BTrack BTrack|BioXSD/GTrack BTrack|BioXSD|GTrack BTrack http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3777 MCPD Bioversity MCPD|Multi-Crop Passport Descriptors|MCPD format|Multi-Crop Passport Descriptors format|FAO MCPD|MCPD V.1|MCPD V.2|IPGRI MCPD The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. FALSE http://edamontology.org/format_3706|http://edamontology.org/format_2330 1.16 https://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/FAO-Bioversity_multi_crop_passport_descriptors_V_2_Final_rev_1526.pdf|https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/FAO_IPGRI_Multi-Crop_Passport_Descriptors__MCPD__124_01.pdf|https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v2-mcpd-v2/|https://www.bioversityinternational.org/e-library/publications/detail/faoipgri-multi-crop-passport-descriptors-mcpd/ format_3777 "Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012)." https://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/FAO-Bioversity_multi_crop_passport_descriptors_V_2_Final_rev_1526.pdf|https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/FAO_IPGRI_Multi-Crop_Passport_Descriptors__MCPD__124_01.pdf|https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v2-mcpd-v2/|https://www.bioversityinternational.org/e-library/publications/detail/faoipgri-multi-crop-passport-descriptors-mcpd/ The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. Bioversity MCPD|Multi-Crop Passport Descriptors|MCPD format|Multi-Crop Passport Descriptors format|FAO MCPD MCPD V.1|MCPD V.2|IPGRI MCPD http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats https://www.bioversityinternational.org/|http://www.fao.org http://edamontology.org/format_3780 Annotated text format "Data format of an annotated text, e.g. with recognised entities, concepts, and relations." FALSE http://edamontology.org/format_2350 1.16 format_3780 "Data format of an annotated text, e.g. with recognised entities, concepts, and relations." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3781 PubAnnotation format JSON format of annotated scientific text used by PubAnnotations and other tools. FALSE http://edamontology.org/format_3780|http://edamontology.org/format_3464 http://dl.acm.org/citation.cfm?id=2391150 1.16 http://www.pubannotation.org/docs/annotation-format/ format_3781 http://www.pubannotation.org/docs/annotation-format/ JSON format of annotated scientific text used by PubAnnotations and other tools. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3782 BioC BioC is a standardised XML format for sharing and integrating text data and annotations. FALSE http://edamontology.org/format_2332|http://edamontology.org/format_3780 http://doi.org/10.1093/database/bat064 1.16 http://bioc.sourceforge.net/ format_3782 http://bioc.sourceforge.net/ BioC is a standardised XML format for sharing and integrating text data and annotations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3783 PubTator format Native textual export format of annotated scientific text from PubTator. FALSE http://edamontology.org/format_3780|http://edamontology.org/format_2330 http://doi.org/10.1093/database/bas041|http://doi.org/10.1093/nar/gkt441 1.16 https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/tutorial/ format_3783 https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/tutorial/ Native textual export format of annotated scientific text from PubTator. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3784 Open Annotation format "A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD." FALSE http://edamontology.org/format_3780|http://edamontology.org/format_2376|http://edamontology.org/format_3749 1.16 http://www.openannotation.org/spec/core/core.html format_3784 http://www.openannotation.org/spec/core/core.html "A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3785 BioNLP Shared Task format BRAT standoff format|BRAT format "A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar." FALSE http://edamontology.org/format_3780|http://edamontology.org/format_2330 1.16 http://2013.bionlp-st.org/file-formats|http://2011.bionlp-st.org/home/file-formats|http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/detail.shtml#format|http://brat.nlplab.org/standoff.html|https://github.com/nlplab/brat/wiki/Annotation-Data-Format http://brat.nlplab.org/examples.html|http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/detail.shtml#format format_3785 http://2013.bionlp-st.org/file-formats|http://2011.bionlp-st.org/home/file-formats|http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/detail.shtml#format|http://brat.nlplab.org/standoff.html|https://github.com/nlplab/brat/wiki/Annotation-Data-Format "A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar." BRAT standoff format|BRAT format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3787 Query language Query format A query language (format) for structured database queries. FALSE http://edamontology.org/format_2350 1.16 format_3787 A query language (format) for structured database queries. Query format http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats Not recommended for annotation in bio.tools. http://edamontology.org/format_3788 SQL Structured Query Language SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. FALSE http://edamontology.org/format_2330 1.16 sql format_3788 http://www.iana.org/assignments/media-types/application/sql|http://filext.com/file-extension/SQL SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. Structured Query Language http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://www.iana.org/assignments/media-types/application/sql http://edamontology.org/format_3789 XQuery XML Query "XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.)." FALSE http://edamontology.org/format_2330 1.16 https://www.w3.org/XML/Query/ xq|xqy|xquery format_3789 https://www.w3.org/XML/Query/ "XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.)." XML Query http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3790 SPARQL SPARQL Protocol and RDF Query Language SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. FALSE http://edamontology.org/format_2330 1.16 https://www.w3.org/TR/sparql11-query/ format_3790 https://www.w3.org/TR/sparql11-query/ SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. SPARQL Protocol and RDF Query Language http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/format_3804 xsd XML format for XML Schema. FALSE http://edamontology.org/format_2332 1.17 format_3804 XML format for XML Schema. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#formats http://edamontology.org/operation_0004 Operation Function|Computational procedure|Computational subroutine|Computational operation|Function (programming)|Lambda abstraction|Mathematical function|Mathematical operation|Computational method|Computational tool|sumo:Function|Process "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." FALSE http://www.w3.org/2002/07/owl#Thing beta12orEarlier operation_0004 Function "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs)." Computational procedure|Computational subroutine|Computational operation|Function (programming)|Lambda abstraction|Mathematical function|Mathematical operation|Computational method Computational tool|sumo:Function|Process http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_0224 Query and retrieval Database retrieval|Query Search or query a data resource and retrieve entries and / or annotation. FALSE http://edamontology.org/operation_2409 beta12orEarlier operation_0224 Search or query a data resource and retrieve entries and / or annotation. Database retrieval Query http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0225 Data retrieval (database cross-reference) Search database to retrieve all relevant references to a particular entity or entry. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0225 http://edamontology.org/operation_2422 Search database to retrieve all relevant references to a particular entity or entry. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0226 Annotation "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.|This is a broad concept and is used a placeholder for other, more specific concepts." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_0226 Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_0227 Indexing Database indexing|Data indexing Generate an index of (typically a file of) biological data. FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_0227 Generate an index of (typically a file of) biological data. Database indexing|Data indexing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_0228 Data index analysis Analyse an index of biological data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0228 http://edamontology.org/operation_0227 Analyse an index of biological data. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0229 Annotation retrieval (sequence) Retrieve basic information about a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0229 http://edamontology.org/operation_2422 Retrieve basic information about a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0230 Sequence generation Generate a molecular sequence by some means. FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_2403 beta12orEarlier operation_0230 Generate a molecular sequence by some means. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0231 Sequence editing "Edit or change a molecular sequence, either randomly or specifically." FALSE http://edamontology.org/operation_3096|http://edamontology.org/operation_2403 beta12orEarlier operation_0231 "Edit or change a molecular sequence, either randomly or specifically." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0232 Sequence merging Sequence splicing|Paired-end stitching|Read merging|Read stitching|Paired-end merging Merge two or more (typically overlapping) molecular sequences. FALSE http://edamontology.org/operation_0231 beta12orEarlier operation_0232 Merge two or more (typically overlapping) molecular sequences. Sequence splicing Paired-end stitching|Read merging|Read stitching|Paired-end merging http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0233 Sequence conversion Convert a molecular sequence from one type to another. FALSE http://edamontology.org/operation_3434|http://edamontology.org/operation_0231 beta12orEarlier operation_0233 Convert a molecular sequence from one type to another. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0234 Sequence complexity calculation "Calculate sequence complexity, for example to find low-complexity regions in sequences." FALSE http://edamontology.org/operation_0236 beta12orEarlier operation_0234 "Calculate sequence complexity, for example to find low-complexity regions in sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0235 Sequence ambiguity calculation "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." FALSE http://edamontology.org/operation_0236 beta12orEarlier operation_0235 "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0236 Sequence composition calculation Calculate character or word composition or frequency of a molecular sequence. FALSE http://edamontology.org/operation_3438|http://edamontology.org/operation_2403 beta12orEarlier operation_0236 Calculate character or word composition or frequency of a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0237 Repeat sequence analysis "Find and/or analyse repeat sequences in (typically nucleotide) sequences.|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." FALSE http://edamontology.org/operation_2403 beta12orEarlier operation_0237 Find and/or analyse repeat sequences in (typically nucleotide) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0238 Sequence motif discovery Motif discovery Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).|Motifs and patterns might be conserved or over-represented (occur with improbable frequency). FALSE http://edamontology.org/operation_0253|http://edamontology.org/operation_2404 beta12orEarlier operation_0238 Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). Motif discovery http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0239 Sequence motif recognition Sequence signature detection|Sequence signature recognition|Motif scanning|Sequence motif search|Motif detection|Motif search|Sequence profile search|Motif recognition|Sequence motif detection "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." FALSE http://edamontology.org/operation_0253|http://edamontology.org/operation_2404 beta12orEarlier operation_0239 "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." Sequence signature detection|Sequence signature recognition|Motif scanning Sequence motif search|Motif detection|Motif search|Sequence profile search|Motif recognition|Sequence motif detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0240 Sequence motif comparison Find motifs shared by molecular sequences. FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_2404 beta12orEarlier operation_0240 Find motifs shared by molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0241 Transcription regulatory sequence analysis "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.|For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0241 http://edamontology.org/operation_0438 "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0242 Conserved transcription regulatory sequence identification "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).|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." FALSE http://edamontology.org/operation_0438|http://edamontology.org/operation_0415 beta12orEarlier operation_0242 "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0243 Protein property calculation (from structure) "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0243 "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0250 1.18 http://edamontology.org/operation_2406|http://edamontology.org/operation_0250 http://edamontology.org/operation_0244 Protein flexibility and motion analysis "Analyse flexibility and motion in protein structure.|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." FALSE http://edamontology.org/operation_2476|http://edamontology.org/operation_0250 beta12orEarlier operation_0244 Analyse flexibility and motion in protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0245 Protein structural motif recognition Protein structural feature identification "Identify or screen for 3D structural motifs in protein structure(s).|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." FALSE http://edamontology.org/operation_2406|http://edamontology.org/operation_3092 beta12orEarlier operation_0245 Identify or screen for 3D structural motifs in protein structure(s). Protein structural feature identification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0246 Protein domain recognition Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). FALSE http://edamontology.org/operation_2406|http://edamontology.org/operation_3092 beta12orEarlier operation_0246 Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0247 Protein architecture analysis Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). FALSE http://edamontology.org/operation_2406 beta12orEarlier operation_0247 Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0248 Residue interaction calculation "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0248 WHATIF:ListContactsRelaxed|WHATIF: SymShellTwoXML|WHATIF: SymShellOneXML|WHATIF:ListSideChainContactsRelaxed|WHATIF:ListSideChainContactsNormal|WHATIF:ListContactsNormal|WHATIF: SymShellTenXML|WHATIF: SymShellFiveXML "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0249 Protein geometry calculation Cysteine torsion angle calculation|Torsion angle calculation|Backbone torsion angle calculation|Tau angle calculation "Calculate, visualise or analyse phi/psi angles of a protein structure." FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0249 WHATIF:CysteineTorsions|WHATIF:ResidueTorsions|WHATIF:ShowTauAngle|WHATIF:ResidueTorsionsBB "Calculate, visualise or analyse phi/psi angles of a protein structure." Cysteine torsion angle calculation|Torsion angle calculation|Backbone torsion angle calculation|Tau angle calculation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0250 Protein property calculation Protein property rendering|Protein property calculation (from structure)|Protein structural property calculation|Protein property calculation (from sequence) "Extract, calculate or predict non-positional (physical or chemical) properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence or 3D structure. |This includes methods to render and visualise the properties of a protein sequence, and a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc." FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_2502|http://edamontology.org/operation_3438 beta12orEarlier operation_0250 "Extract, calculate or predict non-positional (physical or chemical) properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence or 3D structure. " Protein property rendering Protein property calculation (from structure)|Protein structural property calculation|Protein property calculation (from sequence) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0252 Peptide immunogenicity prediction Immunogenicity prediction|Hopp and Woods plotting|MHC peptide immunogenicity prediction "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.|This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot.|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." FALSE http://edamontology.org/operation_2492|http://edamontology.org/operation_0250 beta12orEarlier operation_0252 "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." Immunogenicity prediction Hopp and Woods plotting|MHC peptide immunogenicity prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0253 Sequence feature detection Sequence feature recognition|Sequence feature prediction|Motif database search|SO:0000110 "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.|Look at ""Protein feature detection"" (http://edamontology.org/operation_3092) and ""Nucleic acid feature detection"" (http://edamontology.org/operation_0415) in case more specific terms are needed." FALSE http://edamontology.org/operation_2423|http://edamontology.org/operation_2403 beta12orEarlier operation_0253 "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." Sequence feature recognition|Sequence feature prediction Motif database search SO:0000110 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0254 Data retrieval (feature table) Extract a sequence feature table from a sequence database entry. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0254 http://edamontology.org/operation_2422 Extract a sequence feature table from a sequence database entry. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0255 Feature table query Query the features (in a feature table) of molecular sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0255 http://edamontology.org/operation_2422 Query the features (in a feature table) of molecular sequence(s). http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0256 Sequence feature comparison Feature comparison|Feature table comparison Compare the feature tables of two or more molecular sequences. FALSE http://edamontology.org/operation_2424|http://edamontology.org/operation_2403 beta12orEarlier operation_0256 Compare the feature tables of two or more molecular sequences. Feature comparison|Feature table comparison http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0257 Data retrieval (sequence alignment) Display basic information about a sequence alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0257 http://edamontology.org/operation_2422 Display basic information about a sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0258 Sequence alignment analysis Analyse a molecular sequence alignment. FALSE http://edamontology.org/operation_2403 beta12orEarlier operation_0258 Analyse a molecular sequence alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0259 Sequence alignment comparison Compare (typically by aligning) two molecular sequence alignments.|See also 'Sequence profile alignment'. FALSE http://edamontology.org/operation_0258|http://edamontology.org/operation_2424 beta12orEarlier operation_0259 Compare (typically by aligning) two molecular sequence alignments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0260 Sequence alignment conversion Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). FALSE http://edamontology.org/operation_3434|http://edamontology.org/operation_3081 beta12orEarlier operation_0260 Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0261 Nucleic acid property processing Process (read and / or write) physicochemical property data of nucleic acids. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0261 http://edamontology.org/operation_0262 Process (read and / or write) physicochemical property data of nucleic acids. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0262 Nucleic acid property calculation "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." FALSE http://edamontology.org/operation_2478|http://edamontology.org/operation_3438 beta12orEarlier operation_0262 "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0264 Splice transcript prediction Predict splicing alternatives or transcript isoforms from analysis of sequence data. FALSE http://edamontology.org/operation_2499 beta12orEarlier operation_0264 Predict splicing alternatives or transcript isoforms from analysis of sequence data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0265 Frameshift detection Frameshift error detection "Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.|Methods include sequence alignment (if related sequences are available) and word-based sequence comparison." FALSE http://edamontology.org/operation_3195|http://edamontology.org/operation_3202 beta12orEarlier operation_0265 "Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects." Frameshift error detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0266 Vector sequence detection "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_0415 beta12orEarlier operation_0266 "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0267 Protein secondary structure prediction Secondary structure prediction (protein) "Predict secondary structure of protein sequences.|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." FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_3092|http://edamontology.org/operation_2479 beta12orEarlier operation_0267 Predict secondary structure of protein sequences. Secondary structure prediction (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0268 Protein super-secondary structure prediction "Predict super-secondary structure of protein sequence(s).|Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc." FALSE http://edamontology.org/operation_0267 beta12orEarlier operation_0268 Predict super-secondary structure of protein sequence(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0269 Transmembrane protein prediction Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. FALSE http://edamontology.org/operation_0267|http://edamontology.org/operation_0270 beta12orEarlier operation_0269 Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0270 Transmembrane protein analysis "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.|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)." FALSE http://edamontology.org/operation_2502 beta12orEarlier operation_0270 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0271 Structure prediction Predict tertiary structure of a molecular (biopolymer) sequence. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2423 beta12orEarlier operation_0271 Predict tertiary structure of a molecular (biopolymer) sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0272 Residue interaction prediction "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.|Methods usually involve multiple sequence alignment analysis." FALSE http://edamontology.org/operation_2479|http://edamontology.org/operation_0250 beta12orEarlier operation_0272 "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0273 Protein interaction raw data analysis "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." FALSE http://edamontology.org/operation_2949 beta12orEarlier operation_0273 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0274 Protein-protein interaction prediction (from protein sequence) "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0274 "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2464 1.12 http://edamontology.org/operation_0275 Protein-protein interaction prediction (from protein structure) "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0275 "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2464 1.12 http://edamontology.org/operation_0276 Protein interaction network analysis Analyse a network of protein interactions. FALSE http://edamontology.org/operation_2497|http://edamontology.org/operation_2949 beta12orEarlier operation_0276 Analyse a network of protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0277 Protein interaction network comparison Compare two or more networks of protein interactions. FALSE http://edamontology.org/operation_0276|http://edamontology.org/operation_1778 beta12orEarlier operation_0277 Compare two or more networks of protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0278 RNA secondary structure prediction RNA shape prediction "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).|Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding)." FALSE http://edamontology.org/operation_2439|http://edamontology.org/operation_0415|http://edamontology.org/operation_0279 beta12orEarlier operation_0278 "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." RNA shape prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0279 Nucleic acid folding analysis Nucleic acid folding|Nucleic acid folding prediction|Nucleic acid folding modelling "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_2426|http://edamontology.org/operation_2481 beta12orEarlier operation_0279 "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." Nucleic acid folding|Nucleic acid folding prediction|Nucleic acid folding modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0280 Data retrieval (restriction enzyme annotation) Retrieve information on restriction enzymes or restriction enzyme sites. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0280 http://edamontology.org/operation_2422 Retrieve information on restriction enzymes or restriction enzyme sites. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0281 Genetic marker identification "Identify genetic markers in DNA sequences.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0281 http://edamontology.org/operation_0415 Identify genetic markers in DNA sequences. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0282 Genetic mapping Genetic map construction|Functional mapping|Linkage mapping|Genetic map generation|QTL mapping "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.|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.|This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs)." FALSE http://edamontology.org/operation_2520|http://edamontology.org/operation_3429 beta12orEarlier operation_0282 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. Genetic map construction|Functional mapping|Linkage mapping|Genetic map generation QTL mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0283 Linkage analysis "Analyse genetic linkage.|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." FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_0283 Analyse genetic linkage. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0284 Codon usage table generation Codon usage table construction Calculate codon usage statistics and create a codon usage table. FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_0286 beta12orEarlier operation_0284 Calculate codon usage statistics and create a codon usage table. Codon usage table construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0285 Codon usage table comparison Compare two or more codon usage tables. FALSE http://edamontology.org/operation_2998|http://edamontology.org/operation_0286 beta12orEarlier operation_0285 Compare two or more codon usage tables. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0286 Codon usage analysis synon: Codon usage table analysis|synon: Codon usage data analysis "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_0286 "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." synon: Codon usage table analysis|synon: Codon usage data analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0287 Base position variability plotting Identify and plot third base position variability in a nucleotide sequence. FALSE http://edamontology.org/operation_3441|http://edamontology.org/operation_0286 beta12orEarlier operation_0287 Identify and plot third base position variability in a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0288 Sequence word comparison Find exact character or word matches between molecular sequences without full sequence alignment. FALSE http://edamontology.org/operation_2451 beta12orEarlier operation_0288 Find exact character or word matches between molecular sequences without full sequence alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0289 Sequence distance matrix generation Phylogenetic distance matrix generation|Sequence distance matrix construction Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_3429 beta12orEarlier operation_0289 Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. Phylogenetic distance matrix generation|Sequence distance matrix construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0290 Sequence redundancy removal "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." FALSE http://edamontology.org/operation_2451 beta12orEarlier operation_0290 "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0291 Sequence clustering Sequence cluster construction|Sequence cluster generation "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.|The clusters may be output or used internally for some other purpose." FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_3429|http://edamontology.org/operation_3432 beta12orEarlier operation_0291 "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." Sequence cluster construction|Sequence cluster generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0292 Sequence alignment Sequence alignment construction|Sequence alignment generation|Consensus-based sequence alignment Align (identify equivalent sites within) molecular sequences. FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_2928|http://edamontology.org/operation_2403 beta12orEarlier operation_0292 Align (identify equivalent sites within) molecular sequences. Sequence alignment construction|Sequence alignment generation Consensus-based sequence alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0293 Hybrid sequence alignment construction "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0293 http://edamontology.org/operation_0292 "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0294 Structure-based sequence alignment Sequence alignment generation (structure-based)|Structure-based sequence alignment construction|Structure-based sequence alignment generation|Sequence alignment (structure-based) Align molecular sequences using sequence and structural information. FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0294 Align molecular sequences using sequence and structural information. Sequence alignment generation (structure-based)|Structure-based sequence alignment construction|Structure-based sequence alignment generation|Sequence alignment (structure-based) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0295 Structure alignment Align (superimpose) molecular tertiary structures. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2483|http://edamontology.org/operation_2928 beta12orEarlier operation_0295 Align (superimpose) molecular tertiary structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0296 Sequence profile generation Sequence profile construction Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_0258 beta12orEarlier operation_0296 Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. Sequence profile construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0297 3D profile generation Structural profile construction|Structural profile generation Generate some type of structural (3D) profile or template from a structure or structure alignment. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_3429 beta12orEarlier operation_0297 Generate some type of structural (3D) profile or template from a structure or structure alignment. Structural profile construction|Structural profile generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0298 Profile-profile alignment Sequence profile alignment|Profile-to-profile alignment "Align sequence profiles (representing sequence alignments).|Methods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'." FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0298 Align sequence profiles (representing sequence alignments). Sequence profile alignment|Profile-to-profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0299 3D profile-to-3D profile alignment 3D profile alignment|Structural profile alignment "Align structural (3D) profiles or templates (representing structures or structure alignments).|Methods might perform one-to-one, one-to-many or many-to-many comparisons." FALSE http://edamontology.org/operation_0295 beta12orEarlier operation_0299 Align structural (3D) profiles or templates (representing structures or structure alignments). 3D profile alignment|Structural profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0300 Sequence-to-profile alignment Sequence-profile alignment "Align molecular sequence(s) to sequence profile(s).|A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons." FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0300 Align molecular sequence(s) to sequence profile(s). Sequence-profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0301 Sequence-to-3D-profile alignment Sequence-3D profile alignment "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).|Methods might perform one-to-one, one-to-many or many-to-many comparisons." FALSE http://edamontology.org/operation_0303|http://edamontology.org/operation_2928 beta12orEarlier operation_0301 Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). Sequence-3D profile alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0302 Protein threading Sequence-structure alignment "Align molecular sequence to structure in 3D space (threading).|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." FALSE http://edamontology.org/operation_0303|http://edamontology.org/operation_2928 beta12orEarlier operation_0302 Align molecular sequence to structure in 3D space (threading). Sequence-structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0303 Protein fold recognition Protein fold prediction|Protein domain prediction "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).|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." FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_2406|http://edamontology.org/operation_3092|http://edamontology.org/operation_2479 beta12orEarlier operation_0303 Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). Protein fold prediction|Protein domain prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0304 Metadata retrieval "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.|This includes documentation, general information and other metadata on entities such as databases, database entries and tools." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved." operation_0304 "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2422 1.17 http://edamontology.org/operation_2422 http://edamontology.org/operation_0305 Literature search "Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics." FALSE http://edamontology.org/operation_2421 beta12orEarlier operation_0305 "Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0306 Text mining Text analysis|Literature mining|Text analytics|Text data mining|Article analysis|Literature analysis Process and analyse text (typically scientific literature) to extract information from it. FALSE http://edamontology.org/operation_2945|http://edamontology.org/operation_2423 beta12orEarlier operation_0306 Text analysis Process and analyse text (typically scientific literature) to extract information from it. Literature mining|Text analytics|Text data mining Article analysis|Literature analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0307 Virtual PCR Perform in-silico (virtual) PCR. FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_0307 Perform in-silico (virtual) PCR. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0308 PCR primer design PCR primer prediction|PCR primer design (for genotyping polymorphisms)|PCR primer design (for methylation PCRs)|PCR primer design (for large scale sequencing)|PCR primer design (for gene transcription profiling)|PCR primer design (based on gene structure)|PCR primer design (for conserved primers) "Design or predict oligonucleotide primers for PCR and DNA amplification etc.|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.|This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs." FALSE http://edamontology.org/operation_2419 beta12orEarlier operation_0308 Design or predict oligonucleotide primers for PCR and DNA amplification etc. PCR primer prediction PCR primer design (for genotyping polymorphisms)|PCR primer design (for methylation PCRs)|PCR primer design (for large scale sequencing)|PCR primer design (for gene transcription profiling)|PCR primer design (based on gene structure)|PCR primer design (for conserved primers) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0309 Microarray probe design Microarray probe prediction "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." FALSE http://edamontology.org/operation_2419|http://edamontology.org/operation_2430 beta12orEarlier operation_0309 "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." Microarray probe prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0310 Sequence assembly Metagenomic assembly|Sequence assembly editing "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.|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." FALSE http://edamontology.org/operation_2478|http://edamontology.org/operation_3433 beta12orEarlier operation_0310 Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. Metagenomic assembly|Sequence assembly editing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0311 Microarray data standardisation and normalisation Standardize or normalize microarray data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0311 Standardize or normalize microarray data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3435 1.16 http://edamontology.org/operation_0312 Sequencing-based expression profile data processing "Process (read and / or write) SAGE, MPSS or SBS experimental data." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0312 http://edamontology.org/operation_2495 "Process (read and / or write) SAGE, MPSS or SBS experimental data." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0313 Gene expression profile clustering "Perform cluster analysis of gene expression data to identify groups with similar gene-expression profiles, for example by clustering." FALSE http://edamontology.org/operation_0315|http://edamontology.org/operation_3432 beta12orEarlier operation_0313 "Perform cluster analysis of gene expression data to identify groups with similar gene-expression profiles, for example by clustering." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0314 Gene expression profiling Gene expression quantification|Gene expression profile construction|Gene expression profile generation|Metagenomic inference|RNA profiling|mRNA profiling|Gene transcription profiling|Non-coding RNA profiling|Functional profiling|Protein profiling "The measurement of the gene expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function.|Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function.|Gene expression profiling generates some sort of gene expression profile, for example from microarray data." FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_2495 beta12orEarlier operation_0314 Gene expression quantification "The measurement of the gene expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function." Gene expression profile construction|Gene expression profile generation Metagenomic inference|RNA profiling|mRNA profiling|Gene transcription profiling|Non-coding RNA profiling Functional profiling|Protein profiling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0315 Gene expression profile comparison Comparison of gene expression profiles. FALSE http://edamontology.org/operation_2998|http://edamontology.org/operation_2495 beta12orEarlier operation_0315 Comparison of gene expression profiles. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0316 Functional profiling Interpret (in functional terms) and annotate gene expression data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0316 Interpret (in functional terms) and annotate gene expression data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2495 beta12orEarlier http://edamontology.org/operation_0317 EST and cDNA sequence analysis "Analyse EST or cDNA sequences.|For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0317 http://edamontology.org/operation_2403 Analyse EST or cDNA sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0318 Structural genomics target selection Identify and select targets for protein structural determination.|Methods will typically navigate a graph of protein families of known structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0318 http://edamontology.org/operation_2406 Identify and select targets for protein structural determination. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0319 Protein secondary structure assignment Assign secondary structure from protein coordinate or experimental data. FALSE http://edamontology.org/operation_3023 beta12orEarlier operation_0319 "Includes secondary structure assignment from circular dichroism (CD) spectroscopic data, and from protein coordinate data." Assign secondary structure from protein coordinate or experimental data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0320 Protein structure assignment Assign a protein tertiary structure (3D coordinates) from raw experimental data. FALSE http://edamontology.org/operation_2406|http://edamontology.org/operation_2502 beta12orEarlier operation_0320 Assign a protein tertiary structure (3D coordinates) from raw experimental data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0321 Protein model validation Protein structure validation|Residue validation "Evaluate the quality or correctness a protein three-dimensional model.|This includes methods that calculate poor quality residues. 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).|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.|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." FALSE http://edamontology.org/operation_2428|http://edamontology.org/operation_2406 beta12orEarlier operation_0321 WHATIF: UseFileDB|WHATIF: CorrectedPDBasXML|WHATIF: UseResidueDB Evaluate the quality or correctness a protein three-dimensional model. Protein structure validation Residue validation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0322 Molecular model refinement Protein model refinement "Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc." FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2425 beta12orEarlier operation_0322 WHATIF: CorrectedPDBasXML "Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc." Protein model refinement http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0323 Phylogenetic tree generation Phylogenetic tree construction Construct a phylogenetic tree.|Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. FALSE http://edamontology.org/operation_0324|http://edamontology.org/operation_3429 beta12orEarlier operation_0323 Construct a phylogenetic tree. Phylogenetic tree construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0324 Phylogenetic tree analysis "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_0324 "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0325 Phylogenetic tree comparison "Compare two or more phylogenetic trees.|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." FALSE http://edamontology.org/operation_0324|http://edamontology.org/operation_2424 beta12orEarlier operation_0325 Compare two or more phylogenetic trees. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0326 Phylogenetic tree editing Edit a phylogenetic tree. FALSE http://edamontology.org/operation_0324|http://edamontology.org/operation_3096 beta12orEarlier operation_0326 Edit a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0327 Phylogenetic footprinting / shadowing "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).|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." FALSE http://edamontology.org/operation_0540 beta12orEarlier operation_0327 "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0328 Protein folding simulation Simulate the folding of a protein. FALSE http://edamontology.org/operation_2415 beta12orEarlier operation_0328 Simulate the folding of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0329 Protein folding pathway prediction Predict the folding pathway(s) or non-native structural intermediates of a protein. FALSE http://edamontology.org/operation_2415|http://edamontology.org/operation_3023 beta12orEarlier operation_0329 Predict the folding pathway(s) or non-native structural intermediates of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0330 Protein SNP mapping Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0330 Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0331 1.12 http://edamontology.org/operation_0331 Protein modelling (mutation) Protein mutation modelling|Rotamer likelihood prediction|Protein SNP mapping "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.|This includes 1) rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. 2) Protein SNP mapping, which maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations." FALSE http://edamontology.org/operation_0477|http://edamontology.org/operation_3023 beta12orEarlier operation_0331 "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." Protein mutation modelling Rotamer likelihood prediction|Protein SNP mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0332 Immunogen design Design molecules that elicit an immune response (immunogens). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0332 Design molecules that elicit an immune response (immunogens). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0252 beta12orEarlier http://edamontology.org/operation_0333 Zinc finger prediction Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0333 Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0420 1.18 http://edamontology.org/operation_0420 http://edamontology.org/operation_0334 Enzyme kinetics calculation "Calculate Km, Vmax and derived data for an enzyme reaction." FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0334 "Calculate Km, Vmax and derived data for an enzyme reaction." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0335 Formatting File reformatting|File format conversion|Format conversion|Reformatting|File formatting Reformat a file of data (or equivalent entity in memory). FALSE http://edamontology.org/operation_2409 beta12orEarlier operation_0335 Reformat a file of data (or equivalent entity in memory). File reformatting|File format conversion|Format conversion|Reformatting|File formatting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0336 Format validation File format validation Test and validate the format and content of a data file. FALSE http://edamontology.org/operation_2428 beta12orEarlier operation_0336 Test and validate the format and content of a data file. File format validation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0337 Visualisation Rendering "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_0337 "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." Rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_0338 Sequence database search "Search a sequence database by sequence comparison and retrieve similar sequences. sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.|This excludes direct retrieval methods (e.g. the dbfetch program)." FALSE http://edamontology.org/operation_2421|http://edamontology.org/operation_2403 beta12orEarlier operation_0338 "Search a sequence database by sequence comparison and retrieve similar sequences. sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0339 Structure database search "Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data." FALSE http://edamontology.org/operation_2421 beta12orEarlier operation_0339 "Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0340 Protein secondary database search Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0340 Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3092 1.8 http://edamontology.org/operation_0341 Motif database search Screen a sequence against a motif or pattern database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0341 http://edamontology.org/operation_0253 Screen a sequence against a motif or pattern database. http://purl.obolibrary.org/obo/edam#obsolete 1.8 http://edamontology.org/operation_0342 Sequence profile database search Search a database of sequence profiles with a query sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0342 http://edamontology.org/operation_0239 Search a database of sequence profiles with a query sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/operation_0343 Transmembrane protein database search "Search a database of transmembrane proteins, for example for sequence or structural similarities." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0343 http://edamontology.org/operation_2421 "Search a database of transmembrane proteins, for example for sequence or structural similarities." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0344 Sequence retrieval (by code) Query a database and retrieve sequences with a given entry code or accession number. