diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 680f943..4c61f3d 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -15,10 +15,9 @@ - EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. - topics "EDAM topics" - EDAM_format http://edamontology.org/format_ "EDAM data formats" - Matúš Kalaš - 3347 - Jon Ison + 3424 + 06:10:2014 23:58 + EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics - 1.3 - Jon Ison, Matus Kalas + 1.4 + Jon Ison + Matúš Kalaš + Hervé Ménager + Jon Ison, Matus Kalas, Herve Menager EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. - concept_properties "EDAM concept properties" - EDAM_data http://edamontology.org/data_ "EDAM types of data" - application/rdf+xml - EDAM http://edamontology.org/ "EDAM relations and concept properties" operations "EDAM operations" edam "EDAM" relations "EDAM relations" - 20:02:2014 15:33 bioinformatics "Bioinformatics" data "EDAM types of data" identifiers "EDAM types of identifiers" - EDAM formats "EDAM data formats" + topics "EDAM topics" + concept_properties "EDAM concept properties" + EDAM EDAM_operation http://edamontology.org/operation_ "EDAM operations" EDAM_topic http://edamontology.org/topic_ "EDAM topics" + EDAM_data http://edamontology.org/data_ "EDAM types of data" + EDAM_format http://edamontology.org/format_ "EDAM data formats" + EDAM http://edamontology.org/ "EDAM relations and concept properties" + application/rdf+xml @@ -65,25 +65,11 @@ /////////////////////////////////////////////////////////////////////////////////////// --> - - Regular expression - true - concept_properties - 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. + + - - - + - - - Documentation - concept_properties - true - 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. - Specification - - Obsolete since @@ -91,8 +77,15 @@ concept_properties true + + + + + + + @@ -101,18 +94,54 @@ true 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + + + + + + + + Regular expression + true + concept_properties + 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + + + + + + + + Documentation + concept_properties + true + 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. + Specification + + + + + + Created in concept_properties true Version in which a concept was created. - - - - - - + + + @@ -187,8 +216,14 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + true + In very unusual cases. + + + + OBO_REL:bearer_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. @@ -198,12 +233,6 @@ - - In very unusual cases. - true - - - @@ -214,8 +243,8 @@ false false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. - edam 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. + edam OBO_REL:is_a bioinformatics relations @@ -254,16 +283,16 @@ - In very unusual cases. - true + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant - + - OBO_REL:has_participant - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + In very unusual cases. + true - + @@ -295,8 +324,8 @@ - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:has_participant @@ -338,28 +367,28 @@ - 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. - + In very unusual cases. + true - + - 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. + 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. - + - 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. + 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. + - - true - In very unusual cases. + 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. - + + @@ -415,22 +444,22 @@ - OBO_REL:inheres_in - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of - + - true In very unusual cases. + true - OBO_REL:function_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + OBO_REL:inheres_in - + @@ -478,23 +507,23 @@ - OBO_REL:participates_in + 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). + + + + + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + OBO_REL:participates_in - true In very unusual cases. + true - - 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - - - - @@ -526,14 +555,14 @@ - OBO_REL:participates_in 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:participates_in - In very unusual cases. true + In very unusual cases. @@ -568,17 +597,17 @@ - OBO_REL:quality_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - - - In very unusual cases. true + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of + + + @@ -599,13 +628,11 @@ Resource type true - data - edam A type of computational resource used in bioinformatics. - data