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0344 http://edamontology.org/operation_2422 Query a database and retrieve sequences with a given entry code or accession number. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0345 Sequence retrieval (by keyword) Query a database and retrieve sequences containing a given keyword. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0345 http://edamontology.org/operation_2422 Query a database and retrieve sequences containing a given keyword. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0346 Sequence similarity search Sequence database search (by sequence)|Structure database search (by sequence) Search a sequence database and retrieve sequences that are similar to a query sequence. FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_0338|http://edamontology.org/operation_0339 beta12orEarlier operation_0346 Search a sequence database and retrieve sequences that are similar to a query sequence. Sequence database search (by sequence)|Structure database search (by sequence) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0347 Sequence database search (by motif or pattern) "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0347 "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0239 1.8 http://edamontology.org/operation_0348 Sequence database search (by amino acid composition) Search a sequence database and retrieve sequences of a given amino acid composition. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0348 http://edamontology.org/operation_0338 Search a sequence database and retrieve sequences of a given amino acid composition. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0349 Sequence database search (by property) "Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property." FALSE http://edamontology.org/operation_0338 beta12orEarlier operation_0349 "Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0350 Sequence database search (by sequence using word-based methods) "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0350 http://edamontology.org/operation_0346 Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0351 Sequence database search (by sequence using profile-based methods) "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.|This includes tools based on PSI-BLAST." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0351 http://edamontology.org/operation_0346 "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://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0352 Sequence database search (by sequence using local alignment-based methods) Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.|This includes tools based on the Smith-Waterman algorithm or FASTA. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0352 http://edamontology.org/operation_0346 Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0353 Sequence database search (by sequence using global alignment-based methods) Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.|This includes tools based on the Needleman and Wunsch algorithm. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0353 http://edamontology.org/operation_0346 Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0354 Sequence database search (by sequence for primer sequences) Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.|STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0354 http://edamontology.org/operation_0346 Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0355 Sequence database search (by molecular weight) "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0355 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2929 1.6 http://edamontology.org/operation_0356 Sequence database search (by isoelectric point) Search sequence(s) or a sequence database for sequences of a given isoelectric point. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0356 http://edamontology.org/operation_0338 Search sequence(s) or a sequence database for sequences of a given isoelectric point. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0357 Structure retrieval (by code) Query a tertiary structure database and retrieve entries with a given entry code or accession number. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0357 http://edamontology.org/operation_2422 Query a tertiary structure database and retrieve entries with a given entry code or accession number. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0358 Structure retrieval (by keyword) Query a tertiary structure database and retrieve entries containing a given keyword. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0358 http://edamontology.org/operation_2422 Query a tertiary structure database and retrieve entries containing a given keyword. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0359 Structure database search (by sequence) Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0359 Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0346 1.8 http://edamontology.org/operation_0360 Structural similarity search Structure database search (by structure)|Structure retrieval by structure Search a database of molecular structure and retrieve structures that are similar to a query structure. FALSE http://edamontology.org/operation_2483|http://edamontology.org/operation_0339 beta12orEarlier operation_0360 Search a database of molecular structure and retrieve structures that are similar to a query structure. Structure database search (by structure)|Structure retrieval by structure http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0361 Sequence annotation Annotate a molecular sequence record with terms from a controlled vocabulary. FALSE http://edamontology.org/operation_0226 beta12orEarlier operation_0361 Annotate a molecular sequence record with terms from a controlled vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0362 Genome annotation Metagenome annotation Annotate a genome sequence with terms from a controlled vocabulary. FALSE http://edamontology.org/operation_0361 beta12orEarlier operation_0362 Annotate a genome sequence with terms from a controlled vocabulary. Metagenome annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0363 Nucleic acid sequence reverse and complement Generate the reverse and / or complement of a nucleotide sequence. FALSE http://edamontology.org/operation_2513 beta12orEarlier operation_0363 Generate the reverse and / or complement of a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0364 Random sequence generation "Generate a random sequence, for example, with a specific character composition." FALSE http://edamontology.org/operation_0230 beta12orEarlier operation_0364 "Generate a random sequence, for example, with a specific character composition." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0365 Nucleic acid restriction digest Generate digest fragments for a nucleotide sequence containing restriction sites. FALSE http://edamontology.org/operation_0262|http://edamontology.org/operation_2513 beta12orEarlier operation_0365 Generate digest fragments for a nucleotide sequence containing restriction sites. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0366 Protein sequence cleavage Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. FALSE http://edamontology.org/operation_2514|http://edamontology.org/operation_0250 beta12orEarlier operation_0366 Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0367 Sequence mutation and randomisation Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. FALSE http://edamontology.org/operation_0231 beta12orEarlier operation_0367 Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0368 Sequence masking "Mask characters in a molecular sequence (replacing those characters with a mask character).|For example, SNPs or repeats in a DNA sequence might be masked." FALSE http://edamontology.org/operation_0231 beta12orEarlier operation_0368 Mask characters in a molecular sequence (replacing those characters with a mask character). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0369 Sequence cutting Cut (remove) characters or a region from a molecular sequence. FALSE http://edamontology.org/operation_0231 beta12orEarlier operation_0369 Cut (remove) characters or a region from a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0370 Restriction site creation "Create (or remove) restriction sites in sequences, for example using silent mutations." FALSE http://edamontology.org/operation_0231 beta12orEarlier operation_0370 "Create (or remove) restriction sites in sequences, for example using silent mutations." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0371 DNA translation Translate a DNA sequence into protein. FALSE http://edamontology.org/operation_0233 beta12orEarlier operation_0371 Translate a DNA sequence into protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0372 DNA transcription Transcribe a nucleotide sequence into mRNA sequence(s). FALSE http://edamontology.org/operation_0233 beta12orEarlier operation_0372 Transcribe a nucleotide sequence into mRNA sequence(s). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0377 Sequence composition calculation (nucleic acid) Calculate base frequency or word composition of a nucleotide sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0377 Calculate base frequency or word composition of a nucleotide sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0236 1.8 http://edamontology.org/operation_0378 Sequence composition calculation (protein) Calculate amino acid frequency or word composition of a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0378 Calculate amino acid frequency or word composition of a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0236 1.8 http://edamontology.org/operation_0379 Repeat sequence detection Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. FALSE http://edamontology.org/operation_0415|http://edamontology.org/operation_0237 beta12orEarlier operation_0379 Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0380 Repeat sequence organisation analysis Analyse repeat sequence organisation such as periodicity. FALSE http://edamontology.org/operation_0237|http://edamontology.org/operation_0236 beta12orEarlier operation_0380 Analyse repeat sequence organisation such as periodicity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0383 Protein hydropathy calculation (from structure) "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0383 "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2574 1.12 http://edamontology.org/operation_0384 Accessible surface calculation Protein solvent accessibility calculation "Calculate solvent accessible or buried surface areas in protein or other molecular structures.|Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain)." FALSE http://edamontology.org/operation_3351 beta12orEarlier operation_0384 WHATIF:AtomAccessibilitySolventPlus|WHATIF:AtomAccessibilitySolvent Calculate solvent accessible or buried surface areas in protein or other molecular structures. Protein solvent accessibility calculation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0385 Protein hydropathy cluster calculation Identify clusters of hydrophobic or charged residues in a protein structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0385 Identify clusters of hydrophobic or charged residues in a protein structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0393 1.12 http://edamontology.org/operation_0386 Protein dipole moment calculation Calculate whether a protein structure has an unusually large net charge (dipole moment). FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0386 Calculate whether a protein structure has an unusually large net charge (dipole moment). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0387 Molecular surface calculation Protein atom surface calculation|Protein surface and interior calculation|Protein residue surface calculation|Protein surface calculation Calculate the molecular surface area in proteins and other macromolecules. FALSE http://edamontology.org/operation_3351 beta12orEarlier operation_0387 WHATIF:TotAccessibilityMolecular|WHATIF:TotAccessibilitySolvent|WHATIF:AtomAccessibilityMolecularPlus|WHATIF:ResidueAccessibilitySolvent|WHATIF:AtomAccessibilityMolecular|WHATIF:ResidueAccessibilityMolecular|WHATIF:ResidueAccessibilityVacuum|WHATIF:ResidueAccessibilityVacuumMolecular Calculate the molecular surface area in proteins and other macromolecules. Protein atom surface calculation|Protein surface and interior calculation|Protein residue surface calculation|Protein surface calculation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0388 Protein binding site prediction (from structure) "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0388 "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2575 1.12 http://edamontology.org/operation_0389 Protein-nucleic acid binding site analysis Analyse RNA or DNA-binding sites in protein structure. FALSE http://edamontology.org/operation_2949 beta12orEarlier operation_0389 Analyse RNA or DNA-binding sites in protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0390 Protein peeling Decompose a structure into compact or globular fragments (protein peeling). FALSE http://edamontology.org/operation_0246 beta12orEarlier operation_0390 Decompose a structure into compact or globular fragments (protein peeling). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0391 Protein distance matrix calculation Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. FALSE http://edamontology.org/operation_2950 beta12orEarlier operation_0391 Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0392 Protein contact map calculation Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. FALSE http://edamontology.org/operation_0391 beta12orEarlier operation_0392 Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0393 Residue cluster calculation "Calculate clusters of contacting residues in protein structures.|This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role." FALSE http://edamontology.org/operation_2950 beta12orEarlier operation_0393 Calculate clusters of contacting residues in protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0394 Hydrogen bond calculation "Identify potential hydrogen bonds between amino acids and other groups.|The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy." FALSE http://edamontology.org/operation_0248 beta12orEarlier operation_0394 WHATIF:ShowHydrogenBonds|WHATIF:ShowHydrogenBondsM|WHATIF:HasHydrogenBonds Identify potential hydrogen bonds between amino acids and other groups. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0395 Residue non-canonical interaction detection Calculate non-canonical atomic interactions in protein structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0395 http://edamontology.org/operation_0249 Calculate non-canonical atomic interactions in protein structures. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/operation_0396 Ramachandran plot calculation Calculate a Ramachandran plot of a protein structure. FALSE http://edamontology.org/operation_0249 beta12orEarlier operation_0396 Calculate a Ramachandran plot of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0397 Ramachandran plot validation Validate a Ramachandran plot of a protein structure. FALSE http://edamontology.org/operation_1844 beta12orEarlier operation_0397 Validate a Ramachandran plot of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0398 Protein molecular weight calculation Calculate the molecular weight of a protein sequence or fragments. FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0398 Calculate the molecular weight of a protein sequence or fragments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0399 Protein extinction coefficient calculation Predict extinction coefficients or optical density of a protein sequence. FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0399 Predict extinction coefficients or optical density of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0400 Protein pH-dependent property calculation Calculate pH-dependent properties from pKa calculations of a protein sequence. FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_0400 Calculate pH-dependent properties from pKa calculations of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0401 Protein hydropathy calculation (from sequence) Hydropathy calculation on a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0401 Hydropathy calculation on a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2574 1.12 http://edamontology.org/operation_0402 Protein titration curve plotting Plot a protein titration curve. FALSE http://edamontology.org/operation_0400|http://edamontology.org/operation_3441 beta12orEarlier operation_0402 Plot a protein titration curve. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0403 Protein isoelectric point calculation Calculate isoelectric point of a protein sequence. FALSE http://edamontology.org/operation_0400 beta12orEarlier operation_0403 Calculate isoelectric point of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0404 Protein hydrogen exchange rate calculation Estimate hydrogen exchange rate of a protein sequence. FALSE http://edamontology.org/operation_0400 beta12orEarlier operation_0404 Estimate hydrogen exchange rate of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0405 Protein hydrophobic region calculation Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. FALSE http://edamontology.org/operation_2574 beta12orEarlier operation_0405 Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0406 Protein aliphatic index calculation Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. FALSE http://edamontology.org/operation_2574 beta12orEarlier operation_0406 Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0407 Protein hydrophobic moment plotting Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.|Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. FALSE http://edamontology.org/operation_2574|http://edamontology.org/operation_3441 beta12orEarlier operation_0407 Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0408 Protein globularity prediction "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." FALSE http://edamontology.org/operation_2574 beta12orEarlier operation_0408 "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0409 Protein solubility prediction Predict the solubility or atomic solvation energy of a protein sequence. FALSE http://edamontology.org/operation_2574 beta12orEarlier operation_0409 Predict the solubility or atomic solvation energy of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0410 Protein crystallizability prediction Predict crystallizability of a protein sequence. FALSE http://edamontology.org/operation_2574 beta12orEarlier operation_0410 Predict crystallizability of a protein sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0411 Protein signal peptide detection (eukaryotes) Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier (jison)Too fine-grained. operation_0411 Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0418 1.17 http://edamontology.org/operation_0418 http://edamontology.org/operation_0412 Protein signal peptide detection (bacteria) Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier (jison)Too fine-grained. operation_0412 Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0418 1.17 http://edamontology.org/operation_0418 http://edamontology.org/operation_0413 MHC peptide immunogenicity prediction "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." "true " http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0413 "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0252 1.12 http://edamontology.org/operation_0414 Protein feature prediction (from sequence) "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.|Methods typically involve scanning for known motifs, patterns and regular expressions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0414 http://edamontology.org/operation_3092 "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0415 Nucleic acid feature detection Sequence feature detection (nucleic acid)|Nucleic acid site detection|Nucleic acid feature recognition|Nucleic acid feature prediction|Nucleic acid site recognition|Nucleic acid site prediction "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.|Methods typically involve scanning for known motifs, patterns and regular expressions." FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_2478 beta12orEarlier operation_0415 "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." Sequence feature detection (nucleic acid) Nucleic acid site detection|Nucleic acid feature recognition|Nucleic acid feature prediction|Nucleic acid site recognition|Nucleic acid site prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0416 Epitope mapping Predict antigenic determinant sites (epitopes) in protein sequences.|Epitope mapping is commonly done during vaccine design. FALSE http://edamontology.org/operation_2429|http://edamontology.org/operation_3092 beta12orEarlier operation_0416 Predict antigenic determinant sites (epitopes) in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0417 Protein post-translation modification site prediction "Predict post-translation modification sites in protein sequences.|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." FALSE http://edamontology.org/operation_3092 beta12orEarlier operation_0417 Predict post-translation modification sites in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0418 Protein signal peptide detection "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.|Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc." FALSE http://edamontology.org/operation_2489|http://edamontology.org/operation_3092 beta12orEarlier operation_0418 Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0419 Protein binding site prediction (from sequence) "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0419 "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2575 1.12 http://edamontology.org/operation_0420 Protein-nucleic acid binding prediction Zinc finger prediction Predict RNA and DNA-binding binding sites in protein sequences.|This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). FALSE http://edamontology.org/operation_2575 beta12orEarlier operation_0420 Predict RNA and DNA-binding binding sites in protein sequences. Zinc finger prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0421 Protein folding site prediction "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation." FALSE http://edamontology.org/operation_2415|http://edamontology.org/operation_3092 beta12orEarlier operation_0421 "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0422 Protein cleavage site prediction Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. FALSE http://edamontology.org/operation_3092 beta12orEarlier operation_0422 Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0423 Epitope mapping (MHC Class I) Predict epitopes that bind to MHC class I molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0423 Predict epitopes that bind to MHC class I molecules. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0416 1.8 http://edamontology.org/operation_0424 Epitope mapping (MHC Class II) Predict epitopes that bind to MHC class II molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0424 Predict epitopes that bind to MHC class II molecules. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0416 1.8 http://edamontology.org/operation_0425 Whole gene prediction "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0425 "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2454 1.12 http://edamontology.org/operation_0426 Gene component prediction "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.|Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0426 "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2454 1.12 http://edamontology.org/operation_0427 Transposon prediction "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0427 "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0428 PolyA signal detection Detect polyA signals in nucleotide sequences. FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0428 Detect polyA signals in nucleotide sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0429 Quadruplex formation site detection Quadruplex structure prediction Detect quadruplex-forming motifs in nucleotide sequences.|Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0429 Detect quadruplex-forming motifs in nucleotide sequences. Quadruplex structure prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0430 CpG island and isochore detection CpG island and isochores detection|CpG island and isochores rendering "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.|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." FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0430 Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. CpG island and isochores detection|CpG island and isochores rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0431 Restriction site recognition "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0431 "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0432 Nucleosome formation or exclusion sequence prediction Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0432 Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0433 Splice site prediction "Identify, predict or analyse splice sites in nucleotide sequences.|Methods might require a pre-mRNA or genomic DNA sequence." FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_0433 "Identify, predict or analyse splice sites in nucleotide sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0434 Integrated gene prediction Predict whole gene structure using a combination of multiple methods to achieve better predictions. FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0434 Predict whole gene structure using a combination of multiple methods to achieve better predictions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0435 Operon prediction "Find operons (operators, promoters and genes) in bacteria genes." FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0435 "Find operons (operators, promoters and genes) in bacteria genes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0436 Coding region prediction ORF finding|ORF prediction Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0436 Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. ORF finding|ORF prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0437 Selenocysteine insertion sequence (SECIS) prediction Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.|SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0437 Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0438 Regulatory element prediction Transcription regulatory element prediction|Translational regulatory element prediction "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.|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." FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0438 "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." Transcription regulatory element prediction|Translational regulatory element prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0439 Translation initiation site prediction "Predict translation initiation sites, possibly by searching a database of sites." FALSE http://edamontology.org/operation_0436 beta12orEarlier operation_0439 "Predict translation initiation sites, possibly by searching a database of sites." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0440 Promoter prediction "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.|Methods might recognize CG content, CpG islands, splice sites, polyA signals etc." FALSE http://edamontology.org/operation_0438 beta12orEarlier operation_0440 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0441 Transcription regulatory element prediction (DNA-cis) "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.|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." FALSE http://edamontology.org/operation_0438 beta12orEarlier operation_0441 "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0442 Transcription regulatory element prediction (RNA-cis) "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.|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." FALSE http://edamontology.org/operation_0438 beta12orEarlier operation_0442 "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0443 Transcription regulatory element prediction (trans) Functional RNA identification Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.|Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. FALSE http://edamontology.org/operation_0438 beta12orEarlier operation_0443 Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. Functional RNA identification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0444 Matrix/scaffold attachment site prediction Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.|MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. FALSE http://edamontology.org/operation_0438 beta12orEarlier operation_0444 Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0445 Transcription factor binding site prediction Identify or predict transcription factor binding sites in DNA sequences. FALSE http://edamontology.org/operation_0440 beta12orEarlier operation_0445 Identify or predict transcription factor binding sites in DNA sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0446 Exonic splicing enhancer prediction Identify or predict exonic splicing enhancers (ESE) in exons.|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. FALSE http://edamontology.org/operation_0440 beta12orEarlier operation_0446 Identify or predict exonic splicing enhancers (ESE) in exons. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0447 Sequence alignment validation Sequence alignment quality evaluation Evaluate molecular sequence alignment accuracy.|Evaluation might be purely sequence-based or use structural information. FALSE http://edamontology.org/operation_2428|http://edamontology.org/operation_0258 beta12orEarlier operation_0447 Evaluate molecular sequence alignment accuracy. Sequence alignment quality evaluation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0448 Sequence alignment analysis (conservation) Residue conservation analysis "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.|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." FALSE http://edamontology.org/operation_0258 beta12orEarlier operation_0448 "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." Residue conservation analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0449 Sequence alignment analysis (site correlation) Analyse correlations between sites in a molecular sequence alignment.|This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. FALSE http://edamontology.org/operation_3465|http://edamontology.org/operation_0258 beta12orEarlier operation_0449 Analyse correlations between sites in a molecular sequence alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0450 Chimeric sequence detection Sequence alignment analysis (chimeric sequence detection) Detects chimeric sequences (chimeras) from a sequence alignment.|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. FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_0450 Detects chimeric sequences (chimeras) from a sequence alignment. Sequence alignment analysis (chimeric sequence detection) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0451 Recombination detection Sequence alignment analysis (recombination detection) "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.|Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on." FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_0451 Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. Sequence alignment analysis (recombination detection) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0452 Indel detection Sequence alignment analysis (indel detection)|Indel discovery "Identify insertion, deletion and duplication events from a sequence alignment.|Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on." FALSE http://edamontology.org/operation_2478|http://edamontology.org/operation_3202 beta12orEarlier operation_0452 "Identify insertion, deletion and duplication events from a sequence alignment." Sequence alignment analysis (indel detection)|Indel discovery http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0453 Nucleosome formation potential prediction Predict nucleosome formation potential of DNA sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0453 http://edamontology.org/operation_0432 Predict nucleosome formation potential of DNA sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0455 Nucleic acid thermodynamic property calculation "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." FALSE http://edamontology.org/operation_0262 beta12orEarlier operation_0455 "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0456 Nucleic acid melting profile plotting Calculate and plot a DNA or DNA/RNA melting profile.|A melting profile is used to visualise and analyse partly melted DNA conformations. FALSE http://edamontology.org/operation_0262|http://edamontology.org/operation_3441 beta12orEarlier operation_0456 Calculate and plot a DNA or DNA/RNA melting profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0457 Nucleic acid stitch profile plotting Calculate and plot a DNA or DNA/RNA stitch profile.|A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. FALSE http://edamontology.org/operation_0456 beta12orEarlier operation_0457 Calculate and plot a DNA or DNA/RNA stitch profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0458 Nucleic acid melting curve plotting Calculate and plot a DNA or DNA/RNA melting curve. FALSE http://edamontology.org/operation_0456 beta12orEarlier operation_0458 Calculate and plot a DNA or DNA/RNA melting curve. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0459 Nucleic acid probability profile plotting Calculate and plot a DNA or DNA/RNA probability profile. FALSE http://edamontology.org/operation_0456 beta12orEarlier operation_0459 Calculate and plot a DNA or DNA/RNA probability profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0460 Nucleic acid temperature profile plotting Calculate and plot a DNA or DNA/RNA temperature profile. FALSE http://edamontology.org/operation_0456 beta12orEarlier operation_0460 Calculate and plot a DNA or DNA/RNA temperature profile. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0461 Nucleic acid curvature calculation Calculate curvature and flexibility / stiffness of a nucleotide sequence.|This includes properties such as. FALSE http://edamontology.org/operation_0262 beta12orEarlier operation_0461 Calculate curvature and flexibility / stiffness of a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0463 microRNA detection Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. FALSE http://edamontology.org/operation_0443 beta12orEarlier operation_0463 Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0464 tRNA gene prediction Identify or predict tRNA genes in genomic sequences (tRNA). FALSE http://edamontology.org/operation_2454 beta12orEarlier operation_0464 Identify or predict tRNA genes in genomic sequences (tRNA). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0465 siRNA binding specificity prediction "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." FALSE http://edamontology.org/operation_0443 beta12orEarlier operation_0465 "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0467 Protein secondary structure prediction (integrated) Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0467 Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0267 1.18 http://edamontology.org/operation_0267 http://edamontology.org/operation_0468 Protein secondary structure prediction (helices) Predict helical secondary structure of protein sequences. FALSE http://edamontology.org/operation_0267 beta12orEarlier operation_0468 Predict helical secondary structure of protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0469 Protein secondary structure prediction (turns) Predict turn structure (for example beta hairpin turns) of protein sequences. FALSE http://edamontology.org/operation_0267 beta12orEarlier operation_0469 Predict turn structure (for example beta hairpin turns) of protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0470 Protein secondary structure prediction (coils) "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." FALSE http://edamontology.org/operation_0267 beta12orEarlier operation_0470 "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0471 Disulfide bond prediction Predict cysteine bonding state and disulfide bond partners in protein sequences. FALSE http://edamontology.org/operation_3092 beta12orEarlier operation_0471 Predict cysteine bonding state and disulfide bond partners in protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0472 GPCR prediction G protein-coupled receptor (GPCR) prediction Predict G protein-coupled receptors (GPCR). FALSE http://edamontology.org/operation_0269|http://edamontology.org/operation_0473 beta12orEarlier operation_0472 Predict G protein-coupled receptors (GPCR). G protein-coupled receptor (GPCR) prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0473 GPCR analysis G protein-coupled receptor (GPCR) analysis Analyse G-protein coupled receptor proteins (GPCRs). FALSE http://edamontology.org/operation_0270 beta12orEarlier operation_0473 Analyse G-protein coupled receptor proteins (GPCRs). G protein-coupled receptor (GPCR) analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0474 Protein structure prediction Predict tertiary structure (backbone and side-chain conformation) of protein sequences. FALSE http://edamontology.org/operation_0271|http://edamontology.org/operation_3023|http://edamontology.org/operation_2502|http://edamontology.org/operation_2479 beta12orEarlier operation_0474 Predict tertiary structure (backbone and side-chain conformation) of protein sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0475 Nucleic acid structure prediction Predict tertiary structure of DNA or RNA.|Methods might identify thermodynamically stable or evolutionarily conserved structures. FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_2478|http://edamontology.org/operation_0271 beta12orEarlier operation_0475 Predict tertiary structure of DNA or RNA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0476 Ab initio structure prediction de novo structure prediction Predict tertiary structure of protein sequence(s) without homologs of known structure. FALSE http://edamontology.org/operation_0474 beta12orEarlier operation_0476 Predict tertiary structure of protein sequence(s) without homologs of known structure. de novo structure prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0477 Protein modelling Homology structure modelling|Comparative modelling|Protein structure comparative modelling|Homology modelling "Build a three-dimensional protein model based on known (for example homologs) structures.|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 minimisation etc." FALSE http://edamontology.org/operation_2406|http://edamontology.org/operation_2426|http://edamontology.org/operation_0474 beta12orEarlier operation_0477 Build a three-dimensional protein model based on known (for example homologs) structures. Homology structure modelling|Comparative modelling|Protein structure comparative modelling|Homology modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0478 Molecular docking Protein docking|Docking simulation "Model the structure of a protein in complex with a small molecule or another macromolecule.|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." FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2492 beta12orEarlier operation_0478 Model the structure of a protein in complex with a small molecule or another macromolecule. Protein docking|Docking simulation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0479 Protein modelling (backbone) Model protein backbone conformation.|Methods might require a preliminary C(alpha) trace. FALSE http://edamontology.org/operation_0477 beta12orEarlier operation_0479 Model protein backbone conformation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0480 Protein modelling (side chains) "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.|Methods might use a residue rotamer library." FALSE http://edamontology.org/operation_0477 beta12orEarlier operation_0480 "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0481 Protein modelling (loops) Model loop conformation in protein structures. FALSE http://edamontology.org/operation_0477 beta12orEarlier operation_0481 Model loop conformation in protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0482 Protein-ligand docking Ligand-binding simulation|Virtual ligand screening Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.|Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. FALSE http://edamontology.org/operation_0478 beta12orEarlier operation_0482 Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. Ligand-binding simulation Virtual ligand screening http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0483 Structured RNA prediction and optimisation Nucleic acid folding family identification|RNA inverse folding Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. FALSE http://edamontology.org/operation_3095 beta12orEarlier operation_0483 Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. Nucleic acid folding family identification|RNA inverse folding http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0484 SNP detection SNP discovery|Single nucleotide polymorphism detection "Find single nucleotide polymorphisms (SNPs) between sequences.|This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc." FALSE http://edamontology.org/operation_0415|http://edamontology.org/operation_2478|http://edamontology.org/operation_3202 beta12orEarlier operation_0484 Find single nucleotide polymorphisms (SNPs) between sequences. SNP discovery|Single nucleotide polymorphism detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0485 Radiation Hybrid Mapping Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. FALSE http://edamontology.org/operation_2944 beta12orEarlier operation_0485 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0486 Functional mapping Map the genetic architecture of dynamic complex traits.|This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0486 http://edamontology.org/operation_0282 Map the genetic architecture of dynamic complex traits. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0487 Haplotype mapping Haplotype inference|Haplotype map generation|Haplotype reconstruction "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.|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 optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC)." FALSE http://edamontology.org/operation_0282|http://edamontology.org/operation_0283 beta12orEarlier operation_0487 "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." Haplotype inference|Haplotype map generation|Haplotype reconstruction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0488 Linkage disequilibrium calculation Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).|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. FALSE http://edamontology.org/operation_0283 beta12orEarlier operation_0488 Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0489 Genetic code prediction Predict genetic code from analysis of codon usage data. FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_0286 beta12orEarlier operation_0489 Predict genetic code from analysis of codon usage data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0490 Dotplot plotting Draw a dotplot of sequence similarities identified from word-matching or character comparison. FALSE http://edamontology.org/operation_0564|http://edamontology.org/operation_3441|http://edamontology.org/operation_0288 beta12orEarlier operation_0490 Draw a dotplot of sequence similarities identified from word-matching or character comparison. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0491 Pairwise sequence alignment Pairwise alignment "Align exactly two molecular sequences.|Methods might perform one-to-one, one-to-many or many-to-many comparisons." FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0491 Align exactly two molecular sequences. Pairwise alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0492 Multiple sequence alignment Multiple alignment "Align more than two molecular sequences.|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." FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0492 Align more than two molecular sequences. Multiple alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0493 Pairwise sequence alignment generation (local) Locally align exactly two molecular sequences.|Local alignment methods identify regions of local similarity. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0493 http://edamontology.org/operation_0495|http://edamontology.org/operation_0491 Locally align exactly two molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0494 Pairwise sequence alignment generation (global) Globally align exactly two molecular sequences.|Global alignment methods identify similarity across the entire length of the sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0494 http://edamontology.org/operation_0496|http://edamontology.org/operation_0491 Globally align exactly two molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0495 Local alignment Local sequence alignment|Sequence alignment (local)|Smith-Waterman Locally align two or more molecular sequences.|Local alignment methods identify regions of local similarity. FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0495 Locally align two or more molecular sequences. Local sequence alignment|Sequence alignment (local) Smith-Waterman http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0496 Global alignment Global sequence alignment|Sequence alignment (global) Globally align two or more molecular sequences.|Global alignment methods identify similarity across the entire length of the sequences. FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0496 Globally align two or more molecular sequences. Global sequence alignment|Sequence alignment (global) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0497 Constrained sequence alignment Multiple sequence alignment (constrained)|Sequence alignment (constrained) Align two or more molecular sequences with user-defined constraints. FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0497 Align two or more molecular sequences with user-defined constraints. Multiple sequence alignment (constrained)|Sequence alignment (constrained) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0498 Consensus-based sequence alignment Align two or more molecular sequences using multiple methods to achieve higher quality. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0498 Align two or more molecular sequences using multiple methods to achieve higher quality. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0292 1.16 http://edamontology.org/operation_0499 Tree-based sequence alignment Sequence alignment (phylogenetic tree-based)|Multiple sequence alignment (phylogenetic tree-based)|Sequence alignment generation (phylogenetic tree-based)|Phylogenetic tree-based multiple sequence alignment construction|Multiple sequence alignment construction (phylogenetic tree-based) Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.|This is supposed to give a more biologically meaningful alignment than standard alignments. FALSE http://edamontology.org/operation_0292 beta12orEarlier operation_0499 Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. Sequence alignment (phylogenetic tree-based)|Multiple sequence alignment (phylogenetic tree-based)|Sequence alignment generation (phylogenetic tree-based)|Phylogenetic tree-based multiple sequence alignment construction|Multiple sequence alignment construction (phylogenetic tree-based) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0500 Secondary structure alignment generation Align molecular secondary structure (represented as a 1D string). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0500 http://edamontology.org/operation_2928 Align molecular secondary structure (represented as a 1D string). http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0501 Protein secondary structure alignment generation Align protein secondary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0501 Align protein secondary structures. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2488 1.18 http://edamontology.org/operation_2488 http://edamontology.org/operation_0502 RNA secondary structure alignment RNA secondary structure alignment construction|RNA secondary structure alignment generation|Secondary structure alignment (RNA) Align RNA secondary structures. FALSE http://edamontology.org/operation_2439|http://edamontology.org/operation_3429 beta12orEarlier operation_0502 Align RNA secondary structures. RNA secondary structure alignment construction|RNA secondary structure alignment generation|Secondary structure alignment (RNA) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0503 Pairwise structure alignment Structure alignment (pairwise) Align (superimpose) exactly two molecular tertiary structures. FALSE http://edamontology.org/operation_0295 beta12orEarlier operation_0503 Align (superimpose) exactly two molecular tertiary structures. Structure alignment (pairwise) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0504 Multiple structure alignment Structure alignment (multiple) Align (superimpose) more than two molecular tertiary structures.|This includes methods that use an existing alignment. FALSE http://edamontology.org/operation_0295 beta12orEarlier operation_0504 Align (superimpose) more than two molecular tertiary structures. Structure alignment (multiple) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0505 Structure alignment (protein) Align protein tertiary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0505 http://edamontology.org/operation_0295 Align protein tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0506 Structure alignment (RNA) Align RNA tertiary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0506 http://edamontology.org/operation_0295 Align RNA tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_0507 Pairwise structure alignment generation (local) "Locally align (superimpose) exactly two molecular tertiary structures.|Local alignment methods identify regions of local similarity, common substructures etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0507 http://edamontology.org/operation_0295|http://edamontology.org/operation_0509 Locally align (superimpose) exactly two molecular tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0508 Pairwise structure alignment generation (global) Globally align (superimpose) exactly two molecular tertiary structures.|Global alignment methods identify similarity across the entire structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0508 http://edamontology.org/operation_0295|http://edamontology.org/operation_0510 Globally align (superimpose) exactly two molecular tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0509 Local structure alignment Structure alignment (local) "Locally align (superimpose) two or more molecular tertiary structures.|Local alignment methods identify regions of local similarity, common substructures etc." FALSE http://edamontology.org/operation_0295 beta12orEarlier operation_0509 Locally align (superimpose) two or more molecular tertiary structures. Structure alignment (local) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0510 Global structure alignment Structure alignment (global) Globally align (superimpose) two or more molecular tertiary structures.|Global alignment methods identify similarity across the entire structures. FALSE http://edamontology.org/operation_0295 beta12orEarlier operation_0510 Globally align (superimpose) two or more molecular tertiary structures. Structure alignment (global) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0511 Profile-profile alignment (pairwise) "Align exactly two molecular profiles.|Methods might perform one-to-one, one-to-many or many-to-many comparisons." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0511 Align exactly two molecular profiles. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0298 1.16 http://edamontology.org/operation_0512 Sequence alignment generation (multiple profile) Align two or more molecular profiles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0512 http://edamontology.org/operation_0298 Align two or more molecular profiles. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0513 3D profile-to-3D profile alignment (pairwise) Align exactly two molecular Structural (3D) profiles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0513 Align exactly two molecular Structural (3D) profiles. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0299 1.16 http://edamontology.org/operation_0514 Structural profile alignment generation (multiple) Align two or more molecular 3D profiles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0514 http://edamontology.org/operation_0299 Align two or more molecular 3D profiles. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0515 Data retrieval (tool metadata) "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0515 http://edamontology.org/operation_2422 "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0516 Data retrieval (database metadata) "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0516 http://edamontology.org/operation_2422 "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0517 PCR primer design (for large scale sequencing) Predict primers for large scale sequencing. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0517 Predict primers for large scale sequencing. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0518 PCR primer design (for genotyping polymorphisms) "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0518 "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0519 PCR primer design (for gene transcription profiling) Predict primers for gene transcription profiling. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0519 Predict primers for gene transcription profiling. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0520 PCR primer design (for conserved primers) Predict primers that are conserved across multiple genomes or species. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0520 Predict primers that are conserved across multiple genomes or species. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0521 PCR primer design (based on gene structure) TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0521 http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0522 PCR primer design (for methylation PCRs) Predict primers for methylation PCRs. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0522 Predict primers for methylation PCRs. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0308 1.13 http://edamontology.org/operation_0523 Mapping assembly Sequence assembly (mapping assembly) "Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.|The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers." FALSE http://edamontology.org/operation_0310 beta12orEarlier operation_0523 "Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome." Sequence assembly (mapping assembly) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0524 De-novo assembly De Bruijn graph|Sequence assembly (de-novo assembly) Sequence assembly by combining fragments without the aid of a reference sequence or genome.|De-novo assemblers are much slower and more memory intensive than mapping assemblers. FALSE http://edamontology.org/operation_0310 beta12orEarlier operation_0524 Sequence assembly by combining fragments without the aid of a reference sequence or genome. De Bruijn graph|Sequence assembly (de-novo assembly) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0525 Genome assembly Sequence assembly (genome assembly)|Genomic assembly|Breakend assembly The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. FALSE http://edamontology.org/operation_0310 beta12orEarlier operation_0525 The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. Sequence assembly (genome assembly)|Genomic assembly Breakend assembly http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0526 EST assembly Sequence assembly (EST assembly) "Sequence assembly for EST sequences (transcribed mRNA).|Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification." FALSE http://edamontology.org/operation_0310 beta12orEarlier operation_0526 Sequence assembly for EST sequences (transcribed mRNA). Sequence assembly (EST assembly) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0527 Sequence tag mapping Tag to gene assignment "Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data.|Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome." FALSE http://edamontology.org/operation_2520|http://edamontology.org/operation_0226 beta12orEarlier operation_0527 "Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data." Tag to gene assignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0528 SAGE data processing Process (read and / or write) serial analysis of gene expression (SAGE) data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0528 http://edamontology.org/operation_2495 Process (read and / or write) serial analysis of gene expression (SAGE) data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0529 MPSS data processing Process (read and / or write) massively parallel signature sequencing (MPSS) data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0529 http://edamontology.org/operation_2495 Process (read and / or write) massively parallel signature sequencing (MPSS) data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0530 SBS data processing Process (read and / or write) sequencing by synthesis (SBS) data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0530 http://edamontology.org/operation_2495 Process (read and / or write) sequencing by synthesis (SBS) data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0531 Heat map generation Heat map construction Generate a heat map of gene expression from e.g. microarray data.|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. FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_0571 beta12orEarlier operation_0531 Generate a heat map of gene expression from e.g. microarray data. Heat map construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0532 Gene expression profile analysis "Analyse one or more gene expression profiles, typically to interpret them in functional terms." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0532 http://edamontology.org/operation_2495 "Analyse one or more gene expression profiles, typically to interpret them in functional terms." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_0533 Gene expression profile pathway mapping "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." FALSE http://edamontology.org/operation_2429|http://edamontology.org/operation_2497|http://edamontology.org/operation_2495 beta12orEarlier operation_0533 "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0534 Protein secondary structure assignment (from coordinate data) Assign secondary structure from protein coordinate data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0534 Assign secondary structure from protein coordinate data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0319 1.18 http://edamontology.org/operation_0319 http://edamontology.org/operation_0535 Protein secondary structure assignment (from CD data) Assign secondary structure from circular dichroism (CD) spectroscopic data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0535 Assign secondary structure from circular dichroism (CD) spectroscopic data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0319 1.18 http://edamontology.org/operation_0319 http://edamontology.org/operation_0536 Protein structure assignment (from X-ray crystallographic data) Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0536 Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0320 1.7 http://edamontology.org/operation_0537 Protein structure assignment (from NMR data) Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0537 Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0320 1.7 http://edamontology.org/operation_0538 Phylogenetic tree generation (data centric) Phylogenetic tree construction (data centric) Construct a phylogenetic tree from a specific type of data. FALSE http://edamontology.org/operation_0323 beta12orEarlier operation_0538 Construct a phylogenetic tree from a specific type of data. Phylogenetic tree construction (data centric) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0539 Phylogenetic tree generation (method centric) Phylogenetic tree construction (method centric) Construct a phylogenetic tree using a specific method. FALSE http://edamontology.org/operation_0323 beta12orEarlier operation_0539 Construct a phylogenetic tree using a specific method. Phylogenetic tree construction (method centric) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0540 Phylogenetic tree generation (from molecular sequences) Phylogenetic tree construction (from molecular sequences) Phylogenetic tree construction from molecular sequences.|Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. FALSE http://edamontology.org/operation_0538|http://edamontology.org/operation_2403 beta12orEarlier operation_0540 Phylogenetic tree construction from molecular sequences. Phylogenetic tree construction (from molecular sequences) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0541 Phylogenetic tree generation (from continuous quantitative characters) Phylogenetic tree construction (from continuous quantitative characters) Phylogenetic tree construction from continuous quantitative character data. FALSE http://edamontology.org/operation_0538 beta12orEarlier operation_0541 Phylogenetic tree construction from continuous quantitative character data. Phylogenetic tree construction (from continuous quantitative characters) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0542 Phylogenetic tree generation (from gene frequencies) Phylogenetic tree construction (from gene frequencies) Phylogenetic tree construction from gene frequency data. FALSE http://edamontology.org/operation_0538 beta12orEarlier operation_0542 Phylogenetic tree construction from gene frequency data. Phylogenetic tree construction (from gene frequencies) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0543 Phylogenetic tree construction (from polymorphism data) Phylogenetic tree generation (from polymorphism data) "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." FALSE http://edamontology.org/operation_0538 beta12orEarlier operation_0543 "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." Phylogenetic tree generation (from polymorphism data) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0544 Phylogenetic species tree construction Phylogenetic species tree generation "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." FALSE http://edamontology.org/operation_0540 beta12orEarlier operation_0544 "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." Phylogenetic species tree generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0545 Phylogenetic tree generation (parsimony methods) Phylogenetic tree construction (parsimony methods) 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.|This includes evolutionary parsimony (invariants) methods. FALSE http://edamontology.org/operation_0539 beta12orEarlier operation_0545 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. Phylogenetic tree construction (parsimony methods) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0546 Phylogenetic tree generation (minimum distance methods) Phylogenetic tree construction (minimum distance methods) Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.|This includes neighbor joining (NJ) clustering method. FALSE http://edamontology.org/operation_0539 beta12orEarlier operation_0546 Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. Phylogenetic tree construction (minimum distance methods) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0547 Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetic tree construction (maximum likelihood and Bayesian methods) "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.|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." FALSE http://edamontology.org/operation_0539 beta12orEarlier operation_0547 Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. Phylogenetic tree construction (maximum likelihood and Bayesian methods) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0548 Phylogenetic tree generation (quartet methods) Phylogenetic tree construction (quartet methods) Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. FALSE http://edamontology.org/operation_0539 beta12orEarlier operation_0548 Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. Phylogenetic tree construction (quartet methods) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0549 Phylogenetic tree generation (AI methods) Phylogenetic tree construction (AI methods) "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." FALSE http://edamontology.org/operation_0539 beta12orEarlier operation_0549 "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." Phylogenetic tree construction (AI methods) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0550 DNA substitution modelling Sequence alignment analysis (phylogenetic modelling) Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. FALSE http://edamontology.org/operation_2478|http://edamontology.org/operation_2426 beta12orEarlier operation_0550 Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. Sequence alignment analysis (phylogenetic modelling) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0551 Phylogenetic tree analysis (shape) Phylogenetic tree topology analysis Analyse the shape (topology) of a phylogenetic tree. FALSE http://edamontology.org/operation_0324 beta12orEarlier operation_0551 Analyse the shape (topology) of a phylogenetic tree. Phylogenetic tree topology analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0552 Phylogenetic tree bootstrapping Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. FALSE http://edamontology.org/operation_0324|http://edamontology.org/operation_2428 beta12orEarlier operation_0552 Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0553 Phylogenetic tree analysis (gene family prediction) Predict families of genes and gene function based on their position in a phylogenetic tree. FALSE http://edamontology.org/operation_0324 beta12orEarlier operation_0553 Predict families of genes and gene function based on their position in a phylogenetic tree. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0554 Phylogenetic tree analysis (natural selection) "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).|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." FALSE http://edamontology.org/operation_0324 beta12orEarlier operation_0554 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0555 Phylogenetic tree generation (consensus) Phylogenetic tree construction (consensus) Compare two or more phylogenetic trees to produce a consensus tree.|Methods typically test for topological similarity between trees using for example a congruence index. FALSE http://edamontology.org/operation_0325|http://edamontology.org/operation_0323 beta12orEarlier operation_0555 Compare two or more phylogenetic trees to produce a consensus tree. Phylogenetic tree construction (consensus) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0556 Phylogenetic sub/super tree detection Compare two or more phylogenetic trees to detect subtrees or supertrees. FALSE http://edamontology.org/operation_0325 beta12orEarlier operation_0556 Compare two or more phylogenetic trees to detect subtrees or supertrees. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0557 Phylogenetic tree distances calculation Compare two or more phylogenetic trees to calculate distances between trees. FALSE http://edamontology.org/operation_0325 beta12orEarlier operation_0557 Compare two or more phylogenetic trees to calculate distances between trees. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0558 Phylogenetic tree annotation Annotate a phylogenetic tree with terms from a controlled vocabulary. FALSE http://edamontology.org/operation_0226 beta12orEarlier operation_0558 Annotate a phylogenetic tree with terms from a controlled vocabulary. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0559 Immunogenicity prediction Predict and optimise peptide ligands that elicit an immunological response. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0559 Predict and optimise peptide ligands that elicit an immunological response. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0252 1.12 http://edamontology.org/operation_0560 DNA vaccine design Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. FALSE http://edamontology.org/operation_3095 beta12orEarlier operation_0560 Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0561 Sequence formatting Reformat (a file or other report of) molecular sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0561 Reformat (a file or other report of) molecular sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0335 1.12 http://edamontology.org/operation_0562 Sequence alignment formatting Reformat (a file or other report of) molecular sequence alignment(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0562 Reformat (a file or other report of) molecular sequence alignment(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0335 1.12 http://edamontology.org/operation_0563 Codon usage table formatting Reformat a codon usage table. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0563 Reformat a codon usage table. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0335 1.12 http://edamontology.org/operation_0564 Sequence visualisation Sequence rendering|Sequence alignment visualisation "Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown." FALSE http://edamontology.org/operation_0337|http://edamontology.org/operation_2403 beta12orEarlier operation_0564 "Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown." Sequence rendering Sequence alignment visualisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0565 Sequence alignment visualisation "Visualise, format or print a molecular sequence alignment." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0565 "Visualise, format or print a molecular sequence alignment." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0564 1.15 http://edamontology.org/operation_0566 Sequence cluster visualisation Sequence cluster rendering "Visualise, format or render sequence clusters." FALSE http://edamontology.org/operation_0337 beta12orEarlier operation_0566 "Visualise, format or render sequence clusters." Sequence cluster rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0567 Phylogenetic tree visualisation Phylogenetic tree rendering Render or visualise a phylogenetic tree. FALSE http://edamontology.org/operation_0324|http://edamontology.org/operation_0337 beta12orEarlier operation_0567 Render or visualise a phylogenetic tree. Phylogenetic tree rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0568 RNA secondary structure visualisation "Visualise RNA secondary structure, knots, pseudoknots etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0568 "Visualise RNA secondary structure, knots, pseudoknots etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0570 1.15 http://edamontology.org/operation_0569 Protein secondary structure visualisation Render and visualise protein secondary structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0569 Render and visualise protein secondary structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0570 1.15 http://edamontology.org/operation_0570 Structure visualisation Structure rendering|RNA secondary structure visualisation|Protein secondary structure visualisation "Visualise or render molecular structure, for example a high-quality static picture or animation. This includes secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure." FALSE http://edamontology.org/operation_0337|http://edamontology.org/operation_2480 beta12orEarlier operation_0570 "Visualise or render molecular structure, for example a high-quality static picture or animation. This includes secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure." Structure rendering RNA secondary structure visualisation|Protein secondary structure visualisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0571 Expression data rendering Microarray data rendering Visualise microarray or other expression data. FALSE http://edamontology.org/operation_0337|http://edamontology.org/operation_3441|http://edamontology.org/operation_2495 beta12orEarlier operation_0571 Visualise microarray or other expression data. Microarray data rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0572 Protein interaction network rendering Identify and analyse networks of protein interactions. FALSE http://edamontology.org/operation_3083 beta12orEarlier operation_0572 Identify and analyse networks of protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0573 Map drawing DNA map drawing|Map rendering Draw or visualise a DNA map. FALSE http://edamontology.org/operation_0337 beta12orEarlier operation_0573 Draw or visualise a DNA map. DNA map drawing|Map rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0574 Sequence motif rendering Render a sequence with motifs. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0574 http://edamontology.org/operation_0564 Render a sequence with motifs. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0575 Restriction map drawing Draw or visualise restriction maps in DNA sequences. FALSE http://edamontology.org/operation_0431|http://edamontology.org/operation_0573 beta12orEarlier operation_0575 Draw or visualise restriction maps in DNA sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0577 DNA linear map rendering Draw a linear maps of DNA. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_0577 http://edamontology.org/operation_0573 Draw a linear maps of DNA. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_0578 Plasmid map drawing DNA circular map rendering "Draw a circular maps of DNA, for example a plasmid map." FALSE http://edamontology.org/operation_0573 beta12orEarlier operation_0578 DNA circular map rendering "Draw a circular maps of DNA, for example a plasmid map." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_0579 Operon drawing Operon rendering Visualise operon structure etc. FALSE http://edamontology.org/operation_0573 beta12orEarlier operation_0579 Visualise operon structure etc. Operon rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1768 Nucleic acid folding family identification Identify folding families of related RNAs. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1768 http://edamontology.org/operation_0483 Identify folding families of related RNAs. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_1769 Nucleic acid folding energy calculation "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." FALSE http://edamontology.org/operation_0279 beta12orEarlier operation_1769 "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1774 Annotation retrieval "Retrieve existing annotation (or documentation), typically annotation on a database entity.|Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1774 http://edamontology.org/operation_2422 "Retrieve existing annotation (or documentation), typically annotation on a database entity." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_1777 Protein function prediction "Predict general functional properties of a protein.|For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead." FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_2414 beta12orEarlier operation_1777 Predict general functional properties of a protein. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1778 Protein function comparison Compare the functional properties of two or more proteins. FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_2414 beta12orEarlier operation_1778 Compare the functional properties of two or more proteins. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1780 Sequence submission Submit a molecular sequence to a database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1780 http://edamontology.org/operation_3431 Submit a molecular sequence to a database. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_1781 Gene regulatory network analysis Analyse a known network of gene regulation. FALSE http://edamontology.org/operation_2497 beta12orEarlier operation_1781 Analyse a known network of gene regulation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1812 Loading Data loading Prepare or load a user-specified data file so that it is available for use. FALSE http://edamontology.org/operation_2409 beta12orEarlier operation_1812 WHATIF:UploadPDB Prepare or load a user-specified data file so that it is available for use. Data loading http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1813 Sequence retrieval Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.|This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1813 http://edamontology.org/operation_2422 Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_1814 Structure retrieval "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.|This includes direct retrieval methods but not those that perform calculations on the sequence or structure." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1814 http://edamontology.org/operation_2422 WHATIF:EchoPDB|WHATIF:DownloadPDB "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_1816 Surface rendering "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.|A dot has three coordinates (x,y,z) and (typically) a color." FALSE http://edamontology.org/operation_0570|http://edamontology.org/operation_3351 beta12orEarlier operation_1816 WHATIF:GetSurfaceDots Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1817 Protein atom surface calculation (accessible) Calculate the solvent accessibility ('accessible surface') for each atom in a structure.|Waters are not considered. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1817 Calculate the solvent accessibility ('accessible surface') for each atom in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1818 Protein atom surface calculation (accessible molecular) Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure.|Waters are not considered. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1818 Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1819 Protein residue surface calculation (accessible) "Calculate the solvent accessibility ('accessible surface') for each residue in a structure.|Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1819 Calculate the solvent accessibility ('accessible surface') for each residue in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1820 Protein residue surface calculation (vacuum accessible) "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.|Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1820 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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1821 Protein residue surface calculation (accessible molecular) "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure.|Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1821 Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1822 Protein residue surface calculation (vacuum molecular) "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.|Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1822 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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1823 Protein surface calculation (accessible molecular) Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1823 Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1824 Protein surface calculation (accessible) Calculate the solvent accessibility ('accessible surface') for a structure as a whole. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1824 Calculate the solvent accessibility ('accessible surface') for a structure as a whole. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_1825 Backbone torsion angle calculation Calculate for each residue in a protein structure all its backbone torsion angles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1825 Calculate for each residue in a protein structure all its backbone torsion angles. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0249 1.12 http://edamontology.org/operation_1826 Full torsion angle calculation Calculate for each residue in a protein structure all its torsion angles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1826 Calculate for each residue in a protein structure all its torsion angles. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0249 1.12 http://edamontology.org/operation_1827 Cysteine torsion angle calculation Calculate for each cysteine (bridge) all its torsion angles. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1827 Calculate for each cysteine (bridge) all its torsion angles. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0249 1.12 http://edamontology.org/operation_1828 Tau angle calculation For each amino acid in a protein structure calculate the backbone angle tau.|Tau is the backbone angle N-Calpha-C (angle over the C-alpha). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1828 For each amino acid in a protein structure calculate the backbone angle tau. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0249 1.12 http://edamontology.org/operation_1829 Cysteine bridge detection Detect cysteine bridges (from coordinate data) in a protein structure. FALSE http://edamontology.org/operation_1850 beta12orEarlier operation_1829 WHATIF:ShowCysteineBridge Detect cysteine bridges (from coordinate data) in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1830 Free cysteine detection "Detect free cysteines in a protein structure.|A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal." FALSE http://edamontology.org/operation_1850 beta12orEarlier operation_1830 WHATIF:ShowCysteineFree Detect free cysteines in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1831 Metal-bound cysteine detection Detect cysteines that are bound to metal in a protein structure. FALSE http://edamontology.org/operation_1850|http://edamontology.org/operation_0248 beta12orEarlier operation_1831 WHATIF:ShowCysteineMetal Detect cysteines that are bound to metal in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1832 Residue contact calculation (residue-nucleic acid) Calculate protein residue contacts with nucleic acids in a structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1832 Calculate protein residue contacts with nucleic acids in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_1834 Protein-metal contact calculation Residue-metal contact calculation Calculate protein residue contacts with metal in a structure. FALSE http://edamontology.org/operation_0248 beta12orEarlier operation_1834 Calculate protein residue contacts with metal in a structure. Residue-metal contact calculation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1835 Residue contact calculation (residue-negative ion) Calculate ion contacts in a structure (all ions for all side chain atoms). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1835 Calculate ion contacts in a structure (all ions for all side chain atoms). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_1836 Residue bump detection "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." FALSE http://edamontology.org/operation_0321 beta12orEarlier operation_1836 WHATIF:ShowBumps "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1837 Residue symmetry contact calculation Calculate the number of symmetry contacts made by residues in a protein structure.|A symmetry contact is a contact between two atoms in different asymmetric unit. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1837 WHATIF:SymmetryContact Calculate the number of symmetry contacts made by residues in a protein structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_1838 Residue contact calculation (residue-ligand) Calculate contacts between residues and ligands in a protein structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1838 Calculate contacts between residues and ligands in a protein structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_1839 Salt bridge calculation Calculate (and possibly score) salt bridges in a protein structure.|Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. FALSE http://edamontology.org/operation_0248 beta12orEarlier operation_1839 WHATIF:ShowSaltBridges|WHATIF:HasSaltBridgePlus|WHATIF:ShowSaltBridgesH|WHATIF:HasSaltBridge Calculate (and possibly score) salt bridges in a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1841 Rotamer likelihood prediction "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.|Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1841 WHATIF:ShowLikelyRotamers500|WHATIF:ShowLikelyRotamers200|WHATIF:ShowLikelyRotamers900|WHATIF:ShowLikelyRotamers400|WHATIF:ShowLikelyRotamers800|WHATIF:ShowLikelyRotamers100|WHATIF:ShowLikelyRotamers700|WHATIF:ShowLikelyRotamers|WHATIF:ShowLikelyRotamers600|WHATIF:ShowLikelyRotamers300 Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0480 1.12 http://edamontology.org/operation_1842 Proline mutation value calculation "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1842 WHATIF:ProlineMutationValue "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0331 1.12 http://edamontology.org/operation_1843 Residue packing validation Identify poorly packed residues in protein structures. FALSE http://edamontology.org/operation_0321 beta12orEarlier operation_1843 WHATIF: PackingQuality Identify poorly packed residues in protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1844 Protein geometry validation "Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc." FALSE http://edamontology.org/operation_0321 beta12orEarlier operation_1844 WHATIF: ImproperQualityMax|WHATIF: ImproperQualitySum "Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1845 PDB file sequence retrieval Extract a molecular sequence from a PDB file. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1845 WHATIF: PDB_sequence Extract a molecular sequence from a PDB file. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2422 beta12orEarlier http://edamontology.org/operation_1846 HET group detection "Identify HET groups in PDB files.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1846 Identify HET groups in PDB files. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_1847 DSSP secondary structure assignment Determine for residue the DSSP determined secondary structure in three-state (HSC). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1847 http://edamontology.org/operation_0319 Determine for residue the DSSP determined secondary structure in three-state (HSC). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_1848 Structure formatting Reformat (a file or other report of) tertiary structure data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1848 WHATIF: PDBasXML Reformat (a file or other report of) tertiary structure data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0335 1.12 http://edamontology.org/operation_1850 Protein cysteine and disulfide bond assignment Assign cysteine bonding state and disulfide bond partners in protein structures. FALSE http://edamontology.org/operation_3023 beta12orEarlier operation_1850 Assign cysteine bonding state and disulfide bond partners in protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_1913 Residue validation Identify poor quality amino acid positions in protein structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1913 Identify poor quality amino acid positions in protein structures. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0321 1.12 http://edamontology.org/operation_1914 Structure retrieval (water) Query a tertiary structure database and retrieve water molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_1914 http://edamontology.org/operation_2422 WHATIF:MovedWaterPDB Query a tertiary structure database and retrieve water molecules. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2008 siRNA duplex prediction Identify or predict siRNA duplexes in RNA. FALSE http://edamontology.org/operation_0443 beta12orEarlier operation_2008 Identify or predict siRNA duplexes in RNA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2089 Sequence alignment refinement Refine an existing sequence alignment. FALSE http://edamontology.org/operation_0258|http://edamontology.org/operation_2425 beta12orEarlier operation_2089 Refine an existing sequence alignment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2120 Listfile processing Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2120 http://edamontology.org/operation_2409 Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2121 Sequence file editing "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, creation of subset or a new file of sequences." FALSE http://edamontology.org/operation_0231|http://edamontology.org/operation_2403 beta12orEarlier operation_2121 "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, creation of subset or a new file of sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2122 Sequence alignment file processing "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2122 http://edamontology.org/operation_2409 "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2123 Small molecule data processing Process (read and / or write) physicochemical property data for small molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2123 http://edamontology.org/operation_2480 Process (read and / or write) physicochemical property data for small molecules. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2222 Data retrieval (ontology annotation) Search and retrieve documentation on a bioinformatics ontology. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2222 http://edamontology.org/operation_2422 Search and retrieve documentation on a bioinformatics ontology. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2224 Data retrieval (ontology concept) Query an ontology and retrieve concepts or relations. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2224 http://edamontology.org/operation_2422 Query an ontology and retrieve concepts or relations. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2233 Representative sequence identification "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." FALSE http://edamontology.org/operation_2451 beta12orEarlier operation_2233 "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2234 Structure file processing Perform basic (non-analytical) operations on a file of molecular tertiary structural data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2234 http://edamontology.org/operation_2409 Perform basic (non-analytical) operations on a file of molecular tertiary structural data. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2237 Data retrieval (sequence profile) "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.|This includes direct retrieval methods that retrieve a profile by, e.g. the profile name." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2237 http://edamontology.org/operation_2422 Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2238 Statistical calculation Hypothesis testing|Significance testing|Statistical testing|Statistical analysis|Gibbs sampling|Expectation maximisation|Omnibus test "Perform a statistical data operation of some type, e.g. calibration or validation." FALSE http://edamontology.org/operation_3438 beta12orEarlier operation_2238 "Perform a statistical data operation of some type, e.g. calibration or validation." Hypothesis testing|Significance testing|Statistical testing|Statistical analysis Gibbs sampling|Expectation maximisation|Omnibus test http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2239 3D-1D scoring matrix generation 3D-1D scoring matrix construction Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.|A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. FALSE http://edamontology.org/operation_3429|http://edamontology.org/operation_0250 beta12orEarlier operation_2239 Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. 3D-1D scoring matrix construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2241 Transmembrane protein visualisation Transmembrane protein rendering "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." FALSE http://edamontology.org/operation_0570|http://edamontology.org/operation_0270 beta12orEarlier operation_2241 "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." Transmembrane protein rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2246 Demonstration An operation performing purely illustrative (pedagogical) purposes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2246 An operation performing purely illustrative (pedagogical) purposes. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2264 Data retrieval (pathway or network) Query a biological pathways database and retrieve annotation on one or more pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2264 http://edamontology.org/operation_2422 Query a biological pathways database and retrieve annotation on one or more pathways. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2265 Data retrieval (identifier) Query a database and retrieve one or more data identifiers. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2265 http://edamontology.org/operation_2422 Query a database and retrieve one or more data identifiers. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2284 Nucleic acid density plotting Calculate a density plot (of base composition) for a nucleotide sequence. FALSE http://edamontology.org/operation_0236|http://edamontology.org/operation_3441 beta12orEarlier operation_2284 Calculate a density plot (of base composition) for a nucleotide sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2403 Sequence analysis Sequence analysis (general) Analyse one or more known molecular sequences. FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2403 Analyse one or more known molecular sequences. Sequence analysis (general) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2404 Sequence motif analysis Sequence motif processing Analyse molecular sequence motifs. FALSE http://edamontology.org/operation_2403 beta12orEarlier operation_2404 Analyse molecular sequence motifs. Sequence motif processing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2405 Protein interaction data processing Process (read and / or write) protein interaction data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2405 http://edamontology.org/operation_2949 Process (read and / or write) protein interaction data. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2406 Protein structure analysis Structure analysis (protein) Analyse protein tertiary structural data. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2502 beta12orEarlier operation_2406 Analyse protein tertiary structural data. Structure analysis (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2407 Annotation processing "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2407 http://edamontology.org/operation_2422 "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2408 Sequence feature analysis Analyse features in molecular sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2408 http://edamontology.org/operation_0253 Analyse features in molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2409 Data handling File processing|Report handling|File handling|Utility operation|Processing "Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2409 "Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output." File processing|Report handling|File handling|Utility operation Processing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2410 Gene expression analysis Analyse gene expression and regulation data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2410 http://edamontology.org/operation_2495 Analyse gene expression and regulation data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2411 Structural profile processing Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2411 http://edamontology.org/operation_0297 Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2412 Data index processing Process (read and / or write) an index of (typically a file of) biological data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2412 http://edamontology.org/operation_0227 Process (read and / or write) an index of (typically a file of) biological data. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2413 Sequence profile processing Process (read and / or write) some type of sequence profile. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2413 http://edamontology.org/operation_0296 Process (read and / or write) some type of sequence profile. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2414 Protein function analysis "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." FALSE http://edamontology.org/operation_2502 beta12orEarlier operation_2414 "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2415 Protein folding analysis Protein folding modelling "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." FALSE http://edamontology.org/operation_2426|http://edamontology.org/operation_2502 beta12orEarlier operation_2415 "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." Protein folding modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2416 Protein secondary structure analysis Secondary structure analysis (protein) Analyse known protein secondary structure data. FALSE http://edamontology.org/operation_2502 beta12orEarlier operation_2416 Analyse known protein secondary structure data. Secondary structure analysis (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2417 Physicochemical property data processing Process (read and / or write) data on the physicochemical property of a molecule. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2417 http://edamontology.org/operation_2945 Process (read and / or write) data on the physicochemical property of a molecule. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2419 Primer and probe design Primer and probe prediction Predict oligonucleotide primers or probes. FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_3095 beta12orEarlier operation_2419 Predict oligonucleotide primers or probes. Primer and probe prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2420 Operation (typed) "Process (read and / or write) data of a specific type, for example applying analytical methods." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2420 "Process (read and / or write) data of a specific type, for example applying analytical methods." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2945 1.12 http://edamontology.org/operation_2421 Database search Search "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.|Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database." FALSE http://edamontology.org/operation_0224 beta12orEarlier operation_2421 Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. Search http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2422 Data retrieval Information retrieval|Retrieval|Data retrieval (metadata)|Metadata retrieval "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." FALSE http://edamontology.org/operation_0224 beta12orEarlier operation_2422 Information retrieval "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." Retrieval Data retrieval (metadata)|Metadata retrieval http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2423 Prediction and recognition Prediction|Recognition|Detection "Predict, recognise, detect or identify some properties of a biomolecule." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2423 "Predict, recognise, detect or identify some properties of a biomolecule." Prediction|Recognition|Detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2424 Comparison Compare two or more things to identify similarities. FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2424 Compare two or more things to identify similarities. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2425 Optimisation and refinement Refine or optimise some data model. FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2425 Refine or optimise some data model. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2426 Modelling and simulation Mathematical modelling "Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2426 "Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." Mathematical modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2427 Data handling Perform basic operations on some data or a database. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2427 Perform basic operations on some data or a database. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2409 beta12orEarlier http://edamontology.org/operation_2428 Validation Quality control Validate some data. FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2428 Validate some data. Quality control http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2429 Mapping "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2429 "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2430 Design Design a biological entity (typically a molecular sequence or structure) with specific properties. FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2430 Design a biological entity (typically a molecular sequence or structure) with specific properties. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2432 Microarray data processing Process (read and / or write) microarray data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2432 http://edamontology.org/operation_2495 Process (read and / or write) microarray data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2433 Codon usage table processing Process (read and / or write) a codon usage table. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2433 http://edamontology.org/operation_0284|http://edamontology.org/operation_0285 Process (read and / or write) a codon usage table. http://purl.obolibrary.org/obo/edam#obsolete 1.18 http://edamontology.org/operation_0286 http://edamontology.org/operation_2434 Data retrieval (codon usage table) Retrieve a codon usage table and / or associated annotation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2434 http://edamontology.org/operation_2422 Retrieve a codon usage table and / or associated annotation. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2435 Gene expression profile processing Process (read and / or write) a gene expression profile. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2435 http://edamontology.org/operation_2495 Process (read and / or write) a gene expression profile. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2436 Gene-set enrichment analysis Gene-set over-represenation analysis|GO-term enrichment|Gene Ontology concept enrichment|Gene Ontology term enrichment "Analysis of a set of genes, corresponding e.g. to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed.|The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value." FALSE http://edamontology.org/operation_3501|http://edamontology.org/operation_3224|http://edamontology.org/operation_2495 beta12orEarlier|1.8 operation_2436 "Analysis of a set of genes, corresponding e.g. to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed." Gene-set over-represenation analysis GO-term enrichment|Gene Ontology concept enrichment|Gene Ontology term enrichment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2437 Gene regulatory network prediction Predict a network of gene regulation. FALSE http://edamontology.org/operation_3024|http://edamontology.org/operation_3439 beta12orEarlier operation_2437 Predict a network of gene regulation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2438 Pathway or network processing "Generate, analyse or handle a biological pathway or network." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2438 "Generate, analyse or handle a biological pathway or network." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2497 1.12 http://edamontology.org/operation_2439 RNA secondary structure analysis Process (read and / or write) RNA secondary structure data. FALSE http://edamontology.org/operation_2481 beta12orEarlier operation_2439 Process (read and / or write) RNA secondary structure data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2440 Structure processing (RNA) Process (read and / or write) RNA tertiary structure data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2440 Process (read and / or write) RNA tertiary structure data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2480 beta13 http://edamontology.org/operation_2441 RNA structure prediction Predict RNA tertiary structure. FALSE http://edamontology.org/operation_0475 beta12orEarlier operation_2441 Predict RNA tertiary structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2442 DNA structure prediction Predict DNA tertiary structure. FALSE http://edamontology.org/operation_0475 beta12orEarlier operation_2442 Predict DNA tertiary structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2443 Phylogenetic tree processing "Generate, process or analyse phylogenetic tree or trees." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2443 "Generate, process or analyse phylogenetic tree or trees." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0324 1.12 http://edamontology.org/operation_2444 Protein secondary structure processing Process (read and / or write) protein secondary structure data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2444 http://edamontology.org/operation_2416 Process (read and / or write) protein secondary structure data. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2445 Protein interaction network processing Process (read and / or write) a network of protein interactions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2445 http://edamontology.org/operation_0276 Process (read and / or write) a network of protein interactions. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2446 Sequence processing Process (read and / or write) one or more molecular sequences and associated annotation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2446 http://edamontology.org/operation_2403 Process (read and / or write) one or more molecular sequences and associated annotation. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2447 Sequence processing (protein) Process (read and / or write) a protein sequence and associated annotation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2447 Process (read and / or write) a protein sequence and associated annotation. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2479 1.6 http://edamontology.org/operation_2448 Sequence processing (nucleic acid) Process (read and / or write) a nucleotide sequence and associated annotation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2448 http://edamontology.org/operation_2478 Process (read and / or write) a nucleotide sequence and associated annotation. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2451 Sequence comparison Compare two or more molecular sequences. FALSE http://edamontology.org/operation_2424|http://edamontology.org/operation_2403 beta12orEarlier operation_2451 Compare two or more molecular sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2452 Sequence cluster processing Process (read and / or write) a sequence cluster. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2452 http://edamontology.org/operation_0291 Process (read and / or write) a sequence cluster. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2453 Feature table processing Process (read and / or write) a sequence feature table. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2453 http://edamontology.org/operation_2403 Process (read and / or write) a sequence feature table. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2454 Gene prediction Gene finding|Gene calling|Gene and gene component prediction|Gene component prediction|Whole gene prediction "Detect, predict and identify genes or components of genes in DNA sequences, including 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." FALSE http://edamontology.org/operation_0415 beta12orEarlier operation_2454 "Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. " Gene finding|Gene calling|Gene and gene component prediction Gene component prediction|Whole gene prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2456 GPCR classification Classify G-protein coupled receptors (GPCRs) into families and subfamilies. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2456 Classify G-protein coupled receptors (GPCRs) into families and subfamilies. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2995 1.16 http://edamontology.org/operation_2457 GPCR coupling selectivity prediction Predict G-protein coupled receptor (GPCR) coupling selectivity. FALSE http://edamontology.org/operation_2492|http://edamontology.org/operation_0473|http://edamontology.org/operation_0250 beta12orEarlier operation_2457 Predict G-protein coupled receptor (GPCR) coupling selectivity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2459 Structure processing (protein) Process (read and / or write) a protein tertiary structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2459 Process (read and / or write) a protein tertiary structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2406 1.6 http://edamontology.org/operation_2460 Protein atom surface calculation Calculate the solvent accessibility for each atom in a structure.|Waters are not considered. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2460 Calculate the solvent accessibility for each atom in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_2461 Protein residue surface calculation Calculate the solvent accessibility for each residue in a structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2461 Calculate the solvent accessibility for each residue in a structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_2462 Protein surface calculation Calculate the solvent accessibility of a structure as a whole. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2462 Calculate the solvent accessibility of a structure as a whole. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0387 1.12 http://edamontology.org/operation_2463 Sequence alignment processing Process (read and / or write) a molecular sequence alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2463 http://edamontology.org/operation_0292 Process (read and / or write) a molecular sequence alignment. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2464 Protein-protein interaction prediction "Identify or predict protein-protein interactions, interfaces, binding sites etc." FALSE http://edamontology.org/operation_1777|http://edamontology.org/operation_2492 beta12orEarlier operation_2464 "Identify or predict protein-protein interactions, interfaces, binding sites etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2465 Structure processing Process (read and / or write) a molecular tertiary structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2465 http://edamontology.org/operation_2480 Process (read and / or write) a molecular tertiary structure. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2466 Map annotation Annotate a DNA map of some type with terms from a controlled vocabulary. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2466 http://edamontology.org/operation_0362 Annotate a DNA map of some type with terms from a controlled vocabulary. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2467 Data retrieval (protein annotation) Retrieve information on a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2467 http://edamontology.org/operation_2422 Retrieve information on a protein. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2468 Data retrieval (phylogenetic tree) Retrieve a phylogenetic tree from a data resource. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2468 http://edamontology.org/operation_2422 Retrieve a phylogenetic tree from a data resource. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2469 Data retrieval (protein interaction annotation) Retrieve information on a protein interaction. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2469 http://edamontology.org/operation_2422 Retrieve information on a protein interaction. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2470 Data retrieval (protein family annotation) Retrieve information on a protein family. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2470 http://edamontology.org/operation_2422 Retrieve information on a protein family. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2471 Data retrieval (RNA family annotation) Retrieve information on an RNA family. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2471 http://edamontology.org/operation_2422 Retrieve information on an RNA family. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2472 Data retrieval (gene annotation) Retrieve information on a specific gene. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2472 http://edamontology.org/operation_2422 Retrieve information on a specific gene. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2473 Data retrieval (genotype and phenotype annotation) Retrieve information on a specific genotype or phenotype. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2473 http://edamontology.org/operation_2422 Retrieve information on a specific genotype or phenotype. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2474 Protein architecture comparison Compare the architecture of two or more protein structures. FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_0247 beta12orEarlier operation_2474 Compare the architecture of two or more protein structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2475 Protein architecture recognition Identify the architecture of a protein structure.|Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_2996|http://edamontology.org/operation_0247 beta12orEarlier operation_2475 Identify the architecture of a protein structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2476 Molecular dynamics simulation Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2426|http://edamontology.org/operation_2423 beta12orEarlier operation_2476 Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2478 Nucleic acid sequence analysis Sequence analysis (nucleic acid)|Sequence alignment analysis (nucleic acid)|Nucleic acid sequence alignment analysis Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). FALSE http://edamontology.org/operation_2501|http://edamontology.org/operation_2403 beta12orEarlier operation_2478 Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). Sequence analysis (nucleic acid) Sequence alignment analysis (nucleic acid)|Nucleic acid sequence alignment analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2479 Protein sequence analysis Sequence analysis (protein)|Protein sequence alignment analysis|Sequence alignment analysis (protein) Analyse a protein sequence (using methods that are only applicable to protein sequences). FALSE http://edamontology.org/operation_2502|http://edamontology.org/operation_2403 beta12orEarlier operation_2479 Analyse a protein sequence (using methods that are only applicable to protein sequences). Sequence analysis (protein) Protein sequence alignment analysis|Sequence alignment analysis (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2480 Structure analysis Analyse known molecular tertiary structures. FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2480 Analyse known molecular tertiary structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2481 Nucleic acid structure analysis Analyse nucleic acid tertiary structural data. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2501 beta12orEarlier operation_2481 Analyse nucleic acid tertiary structural data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2482 Secondary structure processing Process (read and / or write) a molecular secondary structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2482 http://edamontology.org/operation_2480 Process (read and / or write) a molecular secondary structure. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2483 Structure comparison Compare two or more molecular tertiary structures. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2424 beta12orEarlier operation_2483 Compare two or more molecular tertiary structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2485 Helical wheel drawing Helical wheel rendering Render a helical wheel representation of protein secondary structure. FALSE http://edamontology.org/operation_0570 beta12orEarlier operation_2485 Render a helical wheel representation of protein secondary structure. Helical wheel rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2486 Topology diagram drawing Topology diagram rendering Render a topology diagram of protein secondary structure. FALSE http://edamontology.org/operation_0570 beta12orEarlier operation_2486 Render a topology diagram of protein secondary structure. Topology diagram rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2487 Protein structure comparison Structure comparison (protein) "Compare protein tertiary structures.|Methods might identify structural neighbors, find structural similarities or define a structural core." FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_2502|http://edamontology.org/operation_2483 beta12orEarlier operation_2487 Compare protein tertiary structures. Structure comparison (protein) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2488 Protein secondary structure comparison Protein secondary structure|Secondary structure comparison (protein)|Protein secondary structure alignment Compare protein secondary structures. FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_2416 beta12orEarlier operation_2488 Compare protein secondary structures. Protein secondary structure|Secondary structure comparison (protein) Protein secondary structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2489 Protein subcellular localisation prediction Protein targeting prediction "Predict the subcellular localisation of a protein sequence.|The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein." FALSE http://edamontology.org/operation_1777|http://edamontology.org/operation_3023 beta12orEarlier operation_2489 Predict the subcellular localisation of a protein sequence. Protein targeting prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2490 Residue contact calculation (residue-residue) Calculate contacts between residues in a protein structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2490 Calculate contacts between residues in a protein structure. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2950 1.12 http://edamontology.org/operation_2491 Hydrogen bond calculation (inter-residue) Identify potential hydrogen bonds between amino acid residues. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2491 Identify potential hydrogen bonds between amino acid residues. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0394 1.12 http://edamontology.org/operation_2492 Protein interaction prediction Predict the interactions of proteins with other molecules. FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_2502 beta12orEarlier operation_2492 Predict the interactions of proteins with other molecules. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2493 Codon usage data processing Process (read and / or write) codon usage data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2493 http://edamontology.org/operation_0286 Process (read and / or write) codon usage data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2495 Gene expression analysis Gene expression data analysis|RNA-seq analysis|Microarray data analysis "Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms." FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2495 "Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms." Gene expression data analysis RNA-seq analysis|Microarray data analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2496 Gene regulatory network processing Process (read and / or write) a network of gene regulation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2496 Process (read and / or write) a network of gene regulation. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_1781 1.6 http://edamontology.org/operation_2497 Pathway or network analysis Network analysis|Pathway analysis "Generate, process or analyse a biological pathway or network." FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2497 "Generate, process or analyse a biological pathway or network." Network analysis|Pathway analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2498 Sequencing-based expression profile data analysis "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2498 http://edamontology.org/operation_2495 "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2499 Splicing model analysis Splicing analysis "Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences." FALSE http://edamontology.org/operation_2451|http://edamontology.org/operation_3024|http://edamontology.org/operation_2426 beta12orEarlier operation_2499 "Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences." Splicing analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2500 Microarray raw data analysis Analyse raw microarray data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2500 http://edamontology.org/operation_2495 Analyse raw microarray data. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/operation_2501 Nucleic acid analysis Nucleic acid data processing Process (read and / or write) nucleic acid sequence or structural data. FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2501 Process (read and / or write) nucleic acid sequence or structural data. Nucleic acid data processing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2502 Protein analysis Protein data processing Process (read and / or write) protein sequence or structural data. FALSE http://edamontology.org/operation_2945 beta12orEarlier operation_2502 Process (read and / or write) protein sequence or structural data. Protein data processing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2503 Sequence data processing Process (read and / or write) molecular sequence data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2503 Process (read and / or write) molecular sequence data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2403 beta13 http://edamontology.org/operation_2504 Structural data processing Process (read and / or write) molecular structural data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2504 http://edamontology.org/operation_2480 Process (read and / or write) molecular structural data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2505 Text processing Process (read and / or write) text. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2505 http://edamontology.org/operation_3778|http://edamontology.org/operation_0306 Process (read and / or write) text. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2506 Protein sequence alignment analysis "Analyse a protein sequence alignment, typically to detect features or make predictions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2506 "Analyse a protein sequence alignment, typically to detect features or make predictions." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2479 1.18 http://edamontology.org/operation_3023|http://edamontology.org/operation_0258|http://edamontology.org/operation_2502 http://edamontology.org/operation_2507 Nucleic acid sequence alignment analysis "Analyse a protein sequence alignment, typically to detect features or make predictions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2507 "Analyse a protein sequence alignment, typically to detect features or make predictions." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2478 1.18 http://edamontology.org/operation_3024|http://edamontology.org/operation_0258|http://edamontology.org/operation_2501 http://edamontology.org/operation_2508 Nucleic acid sequence comparison Compare two or more nucleic acid sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2508 Compare two or more nucleic acid sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2451 1.18 http://edamontology.org/operation_2998|http://edamontology.org/operation_2451|http://edamontology.org/operation_2478 http://edamontology.org/operation_2509 Protein sequence comparison Compare two or more protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2509 Compare two or more protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2451 1.18 http://edamontology.org/operation_2451 http://edamontology.org/operation_2510 DNA back-translation Back-translate a protein sequence into DNA. FALSE http://edamontology.org/operation_0233 beta12orEarlier operation_2510 Back-translate a protein sequence into DNA. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2511 Sequence editing (nucleic acid) "Edit or change a nucleic acid sequence, either randomly or specifically." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2511 "Edit or change a nucleic acid sequence, either randomly or specifically." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0231 1.8 http://edamontology.org/operation_2512 Sequence editing (protein) "Edit or change a protein sequence, either randomly or specifically." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2512 "Edit or change a protein sequence, either randomly or specifically." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0231 1.8 http://edamontology.org/operation_2513 Sequence generation (nucleic acid) Generate a nucleic acid sequence by some means. FALSE http://edamontology.org/operation_0230 beta12orEarlier operation_2513 Generate a nucleic acid sequence by some means. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2514 Sequence generation (protein) Generate a protein sequence by some means. FALSE http://edamontology.org/operation_0230|http://edamontology.org/operation_2502 beta12orEarlier operation_2514 Generate a protein sequence by some means. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2515 Nucleic acid sequence visualisation "Visualise, format or render a nucleic acid sequence.|Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2515 "Visualise, format or render a nucleic acid sequence." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0564 1.8 http://edamontology.org/operation_2516 Protein sequence visualisation "Visualise, format or render a protein sequence.|Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2516 "Visualise, format or render a protein sequence." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0564 1.8 http://edamontology.org/operation_2518 Nucleic acid structure comparison Structure comparison (nucleic acid) Compare nucleic acid tertiary structures. FALSE http://edamontology.org/operation_2998|http://edamontology.org/operation_2481|http://edamontology.org/operation_2483 beta12orEarlier operation_2518 Compare nucleic acid tertiary structures. Structure comparison (nucleic acid) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2519 Structure processing (nucleic acid) Process (read and / or write) nucleic acid tertiary structure data.|http://edamontology.org/operation_2481 TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2519 Process (read and / or write) nucleic acid tertiary structure data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2480 1.6 http://edamontology.org/operation_2520 DNA mapping Generate a map of a DNA sequence annotated with positional or non-positional features of some type. FALSE http://edamontology.org/operation_2429 beta12orEarlier operation_2520 Generate a map of a DNA sequence annotated with positional or non-positional features of some type. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2521 Map data processing Process (read and / or write) a DNA map of some type. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2521 http://edamontology.org/operation_2520 Process (read and / or write) a DNA map of some type. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2574 Protein hydropathy calculation "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." FALSE http://edamontology.org/operation_0250 beta12orEarlier operation_2574 "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2575 Protein binding site prediction Binding site prediction|Protein binding site detection|Ligand-binding site prediction| Active site prediction "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." FALSE http://edamontology.org/operation_2492|http://edamontology.org/operation_3092 beta12orEarlier operation_2575 "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." Binding site prediction|Protein binding site detection Ligand-binding site prediction| Active site prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2871 Sequence tagged site (STS) mapping Sequence mapping "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).|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." FALSE http://edamontology.org/operation_2944 beta12orEarlier operation_2871 Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). Sequence mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2928 Alignment Alignment construction|Alignment generation "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." FALSE http://edamontology.org/operation_0004|http://edamontology.org/operation_3429 beta12orEarlier operation_2928 "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." Alignment construction|Alignment generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2929 Protein fragment weight comparison Protein fingerprinting|PMF|Peptide mass fingerprinting Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification. FALSE http://edamontology.org/operation_2930|http://edamontology.org/operation_0398 beta12orEarlier operation_2929 Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification. Protein fingerprinting|PMF|Peptide mass fingerprinting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2930 Protein property comparison Compare the physicochemical properties of two or more proteins (or reference data). FALSE http://edamontology.org/operation_2997 beta12orEarlier operation_2930 Compare the physicochemical properties of two or more proteins (or reference data). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2931 Secondary structure comparison Compare two or more molecular secondary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2931 http://edamontology.org/operation_2518|http://edamontology.org/operation_2487 Compare two or more molecular secondary structures. http://purl.obolibrary.org/obo/edam#obsolete 1.18 http://edamontology.org/operation_2424 http://edamontology.org/operation_2932 Hopp and Woods plotting Generate a Hopp and Woods plot of antigenicity of a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2932 Generate a Hopp and Woods plot of antigenicity of a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0252 1.12 http://edamontology.org/operation_2934 Cluster textual view generation Microarray cluster textual view generation "Generate a view of clustered quantitative data, annotated with textual information." FALSE http://edamontology.org/operation_3441 beta12orEarlier operation_2934 "In the case of microarray data, visualise gene clusters with gene names." "Generate a view of clustered quantitative data, annotated with textual information." Microarray cluster textual view generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2935 Wave graph plotting Microarray wave graph rendering|Microarray wave graph plotting|Microarray cluster temporal graph rendering "Visualise clustered quantitative data as a set of waves, where each wave corresponds to a certain entity or sample on the X-axis.|In the case of microarray data, visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.|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." FALSE http://edamontology.org/operation_3441 beta12orEarlier operation_2935 "Visualise clustered quantitative data as a set of waves, where each wave corresponds to a certain entity or sample on the X-axis." Microarray wave graph rendering|Microarray wave graph plotting|Microarray cluster temporal graph rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2936 Dendrograph plotting Microarray view rendering|Microarray checks view rendering|Microarray dendrograph rendering|Microarray dendrograph plotting "Generate a dendrograph of raw, preprocessed or clustered expression (e.g. microarray) data." FALSE http://edamontology.org/operation_0571 beta12orEarlier operation_2936 "Generate a dendrograph of raw, preprocessed or clustered expression (e.g. microarray) data." Microarray view rendering|Microarray checks view rendering|Microarray dendrograph rendering|Microarray dendrograph plotting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2937 Proximity map plotting Microarray distance map rendering|Microarray proximity map plotting|Microarray proximity map rendering Generate a plot of distances (distance matrix) between genes. FALSE http://edamontology.org/operation_0571 beta12orEarlier operation_2937 Generate a plot of distances (distance matrix) between genes. Microarray distance map rendering|Microarray proximity map plotting|Microarray proximity map rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2938 Expression data tree or dendrogram rendering Microarray tree or dendrogram rendering|Microarray matrix tree plot rendering|Microarray 2-way dendrogram rendering "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." FALSE http://edamontology.org/operation_0571 beta12orEarlier operation_2938 "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." Microarray tree or dendrogram rendering|Microarray matrix tree plot rendering|Microarray 2-way dendrogram rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2939 Principal component plotting Microarray principal component rendering|Microarray principal component plotting "Generate a line graph drawn as sum of principal components (Eigen value) and, for example in the case of microarray data, individual expression values." FALSE http://edamontology.org/operation_3441 beta12orEarlier operation_2939 "Generate a line graph drawn as sum of principal components (Eigen value) and, for example in the case of microarray data, individual expression values." Microarray principal component rendering|Microarray principal component plotting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2940 Scatter plot plotting Microarray scatter plot rendering|Microarray scatter plot plotting "Generate a scatter plot of quantitative data, typically after principal component analysis." FALSE http://edamontology.org/operation_3441 beta12orEarlier operation_2940 "Generate a scatter plot of quantitative data, typically after principal component analysis." Microarray scatter plot rendering Microarray scatter plot plotting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2941 Whole microarray graph plotting Visualise gene expression data where each band (or line graph) corresponds to a sample. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2941 Visualise gene expression data where each band (or line graph) corresponds to a sample. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0571 1.18 http://edamontology.org/operation_0571 http://edamontology.org/operation_2942 Expression data tree-map rendering Microarray tree-map rendering Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. FALSE http://edamontology.org/operation_0571 beta12orEarlier operation_2942 Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. Microarray tree-map rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2943 Box-Whisker plot plotting Box plot plotting|Microarray Box-Whisker plot plotting "Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles." FALSE http://edamontology.org/operation_3441 beta12orEarlier operation_2943 "In the case of micorarray data, visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." "Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles." Box plot plotting Microarray Box-Whisker plot plotting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2944 Physical mapping "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." FALSE http://edamontology.org/operation_2520 beta12orEarlier operation_2944 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2945 Analysis "Apply analytical methods to existing data of a specific type.|This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling')." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2945 Apply analytical methods to existing data of a specific type. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2946 Alignment analysis Process or analyse an alignment of molecular sequences or structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2946 http://edamontology.org/operation_2928 Process or analyse an alignment of molecular sequences or structures. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2947 Article analysis Analyse a body of scientific text (typically a full text article from a scientific journal.) TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2947 http://edamontology.org/operation_3778|http://edamontology.org/operation_0306 Analyse a body of scientific text (typically a full text article from a scientific journal.) http://purl.obolibrary.org/obo/edam#obsolete 1.16 http://edamontology.org/operation_2948 Molecular interaction analysis Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2948 http://edamontology.org/operation_2949 Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2949 Protein interaction analysis "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." FALSE http://edamontology.org/operation_2502 beta12orEarlier operation_2949 "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2950 Residue distance calculation Residue contact calculation (residue-metal)|WHATIF:SymmetryContact|Residue contact calculation (residue-nucleic acid)|HET group detection|Residue contact calculation (residue-negative ion)|Residue contact calculation (residue-ligand) "Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations.|This includes identifying HET groups, which usually correspond 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. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit." FALSE http://edamontology.org/operation_0248 beta12orEarlier operation_2950 WHATIF:HasNegativeIonContacts|WHATIF:ShowProteiNucleicContacts|WHATIF:ShowDrugContacts|WHATIF:HasNucleicContacts|WHATIF:HasMetalContactsPlus|WHATIF:ShowDrugContactsShort|WHATIF: HETGroupNames|WHATIF:HasNegativeIonContactsPlus|WHATIF:ShowLigandContacts|WHATIF:HasMetalContacts "Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations." Residue contact calculation (residue-metal)|WHATIF:SymmetryContact|Residue contact calculation (residue-nucleic acid)|HET group detection|Residue contact calculation (residue-negative ion)|Residue contact calculation (residue-ligand) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2951 Alignment processing "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2951 http://edamontology.org/operation_0295|http://edamontology.org/operation_0292 "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2952 Structure alignment processing Process (read and / or write) a molecular tertiary (3D) structure alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2952 http://edamontology.org/operation_0295 Process (read and / or write) a molecular tertiary (3D) structure alignment. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_2962 Codon usage bias calculation Calculate codon usage bias. FALSE http://edamontology.org/operation_0286 beta12orEarlier operation_2962 Calculate codon usage bias. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2963 Codon usage bias plotting Generate a codon usage bias plot. FALSE http://edamontology.org/operation_3441|http://edamontology.org/operation_2962 beta12orEarlier operation_2963 Generate a codon usage bias plot. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2964 Codon usage fraction calculation "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." FALSE http://edamontology.org/operation_0286 beta12orEarlier operation_2964 "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2990 Classification "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_2990 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_2993 Molecular interaction data processing Process (read and / or write) molecular interaction data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_2993 http://edamontology.org/operation_2949 Process (read and / or write) molecular interaction data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/operation_2995 Sequence classification Assign molecular sequence(s) to a group or category. FALSE http://edamontology.org/operation_2990|http://edamontology.org/operation_2403 beta12orEarlier operation_2995 Assign molecular sequence(s) to a group or category. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2996 Structure classification Assign molecular structure(s) to a group or category. FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_2990 beta12orEarlier operation_2996 Assign molecular structure(s) to a group or category. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2997 Protein comparison Compare two or more proteins (or some aspect) to identify similarities. FALSE http://edamontology.org/operation_2424 beta12orEarlier operation_2997 Compare two or more proteins (or some aspect) to identify similarities. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_2998 Nucleic acid comparison Compare two or more nucleic acids to identify similarities. FALSE http://edamontology.org/operation_2424 beta12orEarlier operation_2998 Compare two or more nucleic acids to identify similarities. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3023 Prediction and recognition (protein) "Predict, recognise, detect or identify some properties of proteins." FALSE http://edamontology.org/operation_2423 beta12orEarlier operation_3023 "Predict, recognise, detect or identify some properties of proteins." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3024 Prediction and recognition (nucleic acid) "Predict, recognise, detect or identify some properties of nucleic acids." FALSE http://edamontology.org/operation_2423 beta12orEarlier operation_3024 "Predict, recognise, detect or identify some properties of nucleic acids." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3080 Structure editing "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." FALSE http://edamontology.org/operation_3096 beta13 operation_3080 "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3081 Sequence alignment editing "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." FALSE http://edamontology.org/operation_3096 beta13 operation_3081 "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3083 Pathway or network visualisation Pathway or network rendering Render (visualise) a biological pathway or network. FALSE http://edamontology.org/operation_0337|http://edamontology.org/operation_2497 beta13 operation_3083 Render (visualise) a biological pathway or network. Pathway or network rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3084 Protein function prediction (from sequence) "Predict general (non-positional) functional properties of a protein from analysing its sequence.|For functional properties that are positional, use 'Protein site detection' instead." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 operation_3084 http://edamontology.org/operation_1777 Predict general (non-positional) functional properties of a protein from analysing its sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_3087 Protein sequence feature detection "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 "(jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed (consolidate with ""Protein feature detection"")." operation_3087 "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3092 1.17 http://edamontology.org/operation_0253|http://edamontology.org/operation_3092|http://edamontology.org/operation_2479 http://edamontology.org/operation_3088 Protein property calculation (from sequence) "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 operation_3088 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0250 1.18 http://edamontology.org/operation_2479|http://edamontology.org/operation_0250 http://edamontology.org/operation_3090 Protein feature prediction (from structure) "Predict, recognise and identify positional features in proteins from analysing protein structure." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 operation_3090 http://edamontology.org/operation_3092 "Predict, recognise and identify positional features in proteins from analysing protein structure." http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_3092 Protein feature detection Protein feature recognition|Protein feature prediction|Protein site recognition|Sequence profile database search|Protein site detection|Protein site prediction|Sequence feature detection (protein)|Protein secondary database search "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.|Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. " FALSE http://edamontology.org/operation_3023|http://edamontology.org/operation_2502 beta13 operation_3092 "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." Protein feature recognition|Protein feature prediction Protein site recognition|Sequence profile database search|Protein site detection|Protein site prediction|Sequence feature detection (protein)|Protein secondary database search http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3093 Database search (by sequence) Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 operation_3093 http://edamontology.org/operation_2421 Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_3094 Protein interaction network prediction Predict a network of protein interactions. FALSE http://edamontology.org/operation_3439 beta13 operation_3094 Predict a network of protein interactions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3095 Nucleic acid design Design (or predict) nucleic acid sequences with specific chemical or physical properties. FALSE http://edamontology.org/operation_2430|http://edamontology.org/operation_2478 beta13 operation_3095 Design (or predict) nucleic acid sequences with specific chemical or physical properties. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3096 Editing "Edit a data entity, either randomly or specifically." FALSE http://edamontology.org/operation_2409 beta13 operation_3096 "Edit a data entity, either randomly or specifically." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3180 Sequence assembly validation Assembly QC|Sequence assembly QC|Assembly quality evaluation|Sequence assembly quality evaluation "Evaluate a DNA sequence assembly, typically for purposes of quality control." FALSE http://edamontology.org/operation_2428|http://edamontology.org/operation_2478 1.1 operation_3180 "Evaluate a DNA sequence assembly, typically for purposes of quality control." Assembly QC|Sequence assembly QC|Assembly quality evaluation|Sequence assembly quality evaluation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3182 Genome alignment Genome alignment construction Align two or more (tpyically huge) molecular sequences that represent genomes. FALSE http://edamontology.org/operation_0292 1.1 operation_3182 Align two or more (tpyically huge) molecular sequences that represent genomes. Genome alignment construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3183 Localised reassembly Reconstruction of a sequence assembly in a localised area. FALSE http://edamontology.org/operation_0310 1.1 operation_3183 Reconstruction of a sequence assembly in a localised area. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3184 Sequence assembly visualisation Assembly visualisation|Assembly rendering|Sequence assembly rendering Render and visualise a DNA sequence assembly. FALSE http://edamontology.org/operation_0564 1.1 operation_3184 Render and visualise a DNA sequence assembly. Assembly visualisation|Assembly rendering|Sequence assembly rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3185 Base-calling Base calling|Phred base calling|Phred base-calling Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. FALSE http://edamontology.org/operation_2513 1.1 operation_3185 Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. Base calling|Phred base calling|Phred base-calling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3186 Bisulfite mapping Bisulfite sequence alignment|Bisulfite sequence mapping "The mapping of methylation sites in a DNA (genome) sequence.|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." FALSE http://edamontology.org/operation_2944 1.1 operation_3186 The mapping of methylation sites in a DNA (genome) sequence. Bisulfite sequence alignment|Bisulfite sequence mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3187 Sequence contamination filtering Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. FALSE http://edamontology.org/operation_2478 beta12orEarlier operation_3187 Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3189 Trim ends "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.|For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 operation_3189 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3192 1.12 http://edamontology.org/operation_3190 Trim vector "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 operation_3190 "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3192 1.12 http://edamontology.org/operation_3191 Trim to reference Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 operation_3191 Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3192 1.12 http://edamontology.org/operation_3192 Sequence trimming Trimming|Trim vector|Trim ends|Barcode sequence removal|Trim to reference "Cut (remove) the end from a molecular sequence.|This includes ennd trimming Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. trimming to a reference sequence, Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. vector trimming Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. " FALSE http://edamontology.org/operation_0369 1.1 operation_3192 Cut (remove) the end from a molecular sequence. Trimming Trim vector|Trim ends|Barcode sequence removal|Trim to reference http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3194 Genome feature comparison "Compare the features of two genome sequences.|Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on." FALSE http://edamontology.org/operation_0256 1.1 operation_3194 Compare the features of two genome sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3195 Sequencing error detection Short read error correction|Short-read error correction Detect errors in DNA sequences generated from sequencing projects). FALSE http://edamontology.org/operation_2451 beta12orEarlier operation_3195 Detect errors in DNA sequences generated from sequencing projects). Short read error correction|Short-read error correction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3196 Genotyping "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.|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." FALSE http://edamontology.org/operation_3197 1.1 operation_3196 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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3197 Genetic variation analysis Genetic variation annotation|Variant analysis|Sequence variation analysis "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.|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." FALSE http://edamontology.org/operation_0415 1.1 operation_3197 "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." Genetic variation annotation|Variant analysis|Sequence variation analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3198 Read mapping Short oligonucleotide alignment|Oligonucleotide alignment|Short read mapping|Short sequence read mapping|Oligonucleotide alignment generation|Read alignment|Oligonucleotide mapping|Oligonucleotide alignment construction|Short read alignment "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.|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." FALSE http://edamontology.org/operation_0292|http://edamontology.org/operation_2944 1.1 operation_3198 Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. Short oligonucleotide alignment|Oligonucleotide alignment|Short read mapping|Short sequence read mapping|Oligonucleotide alignment generation|Read alignment|Oligonucleotide mapping|Oligonucleotide alignment construction|Short read alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3199 Split read mapping Split-read mapping A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. FALSE http://edamontology.org/operation_3198 1.1 operation_3199 A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. Split-read mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3200 Community profiling Sample barcoding|DNA barcoding Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. FALSE http://edamontology.org/operation_2478 1.1 operation_3200 Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. Sample barcoding DNA barcoding http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3201 SNP calling "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.|Operations usually score confidence in the prediction or some other statistical measure of evidence." FALSE http://edamontology.org/operation_0484 1.1 operation_3201 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3202 Polymorphism detection Polymorphism detection|Mutation detection|de novo mutation detection "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." FALSE http://edamontology.org/operation_3197 1.1 operation_3202 "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." Polymorphism detection Mutation detection|de novo mutation detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3203 Chromatogram visualisation Chromatogram viewing "Visualise, format or render an image of a Chromatogram." FALSE http://edamontology.org/operation_0337 1.1 operation_3203 "Visualise, format or render an image of a Chromatogram." Chromatogram viewing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3204 Methylation analysis Determine cytosine methylation states in nucleic acid sequences. FALSE http://edamontology.org/operation_2478 1.1 operation_3204 Determine cytosine methylation states in nucleic acid sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3205 Methylation calling Determine cytosine methylation status of specific positions in a nucleic acid sequences. FALSE http://edamontology.org/operation_3204|http://edamontology.org/operation_2944 1.1 operation_3205 Determine cytosine methylation status of specific positions in a nucleic acid sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3206 Methylation level analysis (global) Global methylation analysis "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." FALSE http://edamontology.org/operation_3205 1.1 operation_3206 "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." Global methylation analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3207 Methylation level analysis (gene-specific) Gene-specific methylation analysis Measure the level of methyl cytosines in specific genes.|Many different techniques are available for this. FALSE http://edamontology.org/operation_3205 1.1 operation_3207 Measure the level of methyl cytosines in specific genes. Gene-specific methylation analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3208 Genome visualisation Genome rendering|Genome viewing|Genome browser|Genome browsing "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." FALSE http://edamontology.org/operation_0564 1.1 operation_3208 "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." Genome rendering|Genome viewing|Genome browser|Genome browsing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3209 Genome comparison Genomic region matching "Compare the sequence or features of two or more genomes, for example, to find matching regions." FALSE http://edamontology.org/operation_2451 1.1 operation_3209 "Compare the sequence or features of two or more genomes, for example, to find matching regions." Genomic region matching http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3211 Genome indexing Burrows-Wheeler|Genome indexing (Burrows-Wheeler)|Suffix arrays|Genome indexing (suffix arrays) Generate an index of a genome sequence.|Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. FALSE http://edamontology.org/operation_0227 1.1 operation_3211 Generate an index of a genome sequence. Burrows-Wheeler|Genome indexing (Burrows-Wheeler)|Suffix arrays|Genome indexing (suffix arrays) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3212 Genome indexing (Burrows-Wheeler) Generate an index of a genome sequence using the Burrows-Wheeler algorithm.|The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 operation_3212 Generate an index of a genome sequence using the Burrows-Wheeler algorithm. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3211 1.12 http://edamontology.org/operation_3213 Genome indexing (suffix arrays) Generate an index of a genome sequence using a suffix arrays algorithm.|A suffix array consists of the lexicographically sorted list of suffixes of a genome. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 operation_3213 Generate an index of a genome sequence using a suffix arrays algorithm. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3211 1.12 http://edamontology.org/operation_3214 Spectral analysis Spectrum analysis|Mass spectrum analysis Analyse one or more spectra from mass spectrometry (or other) experiments. FALSE http://edamontology.org/operation_2945 1.1 operation_3214 Analyse one or more spectra from mass spectrometry (or other) experiments. Spectrum analysis|Mass spectrum analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3215 Peak detection Peak assignment|Peak finding "Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment." FALSE http://edamontology.org/operation_3214 1.1 operation_3215 "Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment." Peak assignment|Peak finding http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3216 Scaffolding Scaffold construction|Scaffold generation "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.|Scaffold may be positioned along a chromosome physical map to create a ""golden path""." FALSE http://edamontology.org/operation_0310|http://edamontology.org/operation_3429 1.1 operation_3216 "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." Scaffold construction|Scaffold generation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3217 Scaffold gap completion "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.|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." FALSE http://edamontology.org/operation_3216 1.1 operation_3217 Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3218 Sequencing quality control Sequencing QC|Sequencing quality assessment Raw sequence data quality control.|Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems. FALSE http://edamontology.org/operation_2428|http://edamontology.org/operation_2478 1.1 operation_3218 Raw sequence data quality control. Sequencing QC|Sequencing quality assessment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3219 Read pre-processing Sequence read pre-processing "Pre-process sequence reads to ensure (or improve) quality and reliability.|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." FALSE http://edamontology.org/operation_3218|http://edamontology.org/operation_2478 1.1 operation_3219 Pre-process sequence reads to ensure (or improve) quality and reliability. Sequence read pre-processing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3221 Species frequency estimation "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." FALSE http://edamontology.org/operation_2478 1.1 operation_3221 "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3222 Peak calling Protein binding peak detection|Peak-pair calling "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.|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'). ""Peak-pair calling"" is similar to ""Peak calling"" in the context of ChIP-exo." FALSE http://edamontology.org/operation_0415 1.1 operation_3222 Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. Protein binding peak detection Peak-pair calling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3223 Differential gene expression analysis Differentially expressed gene identification|Differential gene analysis "Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.|Differential gene 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." FALSE http://edamontology.org/operation_2998 1.1 operation_3223 Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. Differentially expressed gene identification|Differential gene analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3224 Gene set testing "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.|Gene sets can be defined beforehand by biological function, chromosome locations and so on." FALSE http://edamontology.org/operation_2495 1.1 operation_3224 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3225 Variant classification "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.|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.)" FALSE http://edamontology.org/operation_3197|http://edamontology.org/operation_2995 1.1 operation_3225 "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3226 Variant prioritisation "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.|Variant prioritisation 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." FALSE http://edamontology.org/operation_3197 1.1 operation_3226 "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3227 Variant calling Variant mapping|Genome variant detection|Somatic variant calling|Germ line variant calling|Allele calling|Exome variant detection "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.|Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant.|Variant detection|Methods often utilise a database of aligned reads." FALSE http://edamontology.org/operation_3197 1.1 operation_3227 "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." Variant mapping Genome variant detection|Somatic variant calling|Germ line variant calling|Allele calling|Exome variant detection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3228 Structural variation discovery "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).|Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies." FALSE http://edamontology.org/operation_3197 1.1 operation_3228 "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3229 Exome assembly Exome sequence analysis Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. FALSE http://edamontology.org/operation_0310 1.1 operation_3229 Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. Exome sequence analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3230 Read depth analysis "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." FALSE http://edamontology.org/operation_2478 1.1 operation_3230 "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3232 Gene expression QTL analysis Gene expression quantitative trait loci profiling|Gene expression QTL profiling|eQTL profiling "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." FALSE http://edamontology.org/operation_2495 1.1 operation_3232 "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." Gene expression quantitative trait loci profiling|Gene expression QTL profiling|eQTL profiling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3233 Copy number estimation Transcript copy number estimation "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-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.|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)." FALSE http://edamontology.org/operation_2478 1.1 operation_3233 "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-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." Transcript copy number estimation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3237 Primer removal Adapter removal Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). FALSE http://edamontology.org/operation_0369 1.2 operation_3237 Adapter removal Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3258 Transcriptome assembly Infer a transcriptome sequence by analysis of short sequence reads. FALSE http://edamontology.org/operation_0310 1.2 operation_3258 Infer a transcriptome sequence by analysis of short sequence reads. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3259 Transcriptome assembly (de novo) de novo transcriptome assembly "Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.2 operation_3259 http://edamontology.org/operation_0524 "Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other." de novo transcriptome assembly http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_3260 Transcriptome assembly (mapping) Infer a transcriptome sequence by mapping short reads to a reference genome. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.2 operation_3260 http://edamontology.org/operation_0523 Infer a transcriptome sequence by mapping short reads to a reference genome. http://purl.obolibrary.org/obo/edam#obsolete 1.6 http://edamontology.org/operation_3267 Sequence coordinate conversion "Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc." FALSE http://edamontology.org/operation_3434 1.3 operation_3267 "Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3278 Document similarity calculation Calculate similarity between 2 or more documents. FALSE http://edamontology.org/operation_3437 1.3 operation_3278 Calculate similarity between 2 or more documents. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3279 Document clustering Cluster (group) documents on the basis of their calculated similarity. FALSE http://edamontology.org/operation_3432|http://edamontology.org/operation_3437 1.3 operation_3279 Cluster (group) documents on the basis of their calculated similarity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3280 Named-entity and concept recognition Concept mining|Event extraction|Entity chunking|Named-entity recognition|Entity identification|Entity extraction "Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents." FALSE http://edamontology.org/operation_0306 1.3 operation_3280 "Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents." Concept mining|Event extraction|Entity chunking|Named-entity recognition|Entity identification|Entity extraction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3282 ID mapping Identifier mapping|Accession mapping "Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.|The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence." FALSE http://edamontology.org/operation_2429|http://edamontology.org/operation_2424 1.3 operation_3282 Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. Identifier mapping|Accession mapping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3283 Anonymisation Data anonymisation Process data in such a way that makes it hard to trace to the person which the data concerns. FALSE http://edamontology.org/operation_0004 1.3 operation_3283 Process data in such a way that makes it hard to trace to the person which the data concerns. Data anonymisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3289 ID retrieval "Search for and retrieve a data identifier of some kind, e.g. a database entry accession." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.3 "(jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved." operation_3289 "Search for and retrieve a data identifier of some kind, e.g. a database entry accession." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2422 1.17 http://edamontology.org/operation_0304 http://edamontology.org/operation_3348 Sequence checksum generation Generate a checksum of a molecular sequence. FALSE http://edamontology.org/operation_3429 1.4 operation_3348 Generate a checksum of a molecular sequence. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3349 Bibliography generation Bibliography construction Construct a bibliography from the scientific literature. FALSE http://edamontology.org/operation_3429 1.4 operation_3349 Construct a bibliography from the scientific literature. Bibliography construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3350 Protein quaternary structure prediction Predict the structure of a multi-subunit protein and particularly how the subunits fit together. FALSE http://edamontology.org/operation_0474 1.4 operation_3350 Predict the structure of a multi-subunit protein and particularly how the subunits fit together. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3351 Molecular surface analysis "Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc." FALSE http://edamontology.org/operation_2480 1.4 operation_3351 "Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3352 Ontology comparison "Compare two or more ontologies, e.g. identify differences." FALSE http://edamontology.org/operation_2424 1.4 operation_3352 "Compare two or more ontologies, e.g. identify differences." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3353 Ontology comparison "Compare two or more ontologies, e.g. identify differences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.4 operation_3353 "Compare two or more ontologies, e.g. identify differences." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3352 1.9 http://edamontology.org/operation_3357 Format detection Format recognition|Format identification|Format inference "Recognition of which format the given data is in.|'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology." FALSE http://edamontology.org/operation_2409 1.4 operation_3357 http://edamontology.org/comment_handle Recognition of which format the given data is in. Format recognition|Format identification|Format inference http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3359 Splitting File splitting "Split a file containing multiple data items into many files, each containing one item" FALSE http://edamontology.org/operation_2409 1.4 operation_3359 "Split a file containing multiple data items into many files, each containing one item" File splitting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3429 Generation Construction "Construct some data entity.|For non-analytical operations, see the 'Processing' branch." FALSE http://edamontology.org/operation_0004 beta12orEarlier operation_3429 Construct some data entity. Construction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3430 Nucleic acid sequence feature detection "Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.6 (jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed. operation_3430 "Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0415 1.17 http://edamontology.org/operation_0415|http://edamontology.org/operation_0253 http://edamontology.org/operation_3431 Deposition Data deposition|Data submission|Database submission|Database deposition|Submission "Deposit some data in a database or some other type of repository or software system.|For non-analytical operations, see the 'Processing' branch." FALSE http://edamontology.org/operation_0004 1.6 operation_3431 Deposit some data in a database or some other type of repository or software system. Data deposition|Data submission|Database submission|Database deposition|Submission http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3432 Clustering Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). FALSE http://edamontology.org/operation_0004 1.6 operation_3432 Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3433 Assembly Construct some entity (typically a molecule sequence) from component pieces. FALSE http://edamontology.org/operation_0004 1.6 operation_3433 Construct some entity (typically a molecule sequence) from component pieces. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3434 Conversion Convert a data set from one form to another. FALSE http://edamontology.org/operation_0004 1.6 operation_3434 Convert a data set from one form to another. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3435 Standardisation and normalisation Normalisation|Standardisation "Standardize or normalize data by some statistical method.| In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean. " FALSE http://edamontology.org/operation_2238 1.6 operation_3435 Standardize or normalize data by some statistical method. Normalisation|Standardisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3436 Aggregation Combine multiple files or data items into a single file or object. FALSE http://edamontology.org/operation_2409 1.6 operation_3436 Combine multiple files or data items into a single file or object. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3437 Article comparison Compare two or more scientific articles. FALSE http://edamontology.org/operation_2424 1.6 operation_3437 Compare two or more scientific articles. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3438 Calculation "Mathematical determination of the value of something, typically a properly of a molecule." FALSE http://edamontology.org/operation_0004 1.6 operation_3438 "Mathematical determination of the value of something, typically a properly of a molecule." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3439 Pathway or network prediction Predict a molecular pathway or network. FALSE http://edamontology.org/operation_2497|http://edamontology.org/operation_2423 1.6 operation_3439 Predict a molecular pathway or network. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3440 Genome assembly The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.6 operation_3440 The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0525 1.12 http://edamontology.org/operation_3441 Plotting "Generate a graph, or other visual representation, of data, showing the relationship between two or more variables." FALSE http://edamontology.org/operation_0337 1.6 operation_3441 "Generate a graph, or other visual representation, of data, showing the relationship between two or more variables." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3443 Image analysis Image processing The analysis of a image (typically a digital image) of some type in order to extract information from it. FALSE http://edamontology.org/operation_2945 1.7 operation_3443 Image processing The analysis of a image (typically a digital image) of some type in order to extract information from it. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3445 Diffraction data analysis Analysis of data from a diffraction experiment. FALSE http://edamontology.org/operation_2480 1.7 operation_3445 Analysis of data from a diffraction experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3446 Cell migration analysis "Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression." FALSE http://edamontology.org/operation_3443 1.7 operation_3446 "Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3447 Diffraction data reduction "Processing of diffraction data into a corrected, ordered, and simplified form." FALSE http://edamontology.org/operation_3445 1.7 operation_3447 "Processing of diffraction data into a corrected, ordered, and simplified form." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3450 Neurite measurement "Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images." FALSE http://edamontology.org/operation_3443 1.7 operation_3450 "Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3453 Diffraction data integration Diffraction summation integration|Diffraction profile fitting The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. FALSE http://edamontology.org/operation_3445 1.7 operation_3453 The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. Diffraction summation integration|Diffraction profile fitting http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3454 Phasing "Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods." FALSE http://edamontology.org/operation_3445 1.7 operation_3454 "Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods." http://purl.obolibrary.org/obo/edam#operations|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3455 Molecular replacement "A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form.|The technique solves the phase problem, i.e. retrieve information concern phases of the structure." FALSE http://edamontology.org/operation_0322 1.7 operation_3455 "A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form." http://purl.obolibrary.org/obo/edam#operations|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3456 Rigid body refinement "A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms.|Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data." FALSE http://edamontology.org/operation_0322 1.7 operation_3456 "A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms." http://purl.obolibrary.org/obo/edam#operations|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3457 Single particle analysis "An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.|Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM)." FALSE http://edamontology.org/operation_2480|http://edamontology.org/operation_3443 1.7 operation_3457 "An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3458 Single particle alignment and classification Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. |A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. FALSE http://edamontology.org/operation_2990|http://edamontology.org/operation_3457 1.7 operation_3458 Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3459 Functional clustering Functional sequence clustering "Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype." FALSE http://edamontology.org/operation_0291 1.7 operation_3459 "Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype." Functional sequence clustering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3460 Taxonomic classification Taxonomy assignment|Taxonomic profiling Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy. FALSE http://edamontology.org/operation_2995 1.7 operation_3460 Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy. Taxonomy assignment Taxonomic profiling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3461 Virulence prediction Pathogenicity prediction The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. FALSE http://edamontology.org/operation_2423|http://edamontology.org/operation_2403 1.7 operation_3461 The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. Pathogenicity prediction http://purl.obolibrary.org/obo/edam#operations|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3463 Gene expression correlation analysis Gene co-expression network analysis "Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. " FALSE http://edamontology.org/operation_3465|http://edamontology.org/operation_0315 1.7 operation_3463 "Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. " Gene co-expression network analysis http://purl.obolibrary.org/obo/edam#operations|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3465 Correlation "Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data." FALSE http://edamontology.org/operation_0004 1.7 operation_3465 "Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3469 RNA structure covariance model generation Compute the covariance model for (a family of) RNA secondary structures. FALSE http://edamontology.org/operation_2439|http://edamontology.org/operation_3429 1.7 operation_3469 Compute the covariance model for (a family of) RNA secondary structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3470 RNA secondary structure prediction (shape-based) "Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.7 operation_3470 "Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0278 1.18 http://edamontology.org/operation_0278 http://edamontology.org/operation_3471 Nucleic acid folding prediction (alignment-based) Prediction of nucleic-acid folding using sequence alignments as a source of data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.7 operation_3471 Prediction of nucleic-acid folding using sequence alignments as a source of data. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_0279 1.18 http://edamontology.org/operation_0279 http://edamontology.org/operation_3472 k-mer counting "Count k-mers (substrings of length k) in DNA sequence data.|k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. " FALSE http://edamontology.org/operation_0236 1.7 operation_3472 Count k-mers (substrings of length k) in DNA sequence data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3478 Phylogenetic tree reconstruction Reconstructing the inner node labels of a phylogenetic tree from its leafes.|Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. FALSE http://edamontology.org/operation_0323 1.7 operation_3478 Reconstructing the inner node labels of a phylogenetic tree from its leafes. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3480 Probabilistic data generation "Generate some data from a choosen probibalistic model, possibly to evaluate algorithms." FALSE http://edamontology.org/operation_3429 1.7 operation_3480 "Generate some data from a choosen probibalistic model, possibly to evaluate algorithms." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3481 Probabilistic sequence generation "Generate sequences from some probabilistic model, e.g. a model that simulates evolution." FALSE http://edamontology.org/operation_0230|http://edamontology.org/operation_3480 1.7 operation_3481 "Generate sequences from some probabilistic model, e.g. a model that simulates evolution." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3482 Antimicrobial resistance prediction Identify or predict causes for antibiotic resistance from molecular sequence analysis. FALSE http://edamontology.org/operation_2423|http://edamontology.org/operation_2403 1.7 operation_3482 Identify or predict causes for antibiotic resistance from molecular sequence analysis. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#data http://edamontology.org/operation_3501 Over-representation analysis Enrichment|Enrichment analysis|Functional enrichment "Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed.|Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data." FALSE http://edamontology.org/operation_2945 1.8 operation_3501 "Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed." Enrichment|Enrichment analysis Functional enrichment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3502 Chemical class enrichment Analyse a dataset with respect to concepts from an ontology of chemical structure. FALSE http://edamontology.org/operation_3501 1.8 operation_3502 Analyse a dataset with respect to concepts from an ontology of chemical structure. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3503 Incident curve plotting "Plot an incident curve such as a survival curve, death curve, mortality curve." FALSE http://edamontology.org/operation_3441 1.8 operation_3503 "Plot an incident curve such as a survival curve, death curve, mortality curve." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3504 Variant pattern analysis Identify and map patterns of genomic variations.|Methods often utilise a database of aligned reads. FALSE http://edamontology.org/operation_3197 1.8 operation_3504 Identify and map patterns of genomic variations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3545 Mathematical modelling "Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier operation_3545 "Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_2426 1.12 http://edamontology.org/operation_3552 Microscope image visualisation Visualise images resulting from various types of microscopy. FALSE http://edamontology.org/operation_0337 1.9 operation_3552 Visualise images resulting from various types of microscopy. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3553 Image annotation "Annotate an image of some sort, typically with terms from a controlled vocabulary." FALSE http://edamontology.org/operation_0226 1.9 operation_3553 "Annotate an image of some sort, typically with terms from a controlled vocabulary." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3557 Imputation Data imputation "Replace missing data with substituted values, usually by using some statistical or other mathematical approach." FALSE http://edamontology.org/operation_2238 1.9 operation_3557 "Replace missing data with substituted values, usually by using some statistical or other mathematical approach." Data imputation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3559 Ontology visualisation Ontology browsing "Visualise, format or render data from an ontology, typically a tree of terms." FALSE http://edamontology.org/operation_0337 1.9 operation_3559 "Visualise, format or render data from an ontology, typically a tree of terms." Ontology browsing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3560 Maximum occurence analysis A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. FALSE http://edamontology.org/operation_0321 beta12orEarlier operation_3560 A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3561 Database comparison Data model comparison|Schema comparison "Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves." FALSE http://edamontology.org/operation_2429|http://edamontology.org/operation_2424 1.9 operation_3561 "Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves." Data model comparison|Schema comparison http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3562 Network simulation Pathway simulation|Network topology simulation Simulate the bevaviour of a biological pathway or network. FALSE http://edamontology.org/operation_2426 1.9 operation_3562 Simulate the bevaviour of a biological pathway or network. Pathway simulation|Network topology simulation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3563 RNA-seq read count analysis Analyze read counts from RNA-seq experiments. FALSE http://edamontology.org/operation_3680 1.9 operation_3563 Analyze read counts from RNA-seq experiments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3564 Chemical redundancy removal Identify and remove redudancy from a set of small molecule structures. FALSE http://edamontology.org/operation_2483 1.9 operation_3564 Identify and remove redudancy from a set of small molecule structures. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3565 RNA-seq time series data analysis Analyze time series data from an RNA-seq experiment. FALSE http://edamontology.org/operation_3680 1.9 operation_3565 Analyze time series data from an RNA-seq experiment. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3566 Simulated gene expression data generation "Simulate gene expression data, e.g. for purposes of benchmarking." FALSE http://edamontology.org/operation_2426 1.9 operation_3566 "Simulate gene expression data, e.g. for purposes of benchmarking." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3625 Relation inference Relationship inference "Identify semantic relations among entities and concepts within a text, using text mining techniques." FALSE http://edamontology.org/operation_0306 1.12 operation_3625 "Identify semantic relations among entities and concepts within a text, using text mining techniques." Relationship inference http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3627 Mass spectra calibration Re-adjust the output of mass spectrometry experiments with shifted ppm values. FALSE http://edamontology.org/operation_3214 1.12 operation_3627 Re-adjust the output of mass spectrometry experiments with shifted ppm values. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3628 Chromatographic alignment "Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments." FALSE http://edamontology.org/operation_3214 1.12 operation_3628 "Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3629 Deisotoping Deconvolution "The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point.|Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution." FALSE http://edamontology.org/operation_3214 1.12 operation_3629 "The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point." Deconvolution http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3630 Protein quantification Protein quantitation Technique for determining the amount of proteins in a sample. FALSE http://edamontology.org/operation_3799|http://edamontology.org/operation_3214 1.12 operation_3630 Technique for determining the amount of proteins in a sample. Protein quantitation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3631 Peptide identification Peptide-spectrum-matching Determination of peptide sequence from mass spectrum. FALSE http://edamontology.org/operation_3214 1.12 operation_3631 Determination of peptide sequence from mass spectrum. Peptide-spectrum-matching http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3632 Isotopic distributions calculation Calculate the isotope distribution of a given chemical species. FALSE http://edamontology.org/operation_3438 1.12 operation_3632 Calculate the isotope distribution of a given chemical species. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3633 Retention time prediction Retention time calculation Prediction of retention time in a mass spectrometry experiment based on compositional and structural properties of the separated species. FALSE http://edamontology.org/operation_3438 1.12 operation_3633 Prediction of retention time in a mass spectrometry experiment based on compositional and structural properties of the separated species. Retention time calculation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3634 Label-free quantification Quantification without the use of chemical tags. FALSE http://edamontology.org/operation_3630 1.12 operation_3634 Quantification without the use of chemical tags. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3635 Labeled quantification Quantification based on the use of chemical tags. FALSE http://edamontology.org/operation_3630 1.12 operation_3635 Quantification based on the use of chemical tags. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3636 MRM/SRM Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). FALSE http://edamontology.org/operation_3630 1.12 operation_3636 Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3637 Spectral counting Calculate number of identified MS2 spectra as approximation of peptide / protein quantity. FALSE http://edamontology.org/operation_3634 1.12 operation_3637 Calculate number of identified MS2 spectra as approximation of peptide / protein quantity. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3638 SILAC Quantification analysis using stable isotope labeling by amino acids in cell culture. FALSE http://edamontology.org/operation_3635 1.12 operation_3638 Quantification analysis using stable isotope labeling by amino acids in cell culture. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3639 iTRAQ "Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z." FALSE http://edamontology.org/operation_3635 1.12 operation_3639 "Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3640 18O labeling Quantification analysis using labeling based on 18O-enriched H2O. FALSE http://edamontology.org/operation_3635 1.12 operation_3640 Quantification analysis using labeling based on 18O-enriched H2O. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3641 TMT-tag Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow. FALSE http://edamontology.org/operation_3635 1.12 operation_3641 Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3642 Dimethyl Quantification analysis using chemical labeling by stable isotope dimethylation FALSE http://edamontology.org/operation_3635 1.12 operation_3642 Quantification analysis using chemical labeling by stable isotope dimethylation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3643 Tag-based peptide identification Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry. FALSE http://edamontology.org/operation_3631 1.12 operation_3643 Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3644 de Novo sequencing Analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database. FALSE http://edamontology.org/operation_3631|http://edamontology.org/operation_2514 1.12 operation_3644 Analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3645 PTM identification Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum. FALSE http://edamontology.org/operation_3631 1.12 operation_3645 Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3646 Peptide database search Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences. FALSE http://edamontology.org/operation_2421|http://edamontology.org/operation_3631 1.12 operation_3646 Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3647 Blind peptide database search Unrestricted peptide database search|Modification-tolerant peptide database search Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches. FALSE http://edamontology.org/operation_3646 1.12 operation_3647 Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches. Unrestricted peptide database search|Modification-tolerant peptide database search http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3648 Validation of peptide-spectrum matches "Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search." FALSE http://edamontology.org/operation_2428|http://edamontology.org/operation_3646 1.12 operation_3648 "Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3649 Target-Decoy Estimation of false discovery rate by comparison to search results with a database containing incorrect information. FALSE http://edamontology.org/operation_3648 1.12 operation_3649 Estimation of false discovery rate by comparison to search results with a database containing incorrect information. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3658 Statistical inference Empirical Bayes Analyse data in order to deduce properties of an underlying distribution or population. FALSE http://edamontology.org/operation_2238 1.12 operation_3658 Analyse data in order to deduce properties of an underlying distribution or population. Empirical Bayes http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3659 Regression analysis Regression A statistical calculation to estimate the relationships among variables. FALSE http://edamontology.org/operation_2238 1.12 operation_3659 A statistical calculation to estimate the relationships among variables. Regression http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3660 Metabolic network modelling Metabolic reconstruction|Metabolic network reconstruction|Metabolic network simulation "Model a metabolic network, for example, to reconstruct pathways or to simulate metabolism." FALSE http://edamontology.org/operation_3562 1.12 operation_3660 "Model a metabolic network, for example, to reconstruct pathways or to simulate metabolism." Metabolic reconstruction|Metabolic network reconstruction|Metabolic network simulation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3661 SNP annotation Predict the effect or function of an individual single nucleotide polymorphism (SNP). FALSE http://edamontology.org/operation_0361 1.12 operation_3661 Predict the effect or function of an individual single nucleotide polymorphism (SNP). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3662 Ab-initio gene prediction Gene prediction (ab-initio) "Prediction of genes or gene components from first principles, i.e. without reference to existing genes." FALSE http://edamontology.org/operation_2454 1.12 operation_3662 "Prediction of genes or gene components from first principles, i.e. without reference to existing genes." Gene prediction (ab-initio) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3663 Homology-based gene prediction Gene prediction (homology-based) Prediction of genes or gene components by reference to homologous genes. FALSE http://edamontology.org/operation_2454 1.12 operation_3663 Prediction of genes or gene components by reference to homologous genes. Gene prediction (homology-based) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3664 Statistical modelling "Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data." FALSE http://edamontology.org/operation_2238 1.12 operation_3664 "Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3666 Molecular surface comparison Compare two or more molecular surfaces. FALSE http://edamontology.org/operation_3351|http://edamontology.org/operation_2483 1.12 operation_3666 Compare two or more molecular surfaces. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3672 Gene functional annotation Sequence functional annotation "Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO)." FALSE http://edamontology.org/operation_0361 1.12 operation_3672 "Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO)." Sequence functional annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3675 Variant filtering "Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info." FALSE http://edamontology.org/operation_3218|http://edamontology.org/operation_2478 1.12 operation_3675 "Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3677 Differential binding analysis Differential binding analysis identifies binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups. FALSE http://edamontology.org/operation_2478 1.12 operation_3677 Differential binding analysis identifies binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3680 RNA-Seq analysis Analyze data from RNA-seq experiments. FALSE http://edamontology.org/operation_2478 1.13 operation_3680 Analyze data from RNA-seq experiments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3694 Mass spectrum visualisation "Visualise, format or render a mass spectrum." FALSE http://edamontology.org/operation_0337 1.1 operation_3694 "Visualise, format or render a mass spectrum." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3695 Filtering rRNA filtering|Sequence filtering Filter a set of files or data items according to some property. FALSE http://edamontology.org/operation_2409 1.13 operation_3695 Filter a set of files or data items according to some property. rRNA filtering|Sequence filtering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3703 Reference identification "Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis." FALSE http://edamontology.org/operation_3197 1.1 operation_3703 "Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3704 Ion counting Ion current integration Label-free quantification by integration of ion current (ion counting). FALSE http://edamontology.org/operation_3634 1.14 operation_3704 Label-free quantification by integration of ion current (ion counting). Ion current integration http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3705 Isotope-coded protein label ICPL Chemical tagging free amino groups of intact proteins with stable isotopes. FALSE http://edamontology.org/operation_3635 1.14 operation_3705 Chemical tagging free amino groups of intact proteins with stable isotopes. ICPL http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3715 Metabolic labeling N-15 metabolic labeling|C-13 metabolic labeling Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed.|This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed). FALSE http://edamontology.org/operation_3635 1.14 operation_3715 Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed. N-15 metabolic labeling|C-13 metabolic labeling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3730 Cross-assembly Sequence assembly (cross-assembly) "Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis." FALSE http://edamontology.org/operation_0310 1.15 operation_3730 "Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis." Sequence assembly (cross-assembly) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3731 Sample comparison "The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method." FALSE http://edamontology.org/operation_2424 1.15 operation_3731 "The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3741 Differential protein expression analysis Differential protein analysis "The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup." FALSE http://edamontology.org/operation_2997|http://edamontology.org/operation_3223 1.15 operation_3741 Differential protein analysis "The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3742 Differential gene expression analysis "The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.15 operation_3742 "The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/operation_3223 1.17 http://edamontology.org/operation_2424 http://edamontology.org/operation_3744 Multiple sample visualisation "Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment." FALSE http://edamontology.org/operation_0337 1.15 operation_3744 "Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3745 Ancestral reconstruction Character mapping|Character optimisation "The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors.|Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms." FALSE http://edamontology.org/operation_0324 1.15 operation_3745 "The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors." Character mapping|Character optimisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3755 PTM localisation Site localisation| PTM scoring Site localisation of post-translational modifications in peptide or protein mass spectra. FALSE http://edamontology.org/operation_3645 1.16 operation_3755 Site localisation of post-translational modifications in peptide or protein mass spectra. Site localisation| PTM scoring http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3760 Service management Endpoint management Operations concerning the handling and use of other tools. FALSE http://edamontology.org/operation_0004 1.16 operation_3760 Operations concerning the handling and use of other tools. Endpoint management http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3761 Service discovery An operation supporting the browsing or discovery of other tools and services. FALSE http://edamontology.org/operation_3760 1.16 operation_3761 An operation supporting the browsing or discovery of other tools and services. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3762 Service composition "An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task." FALSE http://edamontology.org/operation_3760 1.16 operation_3762 "An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3763 Service invocation An operation supporting the calling (invocation) of other tools and services. FALSE http://edamontology.org/operation_3760 1.16 operation_3763 An operation supporting the calling (invocation) of other tools and services. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3766 Weighted correlation network analysis WGCNA|Weighted gene co-expression network analysis A data mining method typically used for studying biological networks based on pairwise correlations between variables. FALSE http://edamontology.org/operation_2497 1.16 operation_3766 A data mining method typically used for studying biological networks based on pairwise correlations between variables. WGCNA|Weighted gene co-expression network analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3767 Protein identification Protein inference "Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry." FALSE http://edamontology.org/operation_2502|http://edamontology.org/operation_3214 1.16 operation_3767 "Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry." Protein inference http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3778 Text annotation Literature annotation|Article annotation "Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article)." FALSE http://edamontology.org/operation_0226 1.16 operation_3778 "Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article)." Literature annotation|Article annotation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3791 Collapsing methods "A method whereby data on several variants are ""collapsed"" into a single covariate based on regions such as genes.|Genome-wide association studies (GWAS) analyse a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Traditional association techniques can lack the power to detect the significance of rare variants individually, or measure their compound effect (rare variant burden). ""Collapsing methods"" were developed to overcome these problems. " FALSE http://edamontology.org/operation_3197 1.17 operation_3791 "A method whereby data on several variants are ""collapsed"" into a single covariate based on regions such as genes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3792 miRNA analysis "The analysis of microRNAs (miRNAs) : short, highly conserved small noncoding RNA molecules that are naturally occurring plant and animal genomes." FALSE http://edamontology.org/operation_2495 1.17 operation_3792 "The analysis of microRNAs (miRNAs) : short, highly conserved small noncoding RNA molecules that are naturally occurring plant and animal genomes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3793 Read summarisation Counting and summarising the number of short sequence reads that map to genomic features. FALSE http://edamontology.org/operation_2478 1.17 operation_3793 Counting and summarising the number of short sequence reads that map to genomic features. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3795 In vitro selection "A technique whereby molecules with desired properties and function are isolated from libraries of random molecules, through iterative cycles of selection, amplification, and mutagenesis." FALSE http://edamontology.org/operation_3095 1.17 operation_3795 "A technique whereby molecules with desired properties and function are isolated from libraries of random molecules, through iterative cycles of selection, amplification, and mutagenesis." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3797 Rarefaction "The calculation of species richness for a number of individual samples, based on plots of the number of species as a function of the number of samples (rarefaction curves)." FALSE http://edamontology.org/operation_0004 1.17 operation_3797 "The calculation of species richness for a number of individual samples, based on plots of the number of species as a function of the number of samples (rarefaction curves)." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3798 Read binning Binning An operation which groups reads or contigs and assigns them to operational taxonomic units.|Binning methods use one or a combination of compositional features or sequence similarity. FALSE http://edamontology.org/operation_2478 1.17 operation_3798 Binning An operation which groups reads or contigs and assigns them to operational taxonomic units. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3799 Quantification Quantitation Counting and measuring experimentally determined observations into quantities. FALSE http://edamontology.org/operation_0004 1.17 operation_3799 Counting and measuring experimentally determined observations into quantities. Quantitation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations Not recommended for annotation in bio.tools. http://edamontology.org/operation_3800 RNA-Seq quantification RNA-Seq quantitation "Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study. " FALSE http://edamontology.org/operation_3799 1.17 operation_3800 "Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study. " RNA-Seq quantitation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3801 Spectral library search Match experimentally measured mass spectrum to a spectrum in a spectral library or database. FALSE http://edamontology.org/operation_3631 1.17 operation_3801 Match experimentally measured mass spectrum to a spectrum in a spectral library or database. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3802 Sorting Sort a set of files or data items according to some property. FALSE http://edamontology.org/operation_2409 1.17 operation_3802 Sort a set of files or data items according to some property. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/operation_3803 Natural product identification Metabolite identification "Mass spectra identification of compounds that are produced by living systems. Including polyketides, terpenoids, phenylpropanoids, alkaloids and antibiotics." FALSE http://edamontology.org/operation_3214 1.17 operation_3803 Metabolite identification "Mass spectra identification of compounds that are produced by living systems. Including polyketides, terpenoids, phenylpropanoids, alkaloids and antibiotics." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#operations http://edamontology.org/topic_0003 Topic sumo:FieldOfStudy "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." FALSE http://www.w3.org/2002/07/owl#Thing beta12orEarlier topic_0003 "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." sumo:FieldOfStudy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics Not recommended for annotation in bio.tools. http://edamontology.org/topic_0077 Nucleic acids Nucleic acid informatics|Nucleic acid bioinformatics|Nucleic acid physicochemistry|Nucleic acid properties "The processing and analysis of nucleic acid sequence, structural and other data." FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_0077 "The processing and analysis of nucleic acid sequence, structural and other data." Nucleic acid informatics|Nucleic acid bioinformatics Nucleic acid physicochemistry|Nucleic acid properties http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0078 Proteins Protein informatics|Protein bioinformatics|Protein databases "Archival, processing and analysis of protein data, typically molecular sequence and structural data." FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_0078 "Archival, processing and analysis of protein data, typically molecular sequence and structural data." Protein informatics|Protein bioinformatics Protein databases http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0079 Metabolites "The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0079 "The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0154 1.13 http://edamontology.org/topic_0080 Sequence analysis Sequences|Sequence databases "The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles." FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_0080 "The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles." Sequences Sequence databases http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0081 Structure analysis Structural bioinformatics|Structure databases|Computational structural biology|Structure data resources "The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.|This includes related concepts such as structural properties, alignments and structural motifs." FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_0081 "The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules." Structural bioinformatics Structure databases|Computational structural biology|Structure data resources http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0082 Structure prediction RNA structure prediction|Nucleic acid folding|Nucleic acid design|DNA structure prediction|Protein fold recognition|Protein structure prediction|Nucleic acid structure prediction "The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. |This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." FALSE http://edamontology.org/topic_0081 beta12orEarlier topic_0082 "The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. " RNA structure prediction|Nucleic acid folding|Nucleic acid design|DNA structure prediction|Protein fold recognition|Protein structure prediction|Nucleic acid structure prediction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0083 Alignment "The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0083 http://edamontology.org/topic_0080|http://edamontology.org/topic_0081 "The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0084 Phylogeny Phylogeny reconstruction|Phylogenetic dating|Phylogenetic simulation|Phylogenetic clocks|Phylogenetic stratigraphy "The study of evolutionary relationships amongst organisms.|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, methods for studying gene evolution etc." FALSE http://edamontology.org/topic_3299|http://edamontology.org/topic_3307 beta12orEarlier topic_0084 The study of evolutionary relationships amongst organisms. Phylogeny reconstruction|Phylogenetic dating|Phylogenetic simulation|Phylogenetic clocks|Phylogenetic stratigraphy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0085 Functional genomics "The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc." FALSE http://edamontology.org/topic_0622|http://edamontology.org/topic_1775 beta12orEarlier topic_0085 "The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0089 Ontology and terminology Applied ontology|Ontologies|Terminology|Ontology "The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource." FALSE http://edamontology.org/topic_0605 beta12orEarlier topic_0089 "The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource." Applied ontology|Ontologies|Terminology|Ontology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0090 Information retrieval The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0090 The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3071 1.13 http://edamontology.org/topic_0091 Bioinformatics "The archival, curation, processing and analysis of complex biological data.|This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation." FALSE http://edamontology.org/topic_0605 beta12orEarlier topic_0091 VT 1.5.6 Bioinformatics "The archival, curation, processing and analysis of complex biological data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0092 Data visualisation Computer graphics|Data rendering "Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data." FALSE http://edamontology.org/topic_3316 beta12orEarlier topic_0092 Computer graphics VT 1.2.5 Computer graphics "Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data." Data rendering http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0094 Nucleic acid thermodynamics The study of the thermodynamic properties of a nucleic acid. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass topic_0094 http://edamontology.org/topic_0097 The study of the thermodynamic properties of a nucleic acid. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0097 Nucleic acid structure analysis Nucleic acid structure|Nucleic acid denaturation|Nucleic acid thermodynamics|DNA melting|RNA structure|RNA alignment|RNA structure alignment "The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.|Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc." FALSE http://edamontology.org/topic_0077|http://edamontology.org/topic_0081 beta12orEarlier topic_0097 "The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation." Nucleic acid structure Nucleic acid denaturation|Nucleic acid thermodynamics|DNA melting|RNA structure|RNA alignment|RNA structure alignment http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0099 RNA Small RNA RNA sequences and structures. FALSE http://edamontology.org/topic_0077 beta12orEarlier topic_0099 RNA sequences and structures. Small RNA http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0100 Nucleic acid restriction "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0100 http://edamontology.org/topic_0821 "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0102 Mapping Genetic linkage|Synteny|Linkage|Linkage mapping "The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). |This includes 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. It also includes resources for physical (sequence) maps 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. " FALSE http://edamontology.org/topic_0080 beta12orEarlier topic_0102 "The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). " Genetic linkage|Synteny|Linkage|Linkage mapping http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0107 Genetic codes and codon usage "The study of codon usage in nucleotide sequence(s), genetic codes and so on." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0107 http://edamontology.org/topic_0203 "The study of codon usage in nucleotide sequence(s), genetic codes and so on." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0108 Protein expression Translation The translation of mRNA into protein and subsequent protein processing in the cell. FALSE http://edamontology.org/topic_0078 beta12orEarlier topic_0108 The translation of mRNA into protein and subsequent protein processing in the cell. Translation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0109 Gene finding "Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0109 http://edamontology.org/topic_0114 "Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0110 Transcription The transcription of DNA into mRNA. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0110 http://edamontology.org/topic_0203 The transcription of DNA into mRNA. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0111 Promoters Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0111 http://edamontology.org/topic_0749 Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0112 Nucleic acid folding The folding (in 3D space) of nucleic acid molecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0112 The folding (in 3D space) of nucleic acid molecules. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0097 beta12orEarlier http://edamontology.org/topic_0114 Gene structure Gene features|Fusion genes "Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. |This includes the study of promoters, coding regions etc.|This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information." FALSE http://edamontology.org/topic_3321 beta12orEarlier topic_0114 "Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. " Gene features Fusion genes http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0121 Proteomics Peptide identification|Protein and peptide identification|Metaproteomics "Protein and peptide identification, especially in the study of whole proteomes of organisms.|Includes metaproteomics: proteomics analysis of an environmental sample.|Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues." FALSE http://edamontology.org/topic_3391 beta12orEarlier topic_0121 "Protein and peptide identification, especially in the study of whole proteomes of organisms." Peptide identification|Protein and peptide identification|Metaproteomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0122 Structural genomics The elucidation of the three dimensional structure for all (available) proteins in a given organism. FALSE http://edamontology.org/topic_0622|http://edamontology.org/topic_1317 beta12orEarlier topic_0122 The elucidation of the three dimensional structure for all (available) proteins in a given organism. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0123 Protein properties Protein physicochemistry|Protein hydropathy "The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein." FALSE http://edamontology.org/topic_0078 beta12orEarlier topic_0123 "The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein." Protein physicochemistry Protein hydropathy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0128 Protein interactions Protein-nucleic acid interactions|Protein-RNA interaction|Protein-ligand interactions|Protein-protein interactions|Protein interaction networks|Protein-DNA interaction "Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.|This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques." FALSE http://edamontology.org/topic_0602|http://edamontology.org/topic_0078 beta12orEarlier topic_0128 "Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." Protein-nucleic acid interactions|Protein-RNA interaction|Protein-ligand interactions|Protein-protein interactions|Protein interaction networks|Protein-DNA interaction http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0130 "Protein folding, stability and design" Protein stability|Protein design|Protein residue interactions|Protein folding|Rational protein design "Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." FALSE http://edamontology.org/topic_2814 beta12orEarlier topic_0130 "Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." Protein stability|Protein design|Protein residue interactions|Protein folding|Rational protein design http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0133 Two-dimensional gel electrophoresis Two-dimensional gel electrophoresis image and related data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0133 http://edamontology.org/topic_0121 Two-dimensional gel electrophoresis image and related data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0134 Mass spectrometry An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0134 An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3520 1.13 http://edamontology.org/topic_0135 Protein microarrays Protein microarray data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0135 http://edamontology.org/topic_0121 Protein microarray data. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0137 Protein hydropathy "The study of the hydrophobic, hydrophilic and charge properties of a protein." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0137 http://edamontology.org/topic_0123 "The study of the hydrophobic, hydrophilic and charge properties of a protein." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0140 Protein targeting and localisation Protein sorting|Protein targeting|Protein localisation "The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export." FALSE http://edamontology.org/topic_0108 beta12orEarlier topic_0140 "The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export." Protein sorting|Protein targeting|Protein localisation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0141 Protein cleavage sites and proteolysis Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0141 http://edamontology.org/topic_0121 Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0143 Protein structure comparison The comparison of two or more protein structures.|Use this concept for methods that are exclusively for protein structure. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0143 The comparison of two or more protein structures. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0081 beta12orEarlier http://edamontology.org/topic_0144 Protein residue interactions The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0144 http://edamontology.org/topic_0130 The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0147 Protein-protein interactions "Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0147 http://edamontology.org/topic_0128 "Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0148 Protein-ligand interactions Protein-ligand (small molecule) interactions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0148 http://edamontology.org/topic_0128 Protein-ligand (small molecule) interactions. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0149 Protein-nucleic acid interactions Protein-DNA/RNA interactions. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0149 http://edamontology.org/topic_0128 Protein-DNA/RNA interactions. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0150 Protein design "The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0150 http://edamontology.org/topic_0130 "The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0151 G protein-coupled receptors (GPCR) G-protein coupled receptors (GPCRs). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0151 http://edamontology.org/topic_0820 G-protein coupled receptors (GPCRs). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0152 Carbohydrates "Carbohydrates, typically including structural information." FALSE http://edamontology.org/topic_0081 beta12orEarlier topic_0152 "Carbohydrates, typically including structural information." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0153 Lipids Lipidomics Lipids and their structures. FALSE http://edamontology.org/topic_0081 beta12orEarlier topic_0153 Lipids and their structures. Lipidomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0154 Small molecules Chemical structures|Toxins and targets|Amino acids|Targets|Drugs and target structures|Peptides|Toxins|Peptides and amino acids|Metabolite structures|Metabolites|Target structures|Drug structures|Drug targets|CHEBI:23367 "Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.|This concept excludes macromolecules such as proteins and nucleic acids.|This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances.|Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included." FALSE http://edamontology.org/topic_0081 beta12orEarlier topic_0154 "Small molecules of biological significance, typically archival, curation, processing and analysis of structural information." Chemical structures|Toxins and targets|Amino acids|Targets|Drugs and target structures|Peptides|Toxins|Peptides and amino acids|Metabolite structures|Metabolites|Target structures|Drug structures|Drug targets CHEBI:23367 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0156 Sequence editing "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0156 http://edamontology.org/topic_0080|http://edamontology.org/topic_0091 "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0157 "Sequence composition, complexity and repeats" Protein repeats|Sequence repeats|Nucleic acid repeats|Repeat sequences|Protein sequence repeats|Sequence complexity|Sequence composition|Low complexity sequences "The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.|This includes repetitive elements within a nucleic acid sequence, e.g. long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit.|This includes short repetitive subsequences (repeat sequences) in a protein sequence." FALSE http://edamontology.org/topic_0080 beta12orEarlier topic_0157 "The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences." Protein repeats|Sequence repeats|Nucleic acid repeats|Repeat sequences|Protein sequence repeats|Sequence complexity|Sequence composition|Low complexity sequences http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0158 Sequence motifs Motifs "Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0158 http://edamontology.org/topic_0160 "Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." Motifs http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0159 Sequence comparison "The comparison of two or more molecular sequences, for example sequence alignment and clustering.|The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0159 "The comparison of two or more molecular sequences, for example sequence alignment and clustering." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.12 http://edamontology.org/topic_0160 "Sequence sites, features and motifs" Functional sites|Sequence features|Sequence sites|Sequence profiles|Sequence motifs|HMMs "The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them." FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_0160 "The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them." Functional sites|Sequence features|Sequence sites|Sequence profiles|Sequence motifs|HMMs http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0163 Sequence database search "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).|The query is a sequence-based entity such as another sequence, a motif or profile." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0163 http://edamontology.org/topic_0080 Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0164 Sequence clustering "The comparison and grouping together of molecular sequences on the basis of their similarities.|This includes systems that generate, process and analyse sequence clusters." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0164 The comparison and grouping together of molecular sequences on the basis of their similarities. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.7 http://edamontology.org/topic_0166 Protein structural motifs and surfaces Protein 3D motifs|Protein structural motifs|Protein structural features|Protein surfaces|Structural motifs "Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.|This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc." FALSE http://edamontology.org/topic_2814 beta12orEarlier topic_0166 "Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." Protein 3D motifs Protein structural motifs|Protein structural features|Protein surfaces|Structural motifs http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0167 Structural (3D) profiles "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0167 http://edamontology.org/topic_0081 "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://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0172 Protein structure prediction "The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0172 "The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.12 http://edamontology.org/topic_0173 Nucleic acid structure prediction The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0173 The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0097 1.12 http://edamontology.org/topic_0174 Ab initio structure prediction "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0174 "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://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.7 http://edamontology.org/topic_0175 Homology modelling The modelling of the three-dimensional structure of a protein using known sequence and structural data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0175 http://edamontology.org/topic_2275 The modelling of the three-dimensional structure of a protein using known sequence and structural data. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/topic_0176 Molecular dynamics Molecular motions|Molecular flexibility|Protein dynamics The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.|This includes resources concerning flexibility and motion in protein and other molecular structures. FALSE http://edamontology.org/topic_0082 beta12orEarlier topic_0176 Molecular motions|Molecular flexibility The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. Protein dynamics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0177 Molecular docking The modelling the structure of proteins in complex with small molecules or other macromolecules. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0177 The modelling the structure of proteins in complex with small molecules or other macromolecules. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2275 TRUE 1.12 http://edamontology.org/topic_0178 Protein secondary structure prediction The prediction of secondary or supersecondary structure of protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0178 The prediction of secondary or supersecondary structure of protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.3 http://edamontology.org/topic_0179 Protein tertiary structure prediction The prediction of tertiary structure of protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0179 The prediction of tertiary structure of protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.3 http://edamontology.org/topic_0180 Protein fold recognition The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0180 The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.12 http://edamontology.org/topic_0182 Sequence alignment "The alignment of molecular sequences or sequence profiles (representing sequence alignments).|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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0182 The alignment of molecular sequences or sequence profiles (representing sequence alignments). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.7 http://edamontology.org/topic_0183 Structure alignment "The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).|This includes the generation, storage, analysis, rendering etc. of structure alignments." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0183 The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0081 1.7 http://edamontology.org/topic_0184 Threading "The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0184 "The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0082 1.3 http://edamontology.org/topic_0188 Sequence profiles and HMMs "Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.|Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0188 http://edamontology.org/topic_0160 "Sequence profiles; typically a positional, numerical matrix representing a sequence alignment." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0191 Phylogeny reconstruction "The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.|Currently too specific for the topic sub-ontology (but might be unobsoleted)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0191 http://edamontology.org/topic_3293 "The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0194 Phylogenomics "The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." FALSE http://edamontology.org/topic_0622|http://edamontology.org/topic_0080 beta12orEarlier topic_0194 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0195 Virtual PCR Simulated polymerase chain reaction (PCR). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0195 http://edamontology.org/topic_0077 Simulated polymerase chain reaction (PCR). http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0196 Sequence assembly Assembly "The assembly of fragments of a DNA sequence to reconstruct the original sequence.|Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'." FALSE http://edamontology.org/topic_0080 beta12orEarlier topic_0196 The assembly of fragments of a DNA sequence to reconstruct the original sequence. Assembly http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0199 Genetic variation DNA variation|Polymorphism|Mutation|Somatic mutations "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." FALSE http://edamontology.org/topic_3321 beta12orEarlier topic_0199 "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." DNA variation Polymorphism|Mutation|Somatic mutations http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0200 Microarrays "Microarrays, for example, to process microarray data or design probes and experiments." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0200 http://edamontology.org/topic_0203 "Microarrays, for example, to process microarray data or design probes and experiments." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0202 Pharmacology Computational pharmacology|Pharmacoinformatics The study of drugs and their effects or responses in living systems. FALSE http://edamontology.org/topic_3344 beta12orEarlier topic_0202 VT 3.1.7 Pharmacology and pharmacy The study of drugs and their effects or responses in living systems. Computational pharmacology|Pharmacoinformatics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0203 Gene expression Codon usage|Transcription|Gene expression profiling|DNA microarrays "The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.|Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.|This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on." FALSE http://edamontology.org/topic_3321 beta12orEarlier topic_0203 http://edamontology.org/topic_0197 The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Codon usage|Transcription|Gene expression profiling|DNA microarrays http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0204 Gene regulation Regulatory genomics The regulation of gene expression. FALSE http://edamontology.org/topic_0203 beta12orEarlier topic_0204 The regulation of gene expression. Regulatory genomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0208 Pharmacogenomics Pharmacogenetics "The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." FALSE http://edamontology.org/topic_0622|http://edamontology.org/topic_0202 beta12orEarlier topic_0208 "The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." Pharmacogenetics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0209 Medicinal chemistry Drug design "The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.|This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc." FALSE http://edamontology.org/topic_3336|http://edamontology.org/topic_3371 beta12orEarlier topic_0209 VT 3.1.4 Medicinal chemistry "The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes." Drug design http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0210 Fish "Information on a specific fish genome including molecular sequences, genes and annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0210 http://edamontology.org/topic_0621 "Information on a specific fish genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0211 Flies "Information on a specific fly genome including molecular sequences, genes and annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0211 http://edamontology.org/topic_0621 "Information on a specific fly genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0213 Mice or rats "Information on a specific mouse or rat genome including molecular sequences, genes and annotation.|The resource may be specific to a group of mice / rats or all mice / rats." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_0213 http://edamontology.org/topic_0621 "Information on a specific mouse or rat genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_2820 http://edamontology.org/topic_0215 Worms "Information on a specific worm genome including molecular sequences, genes and annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0215 http://edamontology.org/topic_0621 "Information on a specific worm genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0217 Literature analysis "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0217 "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0218 1.3 http://edamontology.org/topic_0218 Natural language processing NLP|Literature mining|BioNLP|Text analytics|Text data mining|Text mining "The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction." FALSE http://edamontology.org/topic_3068|http://edamontology.org/topic_3316 beta12orEarlier topic_0218 "The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction." NLP Literature mining|BioNLP|Text analytics|Text data mining|Text mining http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0219 "Data submission, annotation and curation" Database curation "Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary." FALSE http://edamontology.org/topic_3071 beta12orEarlier topic_0219 "Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary." Database curation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0220 "Document, record and content management" "The management and manipulation of digital documents, including database records, files and reports." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0220 "The management and manipulation of digital documents, including database records, files and reports." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3489 1.13 http://edamontology.org/topic_0221 Sequence annotation Annotation of a molecular sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0221 http://edamontology.org/topic_0219 Annotation of a molecular sequence. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0222 Genome annotation Annotation of a genome. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0222 http://edamontology.org/topic_0219|http://edamontology.org/topic_0621 Annotation of a genome. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0593 NMR Spectroscopy|NMR spectroscopy|Nuclear magnetic resonance spectroscopy|Nuclear Overhauser Effect Spectroscopy|Heteronuclear Overhauser Effect Spectroscopy|Rotational Frame Nuclear Overhauser Effect Spectroscopy|NOESY|ROESY|HOESY "An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules." FALSE http://edamontology.org/topic_3382|http://edamontology.org/topic_1317 beta12orEarlier topic_0593 Spectroscopy "An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules." NMR spectroscopy|Nuclear magnetic resonance spectroscopy Nuclear Overhauser Effect Spectroscopy|Heteronuclear Overhauser Effect Spectroscopy|Rotational Frame Nuclear Overhauser Effect Spectroscopy|NOESY|ROESY|HOESY http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0594 Sequence classification "The classification of molecular sequences based on some measure of their similarity.|Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0594 The classification of molecular sequences based on some measure of their similarity. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.12 http://edamontology.org/topic_0595 Protein classification "primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0595 http://edamontology.org/topic_0623 "primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0598 Sequence motif or profile "Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.|This includes comparison, discovery, recognition etc. of sequence motifs." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0598 http://edamontology.org/topic_0160 "Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0601 Protein modifications Protein post-translational modification|Post-translation modifications|Protein post-translational modifications|Protein chemical modifications|GO:0006464|MOD:00000 "Protein chemical modifications, e.g. post-translational modifications.|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)" FALSE http://edamontology.org/topic_0108 beta12orEarlier topic_0601 "Protein chemical modifications, e.g. post-translational modifications." Protein post-translational modification Post-translation modifications|Protein post-translational modifications|Protein chemical modifications GO:0006464|MOD:00000 http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0602 "Molecular interactions, pathways and networks" Biological models|Genetic information processing pathways|Interactions|Networks|Signal transduction pathways|Pathways|Biological pathways|Signaling pathways|Gene regulatory networks|Disease pathways|Metabolic pathways|Environmental information processing pathways|Molecular interactions|Biological networks|Cellular process pathways "Molecular interactions, biological pathways, networks and other models." FALSE http://edamontology.org/topic_3307 beta13 topic_0602 http://edamontology.org/topic_3076 "Molecular interactions, biological pathways, networks and other models." Biological models|Genetic information processing pathways|Interactions|Networks|Signal transduction pathways|Pathways|Biological pathways|Signaling pathways|Gene regulatory networks|Disease pathways|Metabolic pathways|Environmental information processing pathways|Molecular interactions|Biological networks|Cellular process pathways http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0605 Informatics Information science|Knowledge management|Information management The study and practice of information processing and use of computer information systems. FALSE http://edamontology.org/topic_0003 beta12orEarlier topic_0605 VT 1.3 Information sciences|VT 1.3.99 Other|VT 1.3.3 Information retrieval|VT 1.3.5 Knowledge management|VT 1.3.4 Information management The study and practice of information processing and use of computer information systems. Information science|Knowledge management|Information management http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0606 Literature data resources "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0606 "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3068 1.3 http://edamontology.org/topic_0607 Laboratory information management Laboratory resources "Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." FALSE http://edamontology.org/topic_0605 beta12orEarlier topic_0607 http://edamontology.org/topic_3071 "Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." Laboratory resources http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0608 Cell and tissue culture General cell culture or data on a specific cell lines. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0608 http://edamontology.org/topic_2229 General cell culture or data on a specific cell lines. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0610 Ecology Environmental science|Ecological informatics|Computational ecology|Ecoinformatics The ecological and environmental sciences and especially the application of information technology (ecoinformatics). FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_0610 Environmental science VT 1.5.15 Ecology The ecological and environmental sciences and especially the application of information technology (ecoinformatics). Ecological informatics|Computational ecology|Ecoinformatics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0611 Electron microscopy Electron diffraction experiment|Transmission electron microscopy|SEM|Scanning electron microscopy|TEM|Electron crystallography|Single particle electron microscopy "The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. " FALSE http://edamontology.org/topic_3382|http://edamontology.org/topic_1317 beta12orEarlier topic_0611 Electron diffraction experiment "The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. " Transmission electron microscopy|SEM|Scanning electron microscopy|TEM|Electron crystallography|Single particle electron microscopy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0612 Cell cycle The cell cycle including key genes and proteins. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0612 http://edamontology.org/topic_2229 The cell cycle including key genes and proteins. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0613 Peptides and amino acids "The physicochemical, biochemical or structural properties of amino acids or peptides." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0613 "The physicochemical, biochemical or structural properties of amino acids or peptides." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0154 1.13 http://edamontology.org/topic_0616 Organelles "A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0616 http://edamontology.org/topic_2229 "A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0617 Ribosomes "Ribosomes, typically of ribosome-related genes and proteins." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0617 http://edamontology.org/topic_2229 "Ribosomes, typically of ribosome-related genes and proteins." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0618 Scents A database about scents. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0618 http://edamontology.org/topic_0154 A database about scents. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0620 Drugs and target structures "The structures of drugs, drug target, their interactions and binding affinities." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0620 "The structures of drugs, drug target, their interactions and binding affinities." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0154 1.13 http://edamontology.org/topic_0621 Model organisms Organisms "A specific organism, or group of organisms, used to study a particular aspect of biology.|This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism." FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_0621 "A specific organism, or group of organisms, used to study a particular aspect of biology." Organisms http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0622 Genomics Personal genomics|Viral genomics "Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." FALSE http://edamontology.org/topic_3391 beta12orEarlier topic_0622 "Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." Personal genomics|Viral genomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0623 Gene and protein families "Genes, gene family or system|Gene system|Gene family|Protein sequence classification|Protein families|Gene families" "Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.|A protein families database might include the classifier (e.g. a sequence profile) used to build the classification." FALSE http://edamontology.org/topic_3321|http://edamontology.org/topic_0078 beta12orEarlier topic_0623 "Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group." "Genes, gene family or system" Gene system|Gene family|Protein sequence classification|Protein families|Gene families http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0624 Chromosomes Study of chromosomes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0624 Study of chromosomes. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0654 1.13 http://edamontology.org/topic_0625 Genotype and phenotype Genotype and phenotype resources|Genotyping|Phenotyping "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." FALSE http://edamontology.org/topic_3053 beta12orEarlier topic_0625 "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." Genotype and phenotype resources Genotyping|Phenotyping http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0629 Gene expression and microarray "Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0629 http://edamontology.org/topic_0203 "Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_0632 Probes and primers Primers|Probes "Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. |This includes the design of primers for PCR and DNA amplification or the design of molecular probes." FALSE http://edamontology.org/topic_0080 beta12orEarlier topic_0632 "Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. " Primers|Probes http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0634 Pathology Disease "Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases." FALSE http://edamontology.org/topic_3303 beta12orEarlier topic_0634 VT 3.1.6 Pathology "Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases." Disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0635 Specific protein resources Specific protein "A particular protein, protein family or other group of proteins." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0635 http://edamontology.org/topic_0623 "A particular protein, protein family or other group of proteins." Specific protein http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0637 Taxonomy "Organism classification, identification and naming." FALSE http://edamontology.org/topic_3299 beta12orEarlier topic_0637 VT 1.5.25 Taxonomy "Organism classification, identification and naming." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0639 Protein sequence analysis "Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0639 "Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.8 http://edamontology.org/topic_0640 Nucleic acid sequence analysis "The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0640 "The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.8 http://edamontology.org/topic_0641 Repeat sequences The repetitive nature of molecular sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0641 http://edamontology.org/topic_0157 The repetitive nature of molecular sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0642 Low complexity sequences "The (character) complexity of molecular sequences, particularly regions of low complexity." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0642 http://edamontology.org/topic_0157 "The (character) complexity of molecular sequences, particularly regions of low complexity." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0644 Proteome A specific proteome including protein sequences and annotation. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0644 http://edamontology.org/topic_0080 A specific proteome including protein sequences and annotation. http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0654 DNA DNA analysis|Ancient DNA|Chromosomes "DNA sequences and structure, including processes such as methylation and replication.