beta12orEarlier beta12orEarlier - bioinformatics + + @@ -619,16 +646,15 @@ Datum - data beta12orEarlier Data set Data record - bioinformatics - data - edam 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. + + + @@ -637,16 +663,22 @@ - Data does however not necessarily contain statements and not necessarily about an entity. + IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. - + - Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). + Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - - + + + + Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. @@ -661,28 +693,22 @@ - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - - - - - GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. + Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). + - - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum + Data does however not necessarily contain statements and not necessarily about an entity. - + + - IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. + GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - + @@ -692,14 +718,11 @@ Tool - edam true beta12orEarlier - beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. - data - bioinformatics - data + beta12orEarlier + @@ -711,12 +734,9 @@ beta12orEarlier true - data beta12orEarlier - bioinformatics A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. - edam - data + @@ -733,11 +753,10 @@ An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. - bioinformatics - edam - data beta12orEarlier - data + + + @@ -747,12 +766,11 @@ Directory metadata - bioinformatics - data - edam beta12orEarlier A directory on disk from which files are read. - data + + + @@ -762,15 +780,12 @@ MeSH vocabulary - data beta12orEarlier - data - bioinformatics + Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. beta12orEarlier true - Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. - edam + @@ -781,14 +796,11 @@ HGNC vocabulary true - beta12orEarlier - bioinformatics - data Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. beta12orEarlier - edam - data + beta12orEarlier + @@ -798,15 +810,12 @@ UMLS vocabulary - data - beta12orEarlier - data - Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). true - edam - bioinformatics + beta12orEarlier beta12orEarlier + Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). + @@ -825,14 +834,13 @@ - identifiers - identifier - data - bioinformatics 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). - edam ID beta12orEarlier + + + + @@ -851,15 +859,12 @@ Database entry - data true An entry (retrievable via URL) from a biological database. - data - bioinformatics beta12orEarlier beta12orEarlier - edam + @@ -869,12 +874,11 @@ Molecular mass - data - bioinformatics - edam - data beta12orEarlier Mass of a molecule. + + + @@ -885,12 +889,11 @@ Molecular charge PDBML:pdbx_formal_charge - bioinformatics - data beta12orEarlier Net charge of a molecule. - edam - data + + + @@ -902,11 +905,10 @@ beta12orEarlier A specification of a chemical structure. - bioinformatics - data Chemical structure specification - edam - data + + + @@ -916,13 +918,12 @@ QSAR descriptor - edam beta12orEarlier - data 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. A QSAR quantitative descriptor (name-value pair) of chemical structure. - data - bioinformatics + + + @@ -933,12 +934,11 @@ Raw sequence Non-sequence characters may be used for example for gaps and translation stop. - data - edam A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. - data - bioinformatics beta12orEarlier + + + @@ -948,12 +948,11 @@ Sequence record - data - data A molecular sequence and associated metadata. - edam beta12orEarlier - bioinformatics + + + @@ -963,14 +962,13 @@ Sequence set - data - bioinformatics - data SO:0001260 beta12orEarlier This concept may be used for arbitrary sequence sets and associated data arising from processing. - edam 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. + + + @@ -981,11 +979,10 @@ Sequence mask character A character used to replace (mask) other characters in a molecular sequence. - data - bioinformatics - edam beta12orEarlier - data + + + @@ -996,13 +993,12 @@ Sequence mask type - bioinformatics - data beta12orEarlier 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. A label (text token) describing the type of sequence masking to perform. - edam - data + + + @@ -1013,15 +1009,14 @@ DNA sense specification - bioinformatics - data beta12orEarlier - edam DNA strand specification - data 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. The