|The DNA sequences might be coding or non-coding sequences." FALSE http://edamontology.org/topic_0077 beta12orEarlier topic_0654 "DNA sequences and structure, including processes such as methylation and replication." DNA analysis Ancient DNA|Chromosomes http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0655 Coding RNA "Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames" TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0655 "Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames" http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_0659 "Functional, regulatory and non-coding RNA" small interfering RNA|Functional RNA|Regulatory RNA|miRNA|microRNA|small nucleolar RNA|Non-coding RNA|ncRNA|siRNA|snoRNA|snRNA|small nuclear RNA|piwi-interacting RNA|piRNA "Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).|Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA)." FALSE http://edamontology.org/topic_0114|http://edamontology.org/topic_0099 beta12orEarlier topic_0659 "Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA)." small interfering RNA|Functional RNA|Regulatory RNA|miRNA|microRNA|small nucleolar RNA|Non-coding RNA|ncRNA|siRNA|snoRNA|snRNA|small nuclear RNA|piwi-interacting RNA|piRNA http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0660 rRNA One or more ribosomal RNA (rRNA) sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass topic_0660 http://edamontology.org/topic_0659 One or more ribosomal RNA (rRNA) sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0663 tRNA One or more transfer RNA (tRNA) sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass topic_0663 http://edamontology.org/topic_0659 One or more transfer RNA (tRNA) sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0694 Protein secondary structure "Protein secondary structure or secondary structure alignments.|This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0694 Protein secondary structure or secondary structure alignments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2814 1.8 http://edamontology.org/topic_0697 RNA structure RNA secondary or tertiary structure and alignments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0697 http://edamontology.org/topic_0097 RNA secondary or tertiary structure and alignments. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0698 Protein tertiary structure Protein tertiary structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0698 Protein tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2814 1.8 http://edamontology.org/topic_0722 Nucleic acid classification Classification of nucleic acid sequences and structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0722 http://edamontology.org/topic_0623 Classification of nucleic acid sequences and structures. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0724 Protein families "Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0724 "Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0623 1.14 http://edamontology.org/topic_0736 Protein folds and structural domains Transmembrane regions|Protein structural domains|Protein membrane regions|Intramembrane regions|Protein folds|Protein topological domains|Protein domains|Protein transmembrane regions "Protein tertiary structural domains and folds in a protein or polypeptide chain.|This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, 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.|This includes topological domains such as cytoplasmic regions in a protein." FALSE http://edamontology.org/topic_2814 beta12orEarlier topic_0736 Protein tertiary structural domains and folds in a protein or polypeptide chain. Transmembrane regions|Protein structural domains|Protein membrane regions|Intramembrane regions|Protein folds|Protein topological domains|Protein domains|Protein transmembrane regions http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0740 Nucleic acid sequence alignment Nucleotide sequence alignments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0740 Nucleotide sequence alignments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.3 http://edamontology.org/topic_0741 Protein sequence alignment Protein sequence alignments.|A sequence profile typically represents a sequence alignment. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0741 http://edamontology.org/topic_0080 Protein sequence alignments. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0747 Nucleic acid sites and features "The archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0747 http://edamontology.org/topic_0160|http://edamontology.org/topic_0640 "The archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0748 Protein sites and features "The detection, identification and analysis of positional features in proteins, such as functional sites." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0748 http://edamontology.org/topic_0639|http://edamontology.org/topic_0160 "The detection, identification and analysis of positional features in proteins, such as functional sites." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0749 Transcription factors and regulatory sites Transcription factors|-35 signals|CpG islands|-10 signals|Enhancers|TFBS|Transcriptional regulatory sites|GC signals|Attenuators|CAAT signals|TATA signals|Terminators|Isochores|CAT box|Promoters|Transcription factor binding sites|CCAAT box "Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.|Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.|This includes CpG rich regions (isochores) in a nucleotide sequence.|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." FALSE http://edamontology.org/topic_0203|http://edamontology.org/topic_3125|http://edamontology.org/topic_0078 beta12orEarlier topic_0749 "Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." Transcription factors|-35 signals|CpG islands|-10 signals|Enhancers|TFBS|Transcriptional regulatory sites|GC signals|Attenuators|CAAT signals|TATA signals|Terminators|Isochores|CAT box|Promoters|Transcription factor binding sites|CCAAT box http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0751 Phosphorylation sites Protein phosphorylation and phosphorylation sites in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0751 http://edamontology.org/topic_0748|http://edamontology.org/topic_0601 Protein phosphorylation and phosphorylation sites in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.0 http://edamontology.org/topic_0753 Metabolic pathways Metabolic pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0753 Metabolic pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_0754 Signaling pathways Signaling pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0754 Signaling pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_0767 Protein and peptide identification TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0767 http://edamontology.org/topic_0121 http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0769 Workflows Pipelines Biological or biomedical analytical workflows or pipelines. FALSE http://edamontology.org/topic_3071 beta12orEarlier topic_0769 Biological or biomedical analytical workflows or pipelines. Pipelines http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0770 Data types and objects Structuring data into basic types and (computational) objects. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0770 http://edamontology.org/topic_0091 Structuring data into basic types and (computational) objects. http://purl.obolibrary.org/obo/edam#obsolete 1.0 http://edamontology.org/topic_0771 Theoretical biology TRUE http://www.w3.org/2002/07/owl#DeprecatedClass topic_0771 http://edamontology.org/topic_3307 http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0779 Mitochondria "Mitochondria, typically of mitochondrial genes and proteins." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0779 http://edamontology.org/topic_2229 "Mitochondria, typically of mitochondrial genes and proteins." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0780 Plant biology Plant science|Plants|Plant science|Botany|Plant "Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.|The resource may be specific to a plant, a group of plants or all plants." FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_0780 Plant science VT 1.5.10 Botany|VT 1.5.22 Plant science "Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." Plants|Plant science|Botany|Plant http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0781 Virology "Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_0781 VT 1.5.28 "Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0782 Fungi Yeast "Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.|The resource may be specific to a fungus, a group of fungi or all fungi." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_0782 http://edamontology.org/topic_0621 VT 1.5.21 Mycology "Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." Yeast http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_2818 http://edamontology.org/topic_0783 Pathogens "Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.|The resource may be specific to a pathogen, a group of pathogens or all pathogens." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). Definition is wrong anyway." topic_0783 http://edamontology.org/topic_0621 "Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_0621 http://edamontology.org/topic_0786 Arabidopsis Arabidopsis-specific data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0786 http://edamontology.org/topic_0780 Arabidopsis-specific data. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0787 Rice Rice-specific data. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0787 http://edamontology.org/topic_0780 Rice-specific data. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0796 Genetic mapping and linkage "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0796 http://edamontology.org/topic_0102 "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://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_0797 Comparative genomics "The study (typically comparison) of the sequence, structure or function of multiple genomes." FALSE http://edamontology.org/topic_0622 beta12orEarlier topic_0797 "The study (typically comparison) of the sequence, structure or function of multiple genomes." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0798 Mobile genetic elements Transposons "Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." FALSE http://edamontology.org/topic_0114 beta12orEarlier topic_0798 "Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." Transposons http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_0803 Human disease "Human diseases, typically describing the genes, mutations and proteins implicated in disease." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0803 http://edamontology.org/topic_0634 "Human diseases, typically describing the genes, mutations and proteins implicated in disease." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_0804 Immunology Computational immunology|Immunoinformatics "The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." FALSE http://edamontology.org/topic_3344 beta12orEarlier topic_0804 VT 3.1.3 Immunology "The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." Computational immunology|Immunoinformatics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0820 Membrane and lipoproteins Membrane proteins|Transmembrane proteins|Lipoproteins "Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane." FALSE http://edamontology.org/topic_0078 beta12orEarlier topic_0820 "Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane." Membrane proteins|Transmembrane proteins|Lipoproteins http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0821 Enzymes Enzymology "Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." FALSE http://edamontology.org/topic_0078 beta12orEarlier topic_0821 "Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." Enzymology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_0922 Primers PCR primers and hybridisation oligos in a nucleic acid sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_0922 PCR primers and hybridisation oligos in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0632 1.13 http://edamontology.org/topic_1302 PolyA signal or sites Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1302 Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_1304 CpG island and isochores CpG rich regions (isochores) in a nucleotide sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1304 CpG rich regions (isochores) in a nucleotide sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_1305 Restriction sites Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1305 Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3125 1.13 http://edamontology.org/topic_1307 Splice sites Splice sites in a nucleotide sequence or alternative RNA splicing events. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1307 http://edamontology.org/topic_3320|http://edamontology.org/topic_3512 Splice sites in a nucleotide sequence or alternative RNA splicing events. http://purl.obolibrary.org/obo/edam#obsolete 1.13 http://edamontology.org/topic_1308 Matrix/scaffold attachment sites Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1308 Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3125 1.13 http://edamontology.org/topic_1311 Operon "Operons (operators, promoters and genes) from a bacterial genome." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1311 "Operons (operators, promoters and genes) from a bacterial genome." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0114 1.13 http://edamontology.org/topic_1312 Promoters "Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1312 "Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0749 1.13 http://edamontology.org/topic_1317 Structural biology Structure determination|Structural assignment|Structural determination "The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.|This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data." FALSE http://edamontology.org/topic_3070 1.3 topic_1317 "This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen." VT 1.5.24 Structural biology "The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids." Structure determination|Structural assignment|Structural determination http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_1456 Protein membrane regions "Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_1456 "Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0736 1.13 http://edamontology.org/topic_1770 Structure comparison "The comparison of two or more molecular structures, for example structure alignment and clustering.|This might involve comparison of secondary or tertiary (3D) structural information." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_1770 "The comparison of two or more molecular structures, for example structure alignment and clustering." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0081 1.13 http://edamontology.org/topic_1775 Function analysis Functional analysis|Protein function prediction|Protein function analysis The study of gene and protein function including the prediction of functional properties of a protein. FALSE http://edamontology.org/topic_3307 beta12orEarlier topic_1775 The study of gene and protein function including the prediction of functional properties of a protein. Functional analysis Protein function prediction|Protein function analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_1811 Prokaryotes and Archaea Bacteriology "Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.|The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_1811 http://edamontology.org/topic_0621 Bacteriology VT 1.5.2 Bacteriology "Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_0621 http://edamontology.org/topic_2225 Protein databases Protein data resources. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2225 http://edamontology.org/topic_0078 Protein data resources. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2226 Structure determination "Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2226 http://edamontology.org/topic_1317 "Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2229 Cell biology Cellular processes "Cells, such as key genes and proteins involved in the cell cycle." FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_2229 VT 1.5.11 Cell biology "Cells, such as key genes and proteins involved in the cell cycle." Cellular processes http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2230 Classification "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2230 http://edamontology.org/topic_0089 "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_2232 Lipoproteins Lipoproteins (protein-lipid assemblies). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2232 http://edamontology.org/topic_0820 Lipoproteins (protein-lipid assemblies). http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2257 Phylogeny visualisation "Visualise a phylogeny, for example, render a phylogenetic tree." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2257 http://edamontology.org/topic_0084 "Visualise a phylogeny, for example, render a phylogenetic tree." http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2258 Cheminformatics Chemoinformatics|Chemical informatics The application of information technology to chemistry in biological research environment. FALSE http://edamontology.org/topic_0605 beta12orEarlier topic_2258 The application of information technology to chemistry in biological research environment. Chemoinformatics|Chemical informatics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2259 Systems biology Biological system modelling|Biological modelling The holistic modelling and analysis of complex biological systems and the interactions therein.|This includes databases of models and methods to construct or analyse a model. FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_2259 The holistic modelling and analysis of complex biological systems and the interactions therein. Biological system modelling|Biological modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2269 Statistics and probability Statistics|Biostatistics|Probability The application of statistical methods to biological problems. FALSE http://edamontology.org/topic_3315 beta12orEarlier topic_2269 The application of statistical methods to biological problems. Statistics|Biostatistics|Probability http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_2271 Structure database search "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).|The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2271 http://edamontology.org/topic_0081 Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2275 Molecular modelling Molecular docking|Homology modeling|Comparative modelling|Homology modelling "The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking)." FALSE http://edamontology.org/topic_0082 beta12orEarlier topic_2275 "The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking)." Molecular docking|Homology modeling|Comparative modelling|Homology modelling http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2276 Protein function prediction The prediction of functional properties of a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2276 http://edamontology.org/topic_1775 The prediction of functional properties of a protein. http://purl.obolibrary.org/obo/edam#obsolete 1.2 http://edamontology.org/topic_2277 SNP "Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2277 "Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2885 1.13 http://edamontology.org/topic_2278 Transmembrane protein prediction Predict transmembrane domains and topology in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2278 http://edamontology.org/topic_0820|http://edamontology.org/topic_0082 Predict transmembrane domains and topology in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2280 Nucleic acid structure comparison The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.|Use this concept for methods that are exclusively for nucleic acid structures. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2280 http://edamontology.org/topic_1770|http://edamontology.org/topic_0097 The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2397 Exons Exons in a nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2397 Exons in a nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_2399 Gene transcription Transcription of DNA into RNA including the regulation of transcription. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2399 Transcription of DNA into RNA including the regulation of transcription. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_2533 DNA mutation DNA mutation. FALSE http://edamontology.org/topic_0654|http://edamontology.org/topic_0199 beta12orEarlier topic_2533 DNA mutation. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_2640 Oncology Cancer biology|Cancer "The study of cancer, for example, genes and proteins implicated in cancer." FALSE http://edamontology.org/topic_3303 beta12orEarlier topic_2640 VT 3.2.16 Oncology "The study of cancer, for example, genes and proteins implicated in cancer." Cancer biology Cancer http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2661 Toxins and targets Structural and associated data for toxic chemical substances. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2661 Structural and associated data for toxic chemical substances. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0154 1.13 http://edamontology.org/topic_2754 Introns Introns in a nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2754 Introns in a nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_2807 Tool topic "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2807 "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0003 beta12orEarlier http://edamontology.org/topic_2809 Study topic "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2809 "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0003 beta12orEarlier http://edamontology.org/topic_2811 Nomenclature "Biological nomenclature (naming), symbols and terminology." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2811 http://edamontology.org/topic_0089 "Biological nomenclature (naming), symbols and terminology." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2813 Disease genes and proteins "The genes, gene variations and proteins involved in one or more specific diseases." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2813 http://edamontology.org/topic_0634 "The genes, gene variations and proteins involved in one or more specific diseases." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2814 Protein structure analysis Protein structure Protein secondary or tertiary structural data and/or associated annotation. FALSE http://edamontology.org/topic_0081|http://edamontology.org/topic_0078 beta12orEarlier topic_2814 http://edamontology.org/topic_3040 Protein secondary or tertiary structural data and/or associated annotation. Protein structure http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2815 Human biology Humans "The study of human beings in general, including the human genome and proteome." FALSE http://edamontology.org/topic_3070 beta12orEarlier topic_2815 "The study of human beings in general, including the human genome and proteome." Humans http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_2816 Gene resources Informatics resource (typically a database) primarily focussed on genes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2816 http://edamontology.org/topic_3053 Informatics resource (typically a database) primarily focussed on genes. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2817 Yeast "Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2817 http://edamontology.org/topic_0621 "Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2818 Eukaryotes "Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.|The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison) Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_2818 http://edamontology.org/topic_0621 "Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_0621 http://edamontology.org/topic_2819 Invertebrates "Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.|The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_2819 http://edamontology.org/topic_0621 "Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_3500 http://edamontology.org/topic_2820 Vertebrates "Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.|The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_2820 http://edamontology.org/topic_0621 "Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_3500 http://edamontology.org/topic_2821 Unicellular eukaryotes "Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.|The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier "(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset)." topic_2821 http://edamontology.org/topic_0621 "Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.17 http://edamontology.org/topic_2818 http://edamontology.org/topic_2826 Protein structure alignment Protein secondary or tertiary structure alignments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2826 http://edamontology.org/topic_2814 Protein secondary or tertiary structure alignments. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2828 X-ray diffraction Crystallography|X-ray microscopy|X-ray crystallography "The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample." FALSE http://edamontology.org/topic_3382|http://edamontology.org/topic_1317 beta12orEarlier topic_2828 "The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample." Crystallography X-ray microscopy|X-ray crystallography http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_2829 "Ontologies, nomenclature and classification" "Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2829 http://edamontology.org/topic_0089 "Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_2830 "Immunoproteins, genes and antigens" Immunogenes|Immunoproteins|Antigens|Immunopeptides "Immunity-related genes, proteins and their ligands.|This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc.""" FALSE http://edamontology.org/topic_0623|http://edamontology.org/topic_0804 beta12orEarlier topic_2830 "Immunity-related genes, proteins and their ligands." Immunogenes|Immunoproteins|Antigens|Immunopeptides http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_2839 Molecules CHEBI:23367 "Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2839 http://edamontology.org/topic_3047 "Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." CHEBI:23367 http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2840 Toxicology Computational toxicology|Toxicoinformatics Toxins and the adverse effects of these chemical substances on living organisms. FALSE http://edamontology.org/topic_3303|http://edamontology.org/topic_3377 beta12orEarlier topic_2840 VT 3.1.9 Toxicology Toxins and the adverse effects of these chemical substances on living organisms. Computational toxicology|Toxicoinformatics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2842 High-throughput sequencing Next-generation sequencing Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2842 http://edamontology.org/topic_3168 Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. Next-generation sequencing http://purl.obolibrary.org/obo/edam#obsolete beta13 http://edamontology.org/topic_2844 Structural clustering "The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2844 "The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0081 1.7 http://edamontology.org/topic_2846 Gene regulatory networks Gene regulatory networks. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2846 Gene regulatory networks. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_2847 Disease (specific) Informatics resources dedicated to one or more specific diseases (not diseases in general). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2847 http://edamontology.org/topic_0634 Informatics resources dedicated to one or more specific diseases (not diseases in general). http://purl.obolibrary.org/obo/edam#obsolete beta12orEarlier http://edamontology.org/topic_2867 VNTR Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2867 Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2885 1.13 http://edamontology.org/topic_2868 Microsatellites Microsatellite polymorphism in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2868 http://edamontology.org/data_2868 Microsatellite polymorphism in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2885 1.13 http://edamontology.org/topic_2869 RFLP Restriction fragment length polymorphisms (RFLP) in a DNA sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2869 http://edamontology.org/data_2869 Restriction fragment length polymorphisms (RFLP) in a DNA sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_2885 1.13 http://edamontology.org/topic_2885 DNA polymorphism Microsatellites|Variable number of tandem repeat polymorphism|snps|RFLP|VNTR|SNP|Single nucleotide polymorphism "DNA polymorphism.|Includes microsatellite polymorphism in a DNA sequence. 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.|Includes restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.|Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.|Includes variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times." FALSE http://edamontology.org/topic_0654|http://edamontology.org/topic_0199 beta12orEarlier topic_2885 DNA polymorphism. Microsatellites|Variable number of tandem repeat polymorphism|snps|RFLP|VNTR|SNP|Single nucleotide polymorphism http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_2953 Nucleic acid design Topic for the design of nucleic acid sequences with specific conformations. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_2953 http://edamontology.org/topic_0097 Topic for the design of nucleic acid sequences with specific conformations. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3032 Primer or probe design The design of primers for PCR and DNA amplification or the design of molecular probes. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3032 http://edamontology.org/topic_0632 The design of primers for PCR and DNA amplification or the design of molecular probes. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3038 Structure databases "Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3038 http://edamontology.org/topic_0081 "Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." http://purl.obolibrary.org/obo/edam#obsolete 1.2 http://edamontology.org/topic_3039 Nucleic acid structure "Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3039 http://edamontology.org/topic_0097 "Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.2 http://edamontology.org/topic_3041 Sequence databases "Molecular sequence data resources, including sequence sites, alignments, motifs and profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3041 http://edamontology.org/topic_0080 "Molecular sequence data resources, including sequence sites, alignments, motifs and profiles." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3042 Nucleic acid sequences "Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3042 http://edamontology.org/topic_0080 "Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3043 Protein sequences "Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3043 "Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.3 http://edamontology.org/topic_3044 Protein interaction networks TRUE http://www.w3.org/2002/07/owl#DeprecatedClass topic_3044 http://edamontology.org/topic_0128 http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3047 Molecular biology "The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life." FALSE http://edamontology.org/topic_3070 beta13 topic_3047 VT 1.5.4 Biochemistry and molecular biology "The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3048 Mammals "Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3048 http://edamontology.org/topic_0621 "Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3050 Biodiversity "The degree of variation of life forms within a given ecosystem, biome or an entire planet." FALSE http://edamontology.org/topic_0610 beta13 topic_3050 VT 1.5.5 Biodiversity conservation "The degree of variation of life forms within a given ecosystem, biome or an entire planet." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3052 Sequence clusters and classification "The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.|This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3052 http://edamontology.org/topic_0080 "The comparison, grouping together and classification of macromolecules on the basis of sequence similarity." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3053 Genetics Heredity "The study of genes, genetic variation and heredity in living organisms." FALSE http://edamontology.org/topic_3070 beta13 topic_3053 "The study of genes, genetic variation and heredity in living organisms." Heredity http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3055 Quantitative genetics The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). FALSE http://edamontology.org/topic_0625 beta13 topic_3055 The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3056 Population genetics "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." FALSE http://edamontology.org/topic_3053 beta13 topic_3056 "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://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3060 Regulatory RNA Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3060 Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0659 1.3 http://edamontology.org/topic_3061 Documentation and help "The documentation of resources such as tools, services and databases and how to get help." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3061 "The documentation of resources such as tools, services and databases and how to get help." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3068 1.13 http://edamontology.org/topic_3062 Genetic organisation The structural and functional organisation of genes and other genetic elements. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3062 http://edamontology.org/topic_0114 The structural and functional organisation of genes and other genetic elements. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3063 Medical informatics Molecular medicine|Translational medicine|Biomedical informatics|Clinical informatics|Health informatics|Healthcare informatics|Health and disease "The application of information technology to health, disease and biomedicine." FALSE http://edamontology.org/topic_0605 beta13 topic_3063 Molecular medicine|Translational medicine "The application of information technology to health, disease and biomedicine." Biomedical informatics|Clinical informatics|Health informatics|Healthcare informatics|Health and disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3064 Developmental biology How organisms grow and develop. FALSE http://edamontology.org/topic_3070 beta13 topic_3064 VT 1.5.14 Developmental biology How organisms grow and develop. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3065 Embryology The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. FALSE http://edamontology.org/topic_3064 beta13 topic_3065 The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3067 Anatomy The form and function of the structures of living organisms. FALSE http://edamontology.org/topic_3344 beta13 topic_3067 VT 3.1.1 Anatomy and morphology The form and function of the structures of living organisms. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3068 Literature and language References|Citations|Documentation|Scientific literature|Bibliography "The scientific literature, language processing, reference information, and documentation.|This includes the documentation of resources such as tools, services and databases, user support, how to get help etc." FALSE http://edamontology.org/topic_0003 beta13 topic_3068 "The scientific literature, language processing, reference information, and documentation." References|Citations|Documentation|Scientific literature|Bibliography http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3070 Biology Biological science|Cryobiology|Aerobiology|Chronobiology|Biological rhythms|Reproductive biology|Behavioural biology "A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." FALSE http://edamontology.org/topic_0003 beta13 topic_3070 "VT 1.5.13 Cryobiology |VT 1.5.8 Biology|VT 1.5.1 Aerobiology|VT 1.5.23 Reproductive biology|VT 1.5.99 Other|VT 1.5 Biological sciences|VT 1.5.3 Behavioural biology|VT 1.5.7 Biological rhythm" "A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." Biological science Cryobiology|Aerobiology|Chronobiology|Biological rhythms|Reproductive biology|Behavioural biology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3071 Data management "The development and use of architectures, policies, practices and procedures for management of data." FALSE http://edamontology.org/topic_0605 beta13 topic_3071 VT 1.3.1 Data management "The development and use of architectures, policies, practices and procedures for management of data." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3072 Sequence feature detection "The detection of the positional features, such as functional and other key sites, in molecular sequences." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3072 http://edamontology.org/topic_0160 "The detection of the positional features, such as functional and other key sites, in molecular sequences." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3073 Nucleic acid feature detection The detection of positional features such as functional sites in nucleotide sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3073 http://edamontology.org/topic_3511 The detection of positional features such as functional sites in nucleotide sequences. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3074 Protein feature detection "The detection, identification and analysis of positional protein sequence features, such as functional sites." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3074 http://edamontology.org/topic_0160 "The detection, identification and analysis of positional protein sequence features, such as functional sites." http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3075 Biological system modelling Topic for modelling biological systems in mathematical terms. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3075 http://edamontology.org/topic_2259 Topic for modelling biological systems in mathematical terms. http://purl.obolibrary.org/obo/edam#obsolete 1.2 http://edamontology.org/topic_3077 Data acquisition "The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means." FALSE http://edamontology.org/topic_3071 beta13 topic_3077 "The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means." http://purl.obolibrary.org/obo/edam#data|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3078 Genes and proteins resources Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3078 http://edamontology.org/topic_0623 Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. http://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3118 Protein topological domains Topological domains such as cytoplasmic regions in a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3118 Topological domains such as cytoplasmic regions in a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0736 1.13 http://edamontology.org/topic_3120 Protein variants "Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." FALSE http://edamontology.org/topic_0108 beta13 topic_3120 http://edamontology.org/data_3120 "Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3123 Expression signals Regions within a nucleic acid sequence containing a signal that alters a biological function. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3123 http://edamontology.org/topic_0749 Regions within a nucleic acid sequence containing a signal that alters a biological function. http://purl.obolibrary.org/obo/edam#obsolete 1.12 http://edamontology.org/topic_3125 DNA binding sites Matrix/scaffold attachment region|Restriction sites|Matrix-attachment region|Scaffold-attachment region|Nucleosome exclusion sequences|Ribosome binding sites "Nucleic acids binding to some other molecule.|This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression).|This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc." FALSE http://edamontology.org/topic_3511|http://edamontology.org/topic_0654 beta13 topic_3125 http://edamontology.org/data_3125 Nucleic acids binding to some other molecule. Matrix/scaffold attachment region|Restriction sites|Matrix-attachment region|Scaffold-attachment region|Nucleosome exclusion sequences|Ribosome binding sites http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3126 Nucleic acid repeats Repetitive elements within a nucleic acid sequence.|This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3126 Repetitive elements within a nucleic acid sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0157 "1,13" http://edamontology.org/topic_3127 DNA replication and recombination DNA replication or recombination. FALSE http://edamontology.org/topic_0654 beta13 topic_3127 DNA replication or recombination. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3135 Signal or transit peptide Coding sequences for a signal or transit peptide. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3135 Coding sequences for a signal or transit peptide. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3512 1.13 http://edamontology.org/topic_3139 Sequence tagged sites Sequence tagged sites (STS) in nucleic acid sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta13 topic_3139 Sequence tagged sites (STS) in nucleic acid sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3511 1.13 http://edamontology.org/topic_3168 Sequencing DNA-Seq|Next gen sequencing|Next generation sequencing|Primer walking|DNase-Seq|Clone verification|Small RNA sequencing|High-throughput sequencing|Amplicon sequencing|Chromosome walking|High throughput sequencing|NGS|Resequencing "The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.|Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions. " FALSE http://edamontology.org/topic_3361 1.1 topic_3168 "The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." DNA-Seq Next gen sequencing|Next generation sequencing|Primer walking|DNase-Seq|Clone verification|Small RNA sequencing|High-throughput sequencing|Amplicon sequencing|Chromosome walking|High throughput sequencing|NGS|Resequencing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3169 ChIP-seq Chip sequencing|Chip-sequencing|Chip Seq|ChIP-exo 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. FALSE http://edamontology.org/topic_3168|http://edamontology.org/topic_3656 1.1 topic_3169 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. Chip sequencing|Chip-sequencing|Chip Seq ChIP-exo http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3170 RNA-Seq RNA sequencing|Small RNA-Seq|WTSS|Whole transcriptome shotgun sequencing|Small RNA-seq|RNA-seq|MicroRNA sequencing|miRNA-seq "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.|This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs." FALSE http://edamontology.org/topic_3168 1.1 topic_3170 "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." RNA sequencing|Small RNA-Seq|WTSS|Whole transcriptome shotgun sequencing|Small RNA-seq|RNA-seq MicroRNA sequencing|miRNA-seq http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3171 DNA methylation "DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 topic_3171 "DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3295 1.3 http://edamontology.org/topic_3172 Metabolomics "The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism." FALSE http://edamontology.org/topic_3391 1.1 topic_3172 "The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3173 Epigenomics "The study of the epigenetic modifications of a whole cell, tissue, organism etc.|Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation." FALSE http://edamontology.org/topic_0622|http://edamontology.org/topic_3295 1.1 topic_3173 "The study of the epigenetic modifications of a whole cell, tissue, organism etc." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3174 Metagenomics Community genomics|Ecogenomics|Environmental genomics|Environmental omics|Environmental sequencing|Biome sequencing|Shotgun metagenomics "The study of genetic material recovered from environmental samples, and associated environmental data." FALSE http://edamontology.org/topic_0610|http://edamontology.org/topic_0622 1.1 topic_3174 Community genomics|Ecogenomics|Environmental genomics|Environmental omics "The study of genetic material recovered from environmental samples, and associated environmental data." Environmental sequencing|Biome sequencing|Shotgun metagenomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3175 DNA structural variation Genomic structural variation|Structural variation "Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." FALSE http://edamontology.org/topic_0654|http://edamontology.org/topic_0199 1.1 topic_3175 "Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." Genomic structural variation|Structural variation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3176 DNA packaging Nucleosome positioning "DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." FALSE http://edamontology.org/topic_0654 beta12orEarlier topic_3176 "DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." Nucleosome positioning http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3177 DNA-Seq "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.1 topic_3177 http://edamontology.org/topic_3168 "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://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3178 RNA-Seq alignment "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." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass beta12orEarlier topic_3178 http://edamontology.org/topic_0196 "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://purl.obolibrary.org/obo/edam#obsolete 1.3 http://edamontology.org/topic_3179 ChIP-on-chip ChIP-Chip|ChIP-chip|ChiP Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. FALSE http://edamontology.org/topic_3656 1.1 topic_3179 Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. ChIP-Chip|ChIP-chip ChiP http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3263 Data security Data privacy "The protection of data, such as patient health data, from damage or unwanted access from unauthorised users." FALSE http://edamontology.org/topic_3071 1.3 topic_3263 "The protection of data, such as patient health data, from damage or unwanted access from unauthorised users." Data privacy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3277 Sample collections Specimen collections|biosamples|samples Biological samples and specimens. FALSE http://edamontology.org/topic_3344 1.3 topic_3277 Biological samples and specimens. Specimen collections biosamples|samples http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3292 Biochemistry Biological chemistry Chemical substances and physico-chemical processes and that occur within living organisms. FALSE http://edamontology.org/topic_3070|http://edamontology.org/topic_3314 1.3 topic_3292 VT 1.5.4 Biochemistry and molecular biology Chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3293 Phylogenetics The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). FALSE http://edamontology.org/topic_0084|http://edamontology.org/topic_0080 1.3 topic_3293 The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3295 Epigenetics DNA methylation|Histone modification "Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.|This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.)" FALSE http://edamontology.org/topic_3053 1.3 topic_3295 "Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence." DNA methylation|Histone modification http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3297 Biotechnology "The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production." FALSE http://edamontology.org/topic_3070 1.3 topic_3297 "The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3298 Phenomics "Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. " FALSE http://edamontology.org/topic_3299|http://edamontology.org/topic_3391|http://edamontology.org/topic_0625 1.3 topic_3298 "Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. " http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3299 Evolutionary biology "The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity." FALSE http://edamontology.org/topic_3070 1.3 topic_3299 VT 1.5.16 Evolutionary biology "The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3300 Physiology The functions of living organisms and their constituent parts. FALSE http://edamontology.org/topic_3303 1.3 topic_3300 VT 3.1.8 Physiology The functions of living organisms and their constituent parts. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3301 Microbiology Antimicrobial stewardship|Microbiological surveillance|Microbial surveillance The biology of microorganisms. FALSE http://edamontology.org/topic_3070 1.3 topic_3301 VT 1.5.20 Microbiology The biology of microorganisms. Antimicrobial stewardship|Microbiological surveillance|Microbial surveillance http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3302 Parasitology The biology of parasites. FALSE http://edamontology.org/topic_3344 1.3 topic_3302 The biology of parasites. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3303 Medicine Biomedical research|Experimental medicine|Clinical medicine|Internal medicine|General medicine "Research in support of healing by diagnosis, treatment, and prevention of disease." FALSE http://edamontology.org/topic_0003 1.3 topic_3303 VT 3.2.9 General and internal medicine|VT 3.2 Clinical medicine|VT 3.1 Basic medicine "Research in support of healing by diagnosis, treatment, and prevention of disease." Biomedical research|Experimental medicine|Clinical medicine Internal medicine|General medicine http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3304 Neurobiology Neuroscience "The study of the nervous system and brain; its anatomy, physiology and function." FALSE http://edamontology.org/topic_3344 1.3 topic_3304 Neuroscience VT 3.1.5 Neuroscience "The study of the nervous system and brain; its anatomy, physiology and function." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3305 Public health and epidemiology Public health|Epidemiology "Topic concerning the the patterns, cause, and effect of disease within populations." FALSE http://edamontology.org/topic_3303 1.3 topic_3305 VT 3.3.1 Epidemiology "Topic concerning the the patterns, cause, and effect of disease within populations." Public health|Epidemiology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3306 Biophysics The use of physics to study biological system. FALSE http://edamontology.org/topic_3070|http://edamontology.org/topic_3318 1.3 topic_3306 VT 1.5.9 Biophysics The use of physics to study biological system. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3307 Computational biology Mathematical biology|Biomathematics|Theoretical biology "The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.|This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology)." FALSE http://edamontology.org/topic_0003 1.3 topic_3307 VT 1.5.19 Mathematical biology|VT 1.5.12 Computational biology|VT 1.5.26 Theoretical biology "The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems." Mathematical biology|Biomathematics|Theoretical biology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3308 Transcriptomics Transcriptome|Metatranscriptomics|Comparative transcriptomics "The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc." FALSE http://edamontology.org/topic_0203|http://edamontology.org/topic_0622 1.3 topic_3308 "The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc." Transcriptome|Metatranscriptomics|Comparative transcriptomics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3314 Chemistry VT 1.7.10 Polymer science|Polymer science|Chemical science|Nuclear chemistry|Physical chemistry|Inorganic chemistry|Organic chemistry|Mathematical chemistry "The composition and properties of matter, reactions, and the use of reactions to create new substances." FALSE http://edamontology.org/topic_0003 1.3 topic_3314 VT 1.7.10 Polymer science|Polymer science|Chemical science VT 1.7.6 Inorganic and nuclear chemistry|VT 1.7.9 Physical chemistry|VT 1.7.2 Chemistry|VT 1.7.5 Electrochemistry|VT 1.7.3 Colloid chemistry|VT 1.7.7 Mathematical chemistry|VT 1.7 Chemical sciences|VT 1.7.8 Organic chemistry "The composition and properties of matter, reactions, and the use of reactions to create new substances." Nuclear chemistry|Physical chemistry|Inorganic chemistry|Organic chemistry|Mathematical chemistry http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3315 Mathematics Maths "The study of numbers (quantity) and other topics including structure, space, and change." FALSE http://edamontology.org/topic_0003 1.3 topic_3315 VT:1.1 Mathematics|VT 1.1.99 Other "The study of numbers (quantity) and other topics including structure, space, and change." Maths http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3316 Computer science The theory and practical use of computer systems. FALSE http://edamontology.org/topic_0003 1.3 topic_3316 VT 1.2.99 Other|VT 1.2 Computer sciences The theory and practical use of computer systems. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3318 Physics "The study of matter, space and time, and related concepts such as energy and force." FALSE http://edamontology.org/topic_0003 1.3 topic_3318 "The study of matter, space and time, and related concepts such as energy and force." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3320 RNA splicing Alternative splicing|Splice sites "RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.|This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc.." FALSE http://edamontology.org/topic_0203|http://edamontology.org/topic_0099 1.3 topic_3320 RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. Alternative splicing Splice sites http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3321 Molecular genetics The structure and function of genes at a molecular level. FALSE http://edamontology.org/topic_3307|http://edamontology.org/topic_3053 1.3 topic_3321 The structure and function of genes at a molecular level. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3322 Respiratory medicine Pulmonary medicine|Pulmonology|Pulmonary disorders|Respiratory disease The study of respiratory system. FALSE http://edamontology.org/topic_3303 1.3 topic_3322 VT 3.2.25 Respiratory systems The study of respiratory system. Pulmonary medicine|Pulmonology Pulmonary disorders|Respiratory disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3323 Metabolic disease The study of metabolic diseases. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.3 topic_3323 http://edamontology.org/topic_3407 The study of metabolic diseases. http://purl.obolibrary.org/obo/edam#obsolete 1.4 http://edamontology.org/topic_3324 Infectious disease Communicable disease|Transmissable disease "The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions)." FALSE http://edamontology.org/topic_0634 1.3 topic_3324 VT 3.3.4 Infectious diseases "The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions)." Communicable disease|Transmissable disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3325 Rare diseases The study of rare diseases. FALSE http://edamontology.org/topic_0634 1.3 topic_3325 The study of rare diseases. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3332 Computational chemistry FALSE http://edamontology.org/topic_3316|http://edamontology.org/topic_3314 1.3 topic_3332 "Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.|VT 1.7.4 Computational chemistry" http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3334 Neurology Neurological disorders "The branch of medicine that deals with the anatomy, functions and disorders of the nervous system." FALSE http://edamontology.org/topic_3303 1.3 topic_3334 "The branch of medicine that deals with the anatomy, functions and disorders of the nervous system." Neurological disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3335 Cardiology Cardiovascular medicine|Heart disease|Cardiovascular disease The diseases and abnormalities of the heart and circulatory system. FALSE http://edamontology.org/topic_3303 1.3 topic_3335 VT 3.2.4 Cardiac and Cardiovascular systems|VT 3.2.22 Peripheral vascular disease The diseases and abnormalities of the heart and circulatory system. Cardiovascular medicine Heart disease|Cardiovascular disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3336 Drug discovery "The discovery and design of drugs or potential drug compounds.|This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc." FALSE http://edamontology.org/topic_3376|http://edamontology.org/topic_3314 1.3 topic_3336 The discovery and design of drugs or potential drug compounds. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3337 Biobank biobanking|Tissue collection "Repositories of biological samples, typically human, for basic biological and clinical research." FALSE http://edamontology.org/topic_3277 1.3 topic_3337 "Repositories of biological samples, typically human, for basic biological and clinical research." biobanking|Tissue collection http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3338 Mouse clinic "Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines." FALSE http://edamontology.org/topic_3277 1.3 topic_3338 "Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3339 Microbial collection "Collections of microbial cells including bacteria, yeasts and moulds." FALSE http://edamontology.org/topic_3277 1.3 topic_3339 "Collections of microbial cells including bacteria, yeasts and moulds." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3340 Cell culture collection "Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells." FALSE http://edamontology.org/topic_3277 1.3 topic_3340 "Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3341 Clone library "Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA." FALSE http://edamontology.org/topic_3277 1.3 topic_3341 "Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3342 Translational medicine "'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice." FALSE http://edamontology.org/topic_3303 1.3 topic_3342 "'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3343 Compound libraries and screening Chemical screening|Compound library|Chemical library|Target identification and validation "Collections of chemicals, typically for use in high-throughput screening experiments." FALSE http://edamontology.org/topic_3336 1.3 topic_3343 "Collections of chemicals, typically for use in high-throughput screening experiments." Chemical screening|Compound library|Chemical library|Target identification and validation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3344 Biomedical science Biomedical sciences|Health science Topic concerning biological science that is (typically) performed in the context of medicine. FALSE http://edamontology.org/topic_0003 1.3 topic_3344 VT 3.3 Health sciences Topic concerning biological science that is (typically) performed in the context of medicine. Biomedical sciences|Health science http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3345 Data identity and mapping "Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases." FALSE http://edamontology.org/topic_3071 1.3 topic_3345 "Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3346 Sequence search Sequence database search The search and retrieval from a database on the basis of molecular sequence similarity. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.3 topic_3346 The search and retrieval from a database on the basis of molecular sequence similarity. Sequence database search http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0080 1.12 http://edamontology.org/topic_3360 Biomarkers Diagnostic markers "Objective indicators of biological state often used to assess health, and determinate treatment." FALSE http://edamontology.org/topic_3070 1.4 topic_3360 "Objective indicators of biological state often used to assess health, and determinate treatment." Diagnostic markers http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3361 Laboratory techniques Lab techniques The procedures used to conduct an experiment. FALSE http://edamontology.org/topic_0003 1.4 topic_3361 The procedures used to conduct an experiment. Lab techniques http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3365 "Data architecture, analysis and design" Data design|Data architecture|Data analysis "The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data." FALSE http://edamontology.org/topic_3071 1.4 topic_3365 "The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data." Data design|Data architecture|Data analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3366 Data integration and warehousing Data integration|Data warehousing "The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. " FALSE http://edamontology.org/topic_3071 1.4 topic_3366 "The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. " Data integration|Data warehousing http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3368 Biomaterials "Any matter, surface or construct that interacts with a biological system." FALSE http://edamontology.org/topic_3297 1.4 topic_3368 "Any matter, surface or construct that interacts with a biological system." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3369 Chemical biology The use of synthetic chemistry to study and manipulate biological systems. FALSE http://edamontology.org/topic_3371|http://edamontology.org/topic_3070 1.4 topic_3369 The use of synthetic chemistry to study and manipulate biological systems. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3370 Analytical chemistry "The study of the separation, identification, and quantification of the chemical components of natural and artificial materials." FALSE http://edamontology.org/topic_3314 1.4 topic_3370 VT 1.7.1 Analytical chemistry "The study of the separation, identification, and quantification of the chemical components of natural and artificial materials." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3371 Synthetic chemistry Synthetic organic chemistry The use of chemistry to create new compounds. FALSE http://edamontology.org/topic_3314 1.4 topic_3371 The use of chemistry to create new compounds. Synthetic organic chemistry http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3372 Software engineering Computer programming|Software development|Data structures| Programming languages|Algorithms The process that leads from an original formulation of a computing problem to executable programs. FALSE http://edamontology.org/topic_3316 1.4 topic_3372 VT 1.2.14 Software engineering|Software engineering|VT 1.2.7 Data structures|1.2.12 Programming languages|VT 1.2.1 Algorithms The process that leads from an original formulation of a computing problem to executable programs. Computer programming|Software development Data structures| Programming languages|Algorithms http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3373 Drug development Drug development science|Medicines development|Medicine development The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. FALSE http://edamontology.org/topic_3376 1.4 topic_3373 The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Drug development science|Medicines development|Medicine development http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3374 Biotherapeutics Drug formulation and delivery|Drug delivery|Drug formulation The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. FALSE http://edamontology.org/topic_3376 1.4 topic_3374 Drug formulation and delivery|Drug delivery|Drug formulation The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3375 Drug metabolism Pharmacodynamics|ADME|Pharmacokinetics and pharmacodynamics|Drug distribution|Pharmacokinetics|Drug absorption|Drug excretion The study of how a drug interacts with the body. FALSE http://edamontology.org/topic_3376 1.4 topic_3375 The study of how a drug interacts with the body. Pharmacodynamics|ADME|Pharmacokinetics and pharmacodynamics|Drug distribution|Pharmacokinetics|Drug absorption|Drug excretion http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3376 Medicines research and development Health care science|Health care research|Drug discovery and development "The discovery, development and approval of medicines." FALSE http://edamontology.org/topic_3344 1.4 topic_3376 Health care science|Health care research "The discovery, development and approval of medicines." Drug discovery and development http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3377 Safety sciences Drug safety The safety (or lack) of drugs and other medical interventions. FALSE http://edamontology.org/topic_3376 1.4 topic_3377 The safety (or lack) of drugs and other medical interventions. Drug safety http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3378 Pharmacovigilence "The detection, assesment, understanding and prevention of adverse effects of medicines.|Pharmacovigilence concerns safety once a drug has gone to market." FALSE http://edamontology.org/topic_3377 1.4 topic_3378 "The detection, assesment, understanding and prevention of adverse effects of medicines." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3379 Preclinical and clinical studies Preclinical studies|Clinical studies|Drug trials|Clinical study|Preclinical study "The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities." FALSE http://edamontology.org/topic_3376|http://edamontology.org/topic_3678 1.4 topic_3379 "The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities." Preclinical studies|Clinical studies|Drug trials|Clinical study|Preclinical study http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3382 Imaging Microscopy imaging|Diffraction experiment|Microscopy "The visual representation of an object.|This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure." FALSE http://edamontology.org/topic_3361 1.4 topic_3382 The visual representation of an object. Microscopy imaging|Diffraction experiment|Microscopy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3383 Biological imaging The use of imaging techniques to understand biology. FALSE http://edamontology.org/topic_3382 1.4 topic_3383 The use of imaging techniques to understand biology. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3384 Medical imaging Radiology|Nuclear medicine The use of imaging techniques for clinical purposes for medical research. FALSE http://edamontology.org/topic_3382 1.4 topic_3384 VT 3.2.14 Nuclear medicine|VT 3.2.13 Medical imaging|VT 3.2.24 Radiology The use of imaging techniques for clinical purposes for medical research. Radiology|Nuclear medicine http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3385 Light microscopy The use of optical instruments to magnify the image of an object. FALSE http://edamontology.org/topic_3382 1.4 topic_3385 The use of optical instruments to magnify the image of an object. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3386 Laboratory animal science The use of animals and alternatives in experimental research. FALSE http://edamontology.org/topic_3344 1.4 topic_3386 The use of animals and alternatives in experimental research. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3387 Marine biology The study of organisms in the ocean or brackish waters. FALSE http://edamontology.org/topic_3070 1.4 topic_3387 VT 1.5.18 Marine and Freshwater biology The study of organisms in the ocean or brackish waters. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3388 Molecular medicine The identification of molecular and genetic causes of disease and the development of interventions to correct them. FALSE http://edamontology.org/topic_3342 1.4 topic_3388 The identification of molecular and genetic causes of disease and the development of interventions to correct them. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3390 Nutritional science Nutrition science|Dietetics "The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices." FALSE http://edamontology.org/topic_3344 1.4 topic_3390 VT 3.3.7 Nutrition and Dietetics "The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices." Nutrition science Dietetics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3391 Omics "The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms." FALSE http://edamontology.org/topic_0003 1.4 topic_3391 "The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3393 Quality affairs Quality assurance|Good laboratory practice|Good clinical practice|Good manufacturing practice The processes that need to be in place to ensure the quality of products for human or animal use. FALSE http://edamontology.org/topic_3376 1.4 topic_3393 The processes that need to be in place to ensure the quality of products for human or animal use. Quality assurance Good laboratory practice|Good clinical practice|Good manufacturing practice http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3394 Regulatory affairs "The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines." FALSE http://edamontology.org/topic_3376 1.4 topic_3394 "The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3395 Regnerative medicine Stem cell research Biomedical approaches to clinical interventions that involve the use of stem cells. FALSE http://edamontology.org/topic_3344 1.4 topic_3395 Biomedical approaches to clinical interventions that involve the use of stem cells. Stem cell research http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3396 Systems medicine "An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life." FALSE http://edamontology.org/topic_3303 1.4 topic_3396 "An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3397 Veterinary medicine "Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals." FALSE http://edamontology.org/topic_3303 1.4 topic_3397 "Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3398 Bioengineering The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. FALSE http://edamontology.org/topic_3297 1.4 topic_3398 The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3399 Geriatric medicine Gerontology|Ageing|Aging|Geriatrics "The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging." FALSE http://edamontology.org/topic_3303 1.4 topic_3399 Gerontology|Ageing|Aging VT 3.2.10 Geriatrics and gerontology "The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging." Geriatrics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3400 "Allergy, clinical immunology and immunotherapeutics" Clinical immunology|Allergy|Immune disorders|Immunomodulators|Immunotherapeutics "Health issues related to the immune system and their prevention, diagnosis and mangement." FALSE http://edamontology.org/topic_3303 1.4 topic_3400 VT 3.2.1 Allergy "Health issues related to the immune system and their prevention, diagnosis and mangement." Clinical immunology|Allergy|Immune disorders|Immunomodulators|Immunotherapeutics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3401 Pain medicine Algiatry "The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain." FALSE http://edamontology.org/topic_3303 1.4 topic_3401 "The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain." Algiatry http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3402 Anaesthesiology Anaesthetics Anaesthesia and anaesthetics. FALSE http://edamontology.org/topic_3303 1.4 topic_3402 VT 3.2.2 Anaesthesiology Anaesthesia and anaesthetics. Anaesthetics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3403 Critical care medicine Acute medicine|Emergency medicine "The multidisciplinary that cares for patients with acute, life-threatening illness or injury." FALSE http://edamontology.org/topic_3303 1.4 topic_3403 VT 3.2.5 Critical care/Emergency medicine "The multidisciplinary that cares for patients with acute, life-threatening illness or injury." Acute medicine|Emergency medicine http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3404 Dermatology Dermatological disorders "The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails." FALSE http://edamontology.org/topic_3303 1.4 topic_3404 VT 3.2.7 Dermatology and venereal diseases "The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails." Dermatological disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3405 Dentistry "The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures." FALSE http://edamontology.org/topic_3303 1.4 topic_3405 "The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3406 "Ear, nose and throat medicine" Audiovestibular medicine|Otorhinolaryngology|Otolaryngology|Head and neck disorders "The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat." FALSE http://edamontology.org/topic_3303 1.4 topic_3406 VT 3.2.20 Otorhinolaryngology "The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat." Audiovestibular medicine|Otorhinolaryngology|Otolaryngology Head and neck disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3407 Endocrinology and metabolism Metabolic disorders|Endocrinology|Metabolism|Endocrine disorders "The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism." FALSE http://edamontology.org/topic_3303 1.4 topic_3407 "The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism." Metabolic disorders|Endocrinology|Metabolism|Endocrine disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3408 Haematology Blood disorders|Haematological disorders "The branch of medicine that deals with the blood, blood-forming organs and blood diseases." FALSE http://edamontology.org/topic_3303 1.4 topic_3408 VT 3.2.11 Hematology "The branch of medicine that deals with the blood, blood-forming organs and blood diseases." Blood disorders|Haematological disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3409 Gastroenterology Gastrointestinal disorders "The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum." FALSE http://edamontology.org/topic_3303 1.4 topic_3409 VT 3.2.8 Gastroenterology and hepatology "The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum." Gastrointestinal disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3410 Gender medicine The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. FALSE http://edamontology.org/topic_3303 1.4 topic_3410 The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3411 Gynaecology and obstetrics Obstetrics|Gynaecology|Gynaecological disorders "The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth." FALSE http://edamontology.org/topic_3303 1.4 topic_3411 VT 3.2.15 Obstetrics and gynaecology "The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth." Obstetrics|Gynaecology|Gynaecological disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3412 Hepatic and biliary medicine Hepatobiliary medicine|Liver disorders "The branch of medicine that deals with the liver, gallbladder, bile ducts and bile." FALSE http://edamontology.org/topic_3303 1.4 topic_3412 "The branch of medicine that deals with the liver, gallbladder, bile ducts and bile." Hepatobiliary medicine Liver disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3413 Infectious tropical disease The branch of medicine that deals with the infectious diseases of the tropics. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.4 topic_3413 The branch of medicine that deals with the infectious diseases of the tropics. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3324 1.13 http://edamontology.org/topic_3414 Trauma medicine "The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident." FALSE http://edamontology.org/topic_3303 1.4 topic_3414 "The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3415 Medical toxicology "The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents." FALSE http://edamontology.org/topic_3303 1.4 topic_3415 "The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3416 Musculoskeletal medicine Rheumatology|Musculoskeletal disorders|Orthopaedics "The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine." FALSE http://edamontology.org/topic_3303 1.4 topic_3416 VT 3.2.26 Rheumatology|VT 3.2.19 Orthopaedics "The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine." Rheumatology|Musculoskeletal disorders|Orthopaedics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3417 Opthalmology Optometry|Eye disoders "The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles." FALSE http://edamontology.org/topic_3303 1.4 topic_3417 Optometry VT 3.2.18 Optometry|VT 3.2.17 Ophthalmology "The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles." Eye disoders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3418 Paediatrics Child health "The branch of medicine that deals with the medical care of infants, children and adolescents." FALSE http://edamontology.org/topic_3303 1.4 topic_3418 VT 3.2.21 Paediatrics "The branch of medicine that deals with the medical care of infants, children and adolescents." Child health http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3419 Psychiatry Mental health|Psychiatric disorders "The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour." FALSE http://edamontology.org/topic_3303 1.4 topic_3419 Mental health VT 3.2.23 Psychiatry "The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour." Psychiatric disorders http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3420 Reproductive health Reproductive disorders|Andrology|Fertility medicine|Family planning "The health of the reproductive processes, functions and systems at all stages of life." FALSE http://edamontology.org/topic_3303 1.4 topic_3420 VT 3.2.3 Andrology "The health of the reproductive processes, functions and systems at all stages of life." Reproductive disorders|Andrology|Fertility medicine|Family planning http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3421 Surgery Transplantation "The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance." FALSE http://edamontology.org/topic_3303 1.4 topic_3421 VT 3.2.28 Transplantation "The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance." Transplantation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3422 Urology and nephrology Urology|Nephrology|Urological disorders|Kidney disease "The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney." FALSE http://edamontology.org/topic_3303 1.4 topic_3422 VT 3.2.29 Urology and nephrology "The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney." Urology|Nephrology|Urological disorders|Kidney disease http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3423 Complementary medicine Alternative medicine|Integrative medicine|Holistic medicine Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. FALSE http://edamontology.org/topic_3303 1.4 topic_3423 Alternative medicine|Integrative medicine|Holistic medicine VT 3.2.12 Integrative and Complementary medicine Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3444 MRI "Magnetic resonance imaging |MRT|Magnetic resonance tomography|NMRI|Nuclear magnetic resonance imaging" "Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body." FALSE http://edamontology.org/topic_3382 1.7 topic_3444 "Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body." "Magnetic resonance imaging |MRT|Magnetic resonance tomography|NMRI|Nuclear magnetic resonance imaging" http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3448 Neutron diffraction Neutron diffraction experiment|Elastic neutron scattering|Neutron microscopy "The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure." FALSE http://edamontology.org/topic_3382|http://edamontology.org/topic_1317 1.7 topic_3448 "The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure." Neutron diffraction experiment Elastic neutron scattering|Neutron microscopy http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3452 Tomography X-ray tomography|Electron tomography "Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram)." FALSE http://edamontology.org/topic_3382 1.7 topic_3452 "Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram)." X-ray tomography|Electron tomography http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3473 Data mining KDD|Knowledge discovery in databases|Pattern recognition The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. FALSE http://edamontology.org/topic_3316 1.7 topic_3473 KDD|Knowledge discovery in databases VT 1.3.2 Data mining The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. Pattern recognition http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3474 Machine learning Artificial Intelligence "A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only." FALSE http://edamontology.org/topic_3316 1.7 topic_3474 Artificial Intelligence "VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)" "A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3489 Database management "Databases|Database administration|Content management|Record management|Document management|File management|Data maintenance|Document, record and content management|Biological databases" "The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. |This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports." FALSE http://edamontology.org/topic_3071 1.8 topic_3489 "The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. " Databases|Database administration "Content management|Record management|Document management|File management|Data maintenance|Document, record and content management|Biological databases" http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3500 Zoology Animal biology|Metazoa|Animal|Animals "Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.|The study of the animal kingdom." FALSE http://edamontology.org/topic_3070 1.8 topic_3500 VT 1.5.29 Zoology "Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation." Animal biology|Metazoa|Animal|Animals http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3510 "Protein sites, features and motifs" Protein sequence features|Signal peptide cleavage sites "The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.|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." FALSE http://edamontology.org/topic_0160|http://edamontology.org/topic_0078 1.8 topic_3510 "The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them." Protein sequence features|Signal peptide cleavage sites http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3511 "Nucleic acid sites, features and motifs" Primer binding sites|Sequence tagged sites|Nucleic acid sequence features|Nucleic acid functional sites "The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.|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." FALSE http://edamontology.org/topic_0160|http://edamontology.org/topic_0077 1.8 topic_3511 "The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them." Primer binding sites|Sequence tagged sites|Nucleic acid sequence features|Nucleic acid functional sites http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3512 Gene transcripts mRNA features|PolyA signal|PolyA site|Fusion transcripts|Gene transcript features|Coding RNA|Transit peptide coding sequence|Signal peptide coding sequence|Introns|Exons|cDNA|mRNA|EST "Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.|This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).|This includes regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. 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.|This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences.|This includes coding sequences for a signal or transit peptide. 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." FALSE http://edamontology.org/topic_0114|http://edamontology.org/topic_0099 1.8 topic_3512 "Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." mRNA features PolyA signal|PolyA site|Fusion transcripts|Gene transcript features|Coding RNA|Transit peptide coding sequence|Signal peptide coding sequence|Introns|Exons|cDNA|mRNA|EST http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3514 Protein-ligand interactions Protein-drug interactions Protein-ligand (small molecule) interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3514 Protein-ligand (small molecule) interaction(s). Protein-drug interactions http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0128 1.13 http://edamontology.org/topic_3515 Protein-drug interactions Protein-drug interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3515 Protein-drug interaction(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0128 1.13 http://edamontology.org/topic_3516 Genotyping experiment "Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." FALSE http://edamontology.org/topic_3361 1.8 topic_3516 "Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3517 GWAS study Genome-wide association study Genome-wide association study experiments. FALSE http://edamontology.org/topic_3678 1.8 topic_3517 Genome-wide association study experiments. Genome-wide association study http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3518 Microarray experiment Microarrays|Multichannel microarray|MicroRNA array|ChIP-on-chip|One channel microarray|miRNA array|mRNA microarray|Proprietary platform micoarray|Methylation array|Reverse phase protein array|Genotyping array|Tissue microarray|Two channel microarray "Microarray experiments including conditions, protocol, sample:data relationships etc.|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." FALSE http://edamontology.org/topic_3361 1.8 topic_3518 "Microarray experiments including conditions, protocol, sample:data relationships etc." Microarrays Multichannel microarray|MicroRNA array|ChIP-on-chip|One channel microarray|miRNA array|mRNA microarray|Proprietary platform micoarray|Methylation array|Reverse phase protein array|Genotyping array|Tissue microarray|Two channel microarray http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3519 PCR experiment "PCR experiments, e.g. quantitative real-time PCR." FALSE http://edamontology.org/topic_3361 1.8 topic_3519 "PCR experiments, e.g. quantitative real-time PCR." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3520 Proteomics experiment Northern blot experiment|2D PAGE experiment|Mass spectrometry "Proteomics experiments.|This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. Also Northern blot experiments." FALSE http://edamontology.org/topic_3361 1.8 topic_3520 Proteomics experiments. Northern blot experiment|2D PAGE experiment|Mass spectrometry http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3521 2D PAGE experiment "Two-dimensional gel electrophoresis experiments, gels or spots in a gel." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3521 "Two-dimensional gel electrophoresis experiments, gels or spots in a gel." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3520 1.13 http://edamontology.org/topic_3522 Northern blot experiment Northern Blot experiments. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3522 Northern Blot experiments. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3520 1.13 http://edamontology.org/topic_3523 RNAi experiment RNAi experiments. FALSE http://edamontology.org/topic_3361 1.8 topic_3523 RNAi experiments. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3524 Simulation experiment "Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction." FALSE http://edamontology.org/topic_3361 1.8 topic_3524 "Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3525 Protein-nucleic acid interactions Protein-DNA/RNA interaction(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3525 Protein-DNA/RNA interaction(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0128 1.13 http://edamontology.org/topic_3526 Protein-protein interactions "Protein-protein interaction(s), including interactions between protein domains." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3526 "Protein-protein interaction(s), including interactions between protein domains." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0128 1.13 http://edamontology.org/topic_3527 Cellular process pathways Cellular process pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3527 Cellular process pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_3528 Disease pathways "Disease pathways, typically of human disease." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3528 "Disease pathways, typically of human disease." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_3529 Environmental information processing pathways Environmental information processing pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3529 Environmental information processing pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_3530 Genetic information processing pathways Genetic information processing pathways. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3530 Genetic information processing pathways. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0602 1.13 http://edamontology.org/topic_3531 Protein super-secondary structure Super-secondary structure of protein sequence(s). TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3531 Super-secondary structure of protein sequence(s). http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3542 1.13 http://edamontology.org/topic_3533 Protein active sites Catalytic residues (active site) of an enzyme. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3533 Catalytic residues (active site) of an enzyme. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3510 1.13 http://edamontology.org/topic_3534 Protein binding sites Protein functional sites|Protein cleavage sites|Enzyme active site|Protein-nucleic acid binding sites|Protein key folding sites "Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc." FALSE http://edamontology.org/topic_3510 1.8 topic_3534 "Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc." Protein functional sites|Protein cleavage sites|Enzyme active site|Protein-nucleic acid binding sites|Protein key folding sites http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3535 Protein-nucleic acid binding sites RNA and DNA-binding proteins and binding sites in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3535 RNA and DNA-binding proteins and binding sites in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3534 1.13 http://edamontology.org/topic_3536 Protein cleavage sites Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3536 Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3510 1.13 http://edamontology.org/topic_3537 Protein chemical modifications Chemical modification of a protein. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3537 Chemical modification of a protein. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0601 1.13 http://edamontology.org/topic_3538 Protein disordered structure Protein features (disordered structure) Disordered structure in a protein. FALSE http://edamontology.org/topic_2814 1.8 topic_3538 Disordered structure in a protein. Protein features (disordered structure) http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3539 Protein domains Structural domains or 3D folds in a protein or polypeptide chain. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3539 Structural domains or 3D folds in a protein or polypeptide chain. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0736 1.13 http://edamontology.org/topic_3540 Protein key folding sites Key residues involved in protein folding. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3540 Key residues involved in protein folding. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3510 1.13 http://edamontology.org/topic_3541 Protein post-translational modifications "Post-translation modifications in a protein sequence, typically describing the specific sites involved." TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3541 "Post-translation modifications in a protein sequence, typically describing the specific sites involved." http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0601 1.13 http://edamontology.org/topic_3542 Protein secondary structure Protein features (secondary structure)|Protein super-secondary structure "Secondary structure (predicted or real) of a protein, including super-secondary structure.|Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.|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)." FALSE http://edamontology.org/topic_2814 1.8 topic_3542 "Secondary structure (predicted or real) of a protein, including super-secondary structure." Protein features (secondary structure) Protein super-secondary structure http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3543 Protein sequence repeats Short repetitive subsequences (repeat sequences) in a protein sequence. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3543 Short repetitive subsequences (repeat sequences) in a protein sequence. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_0157 1.13 http://edamontology.org/topic_3544 Protein signal peptides Signal peptides or signal peptide cleavage sites in protein sequences. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.8 topic_3544 Signal peptides or signal peptide cleavage sites in protein sequences. http://purl.obolibrary.org/obo/edam#obsolete http://edamontology.org/topic_3510 1.13 http://edamontology.org/topic_3557 Protein interaction experiment Phage display|Yeast two-hybrid|Yeast one-hybrid|Co-immunoprecipitation An experiment for studying protein-protein interactions. FALSE http://edamontology.org/topic_3361 1.12 topic_3557 An experiment for studying protein-protein interactions. Phage display|Yeast two-hybrid|Yeast one-hybrid|Co-immunoprecipitation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3569 Applied mathematics "The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models." FALSE http://edamontology.org/topic_3315 1.10 topic_3569 VT 1.1.1 Applied mathematics "The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models." http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3570 Pure mathematics The study of abstract mathematical concepts. FALSE http://edamontology.org/topic_3315 1.10 topic_3570 VT 1.1.1 Pure mathematics The study of abstract mathematical concepts. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3571 Data governance Data stewardship "The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints." FALSE http://edamontology.org/topic_3071 1.10 topic_3571 "The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints." Data stewardship http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3572 Data quality management Data clean-up|Data integrity|Data quality "The quality, integrity, and cleaning up of data. " FALSE http://edamontology.org/topic_3071 1.10 topic_3572 "The quality, integrity, and cleaning up of data. " Data clean-up|Data integrity|Data quality http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3573 Freshwater biology The study of organisms in freshwater ecosystems. FALSE http://edamontology.org/topic_3070 1.10 topic_3573 VT 1.5.18 Marine and Freshwater biology The study of organisms in freshwater ecosystems. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3574 Human genetics The study of inheritatnce in human beings. FALSE http://edamontology.org/topic_3053 1.10 topic_3574 VT 3.1.2 Human genetics The study of inheritatnce in human beings. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3575 Tropical medicine Health problems that are prevalent in tropical and subtropical regions. FALSE http://edamontology.org/topic_3303 1.10 topic_3575 VT 3.3.14 Tropical medicine Health problems that are prevalent in tropical and subtropical regions. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3576 Medical biotechnology Pharmaceutical biotechnology Biotechnology applied to the medical sciences and the development of medicines. FALSE http://edamontology.org/topic_3297 1.10 topic_3576 VT 3.4.1 Biomedical devices|VT 3.4 Medical biotechnology|VT 3.4.2 Health-related biotechnology|VT 3.3.14 Tropical medicine Biotechnology applied to the medical sciences and the development of medicines. Pharmaceutical biotechnology http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3577 Personalised medicine Molecular diagnostics Health problems that are prevalent in tropical and subtropical regions. FALSE http://edamontology.org/topic_3303 1.10 topic_3577 VT 3.4.5 Molecular diagnostics Health problems that are prevalent in tropical and subtropical regions. Molecular diagnostics http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3656 Immunoprecipitation experiment Chromatin immunoprecipitation| "Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq." FALSE http://edamontology.org/topic_3361 1.12 topic_3656 "Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq." Chromatin immunoprecipitation http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3673 Whole genome sequencing WGS|Whole genome resequencing Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. FALSE http://edamontology.org/topic_3168 1.12 https://en.wikipedia.org/wiki/Whole_genome_sequencing topic_3673 Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. WGS Whole genome resequencing http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3674 Methylated DNA immunoprecipitation MeDIP-seq|MeDIP-chip|mDIP|WGBS|methyl-seq|methy-seq|Whole-genome bisulfite sequencing|MeDIP|Methylation sequencing|Bisulfite sequencing|Methylated DNA immunoprecipitation (MeDIP) Laboratory technique to sequence the methylated regions in DNA. FALSE http://edamontology.org/topic_3656 1.12 https://en.wikipedia.org/wiki/Whole_genome_sequencing topic_3674 Laboratory technique to sequence the methylated regions in DNA. MeDIP-seq|MeDIP-chip|mDIP WGBS|methyl-seq|methy-seq|Whole-genome bisulfite sequencing|MeDIP|Methylation sequencing|Bisulfite sequencing|Methylated DNA immunoprecipitation (MeDIP) http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3676 Exome sequencing Exome|Targeted exome capture|Exome analysis|Exome capture "Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome.|Exome sequencing is considered a cheap alternative to whole genome sequencing." FALSE http://edamontology.org/topic_3168 1.1 https://en.wikipedia.org/wiki/Exome_sequencing topic_3676 "Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome." Exome|Targeted exome capture|Exome analysis|Exome capture http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3678 Experimental design and studies Design of experiments|Studies|Experimental design "The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions." FALSE http://edamontology.org/topic_0003 1.12 https://en.wikipedia.org/wiki/Design_of_experiments topic_3678 "The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions." Design of experiments|Studies|Experimental design http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3679 Animal study Challenge study The design of an experiment involving non-human animals. FALSE http://edamontology.org/topic_3386|http://edamontology.org/topic_3678 1.12 topic_3679 The design of an experiment involving non-human animals. Challenge study http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3697 Microbial ecology Environmental microbiology|Microbiome|Molecular community analysis|Community analysis The ecology of microorganisms including their relationship with one another and their environment. FALSE http://edamontology.org/topic_0610|http://edamontology.org/topic_3301 1.13 topic_3697 The ecology of microorganisms including their relationship with one another and their environment. Environmental microbiology Microbiome|Molecular community analysis|Community analysis http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#topics TRUE http://edamontology.org/topic_3794 RNA immunoprecipitation RIP|iCLIP|HITS-CLIP|CLIP-seq|CLIP|PAR-CLIP An antibody-based technique used to map in vivo RNA-protein interactions. FALSE http://edamontology.org/topic_3656 1.17 topic_3794 An antibody-based technique used to map in vivo RNA-protein interactions. RIP iCLIP|HITS-CLIP|CLIP-seq|CLIP|PAR-CLIP http://purl.obolibrary.org/obo/edam#topics http://edamontology.org/topic_3796 Population genomics Large-scale study (typically comparison) of DNA sequences of populations. FALSE http://edamontology.org/topic_0622 1.17 topic_3796 Large-scale study (typically comparison) of DNA sequences of populations. http://purl.obolibrary.org/obo/edam#edam|http://purl.obolibrary.org/obo/edam#events|http://purl.obolibrary.org/obo/edam#topics http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete concept (EDAM) An obsolete concept (redefined in EDAM).|Needed for conversion to the OBO format. TRUE http://www.w3.org/2002/07/owl#DeprecatedClass 1.2 oboInOwl:ObsoleteClass An obsolete concept (redefined in EDAM). http://www.w3.org/2002/07/owl#DeprecatedClass http://www.w3.org/2002/07/owl#DeprecatedClass DeprecatedClass FALSE http://www.w3.org/2002/07/owl#Thing owl:DeprecatedClass