strand of a DNA sequence (forward or reverse). Strand + + + @@ -1031,12 +1026,11 @@ Sequence length specification - bioinformatics - data beta12orEarlier A specification of sequence length(s). - data - edam + + + @@ -1051,10 +1045,9 @@ This is used for such things as a report including the sequence identifier, type and length. Basic or general information concerning molecular sequences. beta12orEarlier - data - edam - data - bioinformatics + + + @@ -1065,13 +1058,12 @@ Sequence feature source - data beta12orEarlier How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. - edam 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). - data - bioinformatics + + + @@ -1081,13 +1073,12 @@ Database hits (sequence) - data A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. 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. - edam - data - bioinformatics beta12orEarlier + + + @@ -1097,13 +1088,12 @@ Database hits (secondary) - bioinformatics A report of hits from a search of a protein secondary or domain database. - data - data - edam beta12orEarlier Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. + + + @@ -1113,15 +1103,12 @@ Sequence signature model - data true beta12orEarlier - data - bioinformatics - edam beta12orEarlier Data files used by motif or profile methods. + @@ -1131,16 +1118,13 @@ Sequence signature - data - edam - beta12orEarlier A classifier of sequences such as a sequence motif, profile or other diagnostic element. + beta12orEarlier beta12orEarlier - data true - bioinformatics + @@ -1151,12 +1135,11 @@ Sequence alignment (words) Alignment of exact matches between subsequences (words) within two or more molecular sequences. - data Sequence word alignment - data beta12orEarlier - edam - bioinformatics + + + @@ -1166,12 +1149,11 @@ Dotplot - data beta12orEarlier - edam - bioinformatics A dotplot of sequence similarities identified from word-matching or character comparison. - data + + + @@ -1188,13 +1170,12 @@ Alignment of multiple molecular sequences. - data beta12orEarlier - bioinformatics - edam - data + + + @@ -1206,11 +1187,10 @@ Sequence alignment parameter beta12orEarlier - bioinformatics - edam - data - data Some simple value controlling a sequence alignment (or similar 'match') operation. + + + @@ -1220,12 +1200,11 @@ Sequence similarity score - edam - data beta12orEarlier - bioinformatics - data A value representing molecular sequence similarity. + + + @@ -1236,12 +1215,11 @@ Sequence alignment metadata - bioinformatics - edam - data - data beta12orEarlier Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. + + + @@ -1252,12 +1230,11 @@ Sequence alignment report beta12orEarlier - edam - data An informative report of molecular sequence alignment-derived data or metadata. - bioinformatics This is a broad data type and is used a placeholder for other, more specific types. - data + + + @@ -1267,12 +1244,11 @@ Sequence profile alignment - bioinformatics - data - data A profile-profile alignment (each profile typically representing a sequence alignment). beta12orEarlier - edam + + + @@ -1283,12 +1259,11 @@ Sequence-profile alignment Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. - bioinformatics - data - edam - data Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). beta12orEarlier + + + @@ -1299,14 +1274,13 @@ Sequence distance matrix Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. - data - A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. - bioinformatics - edam Phylogenetic distance matrix - data + A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. Moby:phylogenetic_distance_matrix beta12orEarlier + + + @@ -1316,13 +1290,12 @@ Phylogenetic character data - data beta12orEarlier - edam - bioinformatics - 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 + + + @@ -1339,18 +1312,17 @@ - bioinformatics Moby:myTree beta12orEarlier - data 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. Moby:phylogenetic_tree - data 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'. Moby:Tree Phylogeny - edam + + + @@ -1361,14 +1333,13 @@ Comparison matrix - data - bioinformatics Substitution matrix - edam Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. beta12orEarlier - data 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). + + + @@ -1378,16 +1349,13 @@ Protein topology - edam + The location and size of the secondary structure elements and intervening loop regions is usually indicated. true + Predicted or actual protein topology represented as a string of protein secondary structure elements. beta12orEarlier - bioinformatics beta12orEarlier - The location and size of the secondary structure elements and intervening loop regions is usually indicated. - data - data - Predicted or actual protein topology represented as a string of protein secondary structure elements. + @@ -1404,14 +1372,13 @@ - edam beta12orEarlier - data - bioinformatics - data 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). Protein secondary structure Secondary structure assignment (predicted or real) of a protein. + + + @@ -1422,14 +1389,13 @@ Protein features (super-secondary) - data - bioinformatics - edam - A report of predicted or actual super-secondary structure of protein sequence(s). - data Protein structure report (super-secondary) beta12orEarlier Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + A report of predicted or actual super-secondary structure of protein sequence(s). + + + @@ -1442,10 +1408,9 @@ beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more proteins. - data - bioinformatics - edam - data + + + @@ -1456,14 +1421,11 @@ Secondary structure alignment metadata (protein) true - edam - beta12orEarlier beta12orEarlier - data + beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. - bioinformatics - data + @@ -1480,13 +1442,12 @@ beta12orEarlier - bioinformatics - data - edam Moby:RNAStructML This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. - data An informative report of secondary structure (predicted or real) of an RNA molecule. + + + @@ -1496,13 +1457,12 @@ Secondary structure alignment (RNA) - edam beta12orEarlier - data Alignment of the (1D representations of) secondary structure of two or more RNA molecules. - data - bioinformatics Moby:RNAStructAlignmentML + + + @@ -1512,15 +1472,12 @@ Secondary structure alignment metadata (RNA) - edam - beta12orEarlier - bioinformatics - true beta12orEarlier - data - data An informative report of RNA secondary structure alignment-derived data or metadata. + beta12orEarlier + true + @@ -1538,14 +1495,13 @@ 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. Structure data - data The coordinate data may be predicted or real. - bioinformatics - data beta12orEarlier - edam Coordinate model + + + @@ -1558,12 +1514,9 @@ An entry from a molecular tertiary (3D) structure database. beta12orEarlier beta12orEarlier - bioinformatics - edam - data true - data + @@ -1574,12 +1527,11 @@ Database hits (structure) This includes alignment and score data. - edam beta12orEarlier Results (hits) from searching a database of tertiary structure. - data - data - bioinformatics + + + @@ -1596,13 +1548,12 @@ - edam - data - bioinformatics - Alignment (superimposition) of molecular tertiary (3D) structures. - data beta12orEarlier 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. + Alignment (superimposition) of molecular tertiary (3D) structures. + + + @@ -1612,13 +1563,12 @@ Structure alignment report - bioinformatics - data - An informative report on molecular tertiary structure alignment-derived data. - edam - data + 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. beta12orEarlier + + + @@ -1628,12 +1578,11 @@ Structure similarity score - data - bioinformatics - edam A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. - data beta12orEarlier + + + @@ -1649,13 +1598,12 @@ - bioinformatics - edam - data - data Some type of structural (3D) profile or template (representing a structure or structure alignment). beta12orEarlier 3D profile + + + @@ -1666,12 +1614,11 @@ Structural (3D) profile alignment A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). - data - data - edam - bioinformatics Structural profile alignment beta12orEarlier + + + @@ -1682,12 +1629,11 @@ Sequence-3D profile alignment beta12orEarlier - data - bioinformatics - data An alignment of a sequence to a 3D profile (representing structures or a structure alignment). - edam Sequence-structural profile alignment + + + @@ -1697,12 +1643,11 @@ Protein sequence-structure scoring matrix - edam Matrix of values used for scoring sequence-structure compatibility. - data beta12orEarlier - bioinformatics - data + + + @@ -1712,12 +1657,11 @@ Sequence-structure alignment - data An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). - data beta12orEarlier - bioinformatics - edam + + + @@ -1726,14 +1670,13 @@ Amino acid annotation - - + beta12orEarlier - data - edam - bioinformatics + 1.4 + true An informative report about a specific amino acid. - data + + @@ -1742,20 +1685,13 @@ Peptide annotation - - - - - - - - + beta12orEarlier - data An informative report about a specific peptide. - bioinformatics - edam - data + true + 1.4 + + @@ -1771,13 +1707,12 @@ - bioinformatics - edam - data Gene product annotation beta12orEarlier An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. - data + + + @@ -1788,14 +1723,13 @@ Protein property - data - edam - A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. - bioinformatics 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. - data beta12orEarlier + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. Protein physicochemical property + + + @@ -1813,13 +1747,12 @@ beta12orEarlier - data Protein structure report (3D motif) - edam - data An informative report on the 3D structural motifs in a protein. This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. - bioinformatics + + + @@ -1835,12 +1768,11 @@ - bioinformatics beta12orEarlier - data Data concerning the classification of the sequences and/or structures of protein structural domain(s). - edam - data + + + @@ -1856,15 +1788,14 @@ - edam - beta12orEarlier - The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. Protein structural domains + The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + beta12orEarlier Protein domain assignment Summary of structural domains or 3D folds in a protein or polypeptide chain. - bioinformatics - data - data + + + @@ -1873,16 +1804,15 @@ Protein architecture report - - + + true beta12orEarlier - bioinformatics - edam - data - data Protein structure report (architecture) Protein property (architecture) An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. + 1.4 + + @@ -1893,14 +1823,13 @@ Protein folding report 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. - Protein report (folding) - data - data - edam - bioinformatics Protein property (folding) A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. + Protein report (folding) beta12orEarlier + + + @@ -1913,16 +1842,13 @@ Protein report (mutation) beta13 Protein structure report (mutation) - data - data Protein property (mutation) beta12orEarlier - bioinformatics true 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. - edam + @@ -1932,13 +1858,12 @@ Protein interaction raw data - data beta12orEarlier - edam Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. - bioinformatics - data 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. + + + @@ -1955,13 +1880,12 @@ - bioinformatics - data - data Protein report (interaction) beta12orEarlier An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand. - edam + + + @@ -1977,13 +1901,12 @@ - edam Protein family annotation - bioinformatics - data beta12orEarlier - data An informative report on a specific protein family or other group of classified proteins. + + + @@ -1994,11 +1917,10 @@ Vmax The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. - data - data - edam beta12orEarlier - bioinformatics + + + @@ -2008,12 +1930,11 @@ Km - data beta12orEarlier - data Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. - edam - bioinformatics + + + @@ -2022,13 +1943,13 @@ Nucleotide base annotation - - bioinformatics + + 1.4 An informative report about a specific nucleotide base. - data - edam + true beta12orEarlier - data + + @@ -2039,14 +1960,13 @@ Nucleic acid property - Nucleic acid physicochemical property - data - bioinformatics - data beta12orEarlier + Nucleic acid physicochemical property 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. A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. - edam + + + @@ -2063,12 +1983,11 @@ This is a broad data type and is used a placeholder for other, more specific types. - data - bioinformatics - data Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. - edam beta12orEarlier + + + @@ -2084,18 +2003,17 @@ - data - bioinformatics Gene annotation (functional) - data Moby:GeneInfo Moby_namespace:Human_Readable_Description beta12orEarlier - edam 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). Moby:gene Gene report An informative report on a particular locus, gene, gene system or groups of genes. + + + @@ -2105,15 +2023,12 @@ Gene classification - edam + beta12orEarlier A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. true beta12orEarlier - data - beta12orEarlier - bioinformatics - data + @@ -2130,13 +2045,12 @@ beta12orEarlier - data A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - bioinformatics Sequence variation annotation - data - edam SO:0001059 + + + @@ -2153,12 +2067,11 @@ This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. - data - data An informative report on a specific chromosome. - edam beta12orEarlier - bioinformatics + + + @@ -2169,11 +2082,10 @@ Genotype/phenotype annotation beta12orEarlier - data - data - edam - bioinformatics 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. + + + @@ -2189,12 +2101,11 @@ - edam - data beta12orEarlier - bioinformatics - data Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence. + + + @@ -2210,13 +2121,12 @@ - data PCR assay data beta12orEarlier - bioinformatics Data on a PCR assay or electronic / virtual PCR. - edam - data + + + @@ -2227,13 +2137,12 @@ Sequence trace - edam beta12orEarlier - data - bioinformatics This is the raw data produced by a DNA sequencing machine. 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. - data + + + @@ -2243,16 +2152,15 @@ Sequence assembly - data - data 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. - edam - bioinformatics SO:0000353 - An assembly of fragments of a (typically genomic) DNA sequence. SO:0001248 + An assembly of fragments of a (typically genomic) DNA sequence. beta12orEarlier + + + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. @@ -2268,13 +2176,12 @@ Radiation Hybrid (RH) scores - bioinformatics - data - edam Radiation hybrid scores (RH) scores for one or more markers. - data Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. beta12orEarlier + + + @@ -2285,11 +2192,10 @@ Gene annotation (linkage) An informative report on the linkage of alleles. - data - data beta12orEarlier - edam - bioinformatics + + + @@ -2300,12 +2206,11 @@ Gene expression profile Gene expression pattern - bioinformatics Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. beta12orEarlier - edam - data - data + + + @@ -2323,12 +2228,11 @@ beta12orEarlier 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. - data - bioinformatics - edam - Information on a microarray experiment such as conditions, protocol, sample:data relationships etc. - data Experimental design annotation + Information on a microarray experiment such as conditions, protocol, sample:data relationships etc. + + + @@ -2338,15 +2242,12 @@ Oligonucleotide probe data - bioinformatics - beta13 - data Data on oligonucleotide probes (typically for use with DNA microarrays). true - data - edam + beta13 beta12orEarlier + @@ -2356,16 +2257,13 @@ SAGE experimental data - edam - data - true - beta12orEarlier - data beta12orEarlier - bioinformatics Serial analysis of gene expression (SAGE) experimental data Output from a serial analysis of gene expression (SAGE) experiment. + true + beta12orEarlier + @@ -2376,15 +2274,12 @@ MPSS experimental data true - data - edam - beta12orEarlier - beta12orEarlier Massively parallel signature sequencing (MPSS) experimental data + beta12orEarlier Massively parallel signature sequencing (MPSS) data. - bioinformatics - data + beta12orEarlier + @@ -2394,16 +2289,13 @@ SBS experimental data + Sequencing by synthesis (SBS) experimental data + Sequencing by synthesis (SBS) data. true - data - edam - bioinformatics beta12orEarlier - Sequencing by synthesis (SBS) data. - Sequencing by synthesis (SBS) experimental data - data beta12orEarlier + @@ -2414,11 +2306,10 @@ 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. - bioinformatics - data beta12orEarlier - edam - data + + + @@ -2429,11 +2320,10 @@ Protein X-ray crystallographic data beta12orEarlier - data X-ray crystallography data. - bioinformatics - edam - data + + + @@ -2443,12 +2333,11 @@ Protein NMR data - bioinformatics beta12orEarlier - data - edam - data Protein nuclear magnetic resonance (NMR) raw data. + + + @@ -2458,12 +2347,11 @@ Protein circular dichroism (CD) spectroscopic data - data - data Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. - bioinformatics beta12orEarlier - edam + + + @@ -2479,13 +2367,12 @@ - edam EM volume map Volume map data from electron microscopy. - bioinformatics - data beta12orEarlier - data + + + @@ -2503,11 +2390,10 @@ This might include the location in the model of the known features of a particular macromolecule. Annotation on a structural 3D model (volume map) from electron microscopy. - data - edam beta12orEarlier - bioinformatics - data + + + @@ -2524,13 +2410,12 @@ - beta12orEarlier Two-dimensional gel electrophoresis image. - edam - data - data + beta12orEarlier Two-dimensional gel electrophoresis image - bioinformatics + + + @@ -2546,12 +2431,11 @@ - data Spectra from mass spectrometry. beta12orEarlier - data - edam - bioinformatics + + + @@ -2568,14 +2452,13 @@ - edam beta12orEarlier A set of peptide masses (peptide mass fingerprint) from mass spectrometry. - bioinformatics - data - data Protein fingerprint Peak list + + + @@ -2592,11 +2475,10 @@ beta12orEarlier - bioinformatics - data Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. - edam - data + + + @@ -2607,14 +2489,11 @@ Pathway or network annotation beta12orEarlier - bioinformatics - data - true - data An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. - edam + true beta12orEarlier + @@ -2624,15 +2503,12 @@ Biological pathway map - edam beta12orEarlier - data A map (typically a diagram) of a biological pathway. - data - bioinformatics true beta12orEarlier + @@ -2642,12 +2518,11 @@ Data resource definition - edam - data A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. - bioinformatics - data beta12orEarlier + + + @@ -2658,11 +2533,10 @@ Workflow metadata beta12orEarlier - edam - data - bioinformatics - data Basic information, annotation or documentation concerning a workflow (but not the workflow itself). + + + @@ -2678,12 +2552,11 @@ - edam - data - bioinformatics beta12orEarlier A biological model which can be represented in mathematical terms. - data + + + @@ -2694,12 +2567,11 @@ Statistical estimate score - data - bioinformatics A value representing estimated statistical significance of some observed data; typically sequence database hits. beta12orEarlier - data - edam + + + @@ -2709,12 +2581,11 @@ EMBOSS database resource definition - data - edam beta12orEarlier Resource definition for an EMBOSS database. - bioinformatics - data + + + @@ -2724,14 +2595,13 @@ Version information - edam - data - Information on a version of software or data, for example name, version number and release date. beta12orEarlier - bioinformatics + 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. - data + + + @@ -2752,11 +2622,10 @@ 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. A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. - data - edam - data - bioinformatics beta12orEarlier + + + @@ -2773,11 +2642,10 @@ beta12orEarlier - bioinformatics An index of data of biological relevance. - data - edam - data + + + @@ -2794,12 +2662,11 @@ beta12orEarlier - data - data - edam - bioinformatics Database index annotation A report of an analysis of an index of biological data. + + + @@ -2809,12 +2676,11 @@ Database metadata - bioinformatics - edam - data - data beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. + + + @@ -2824,12 +2690,11 @@ Tool metadata - data - edam - data Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. beta12orEarlier - bioinformatics + + + @@ -2839,13 +2704,12 @@ Job metadata - data Textual metadata on a submitted or completed job. - edam Moby:PDGJOB - data - bioinformatics beta12orEarlier + + + @@ -2855,12 +2719,11 @@ User metadata - data - edam - data Textual metadata on a software author or end-user, for example a person or other software. - bioinformatics beta12orEarlier + + + @@ -2868,7 +2731,7 @@ - Small molecule annotation + Small molecule report @@ -2877,14 +2740,14 @@ - data - data An informative report on a specific chemical compound. Small molecule report - bioinformatics Chemical compound annotation beta12orEarlier - edam + Small molecule annotation + + + @@ -2892,15 +2755,15 @@ - Cell line annotation + Cell line report beta12orEarlier 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. - bioinformatics - data - data - edam + Cell line annotation Organism strain data + + + @@ -2909,13 +2772,13 @@ Scent annotation - - bioinformatics - data + + true + 1.4 An informative report about a specific scent. - edam beta12orEarlier - data + + @@ -2925,12 +2788,12 @@ Ontology term - bioinformatics A term (name) from an ontology. - edam - data beta12orEarlier - data + Ontology class name + + + @@ -2946,12 +2809,13 @@ - bioinformatics - data Data concerning or derived from a concept from a biological ontology. - data + Ontology term metadata beta12orEarlier - edam + Ontology class metadata + + + @@ -2964,14 +2828,13 @@ Moby:Global_Keyword Moby:Wildcard_Query Moby:BooleanQueryString - data beta12orEarlier - data Moby:QueryString - bioinformatics - edam Keyword(s) or phrase(s) used (typically) for text-searching purposes. Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + + + @@ -2979,20 +2842,19 @@ - Bibliographic reference + Citation beta12orEarlier Moby:Publication - edam - Citation + Bibliographic reference Reference - data 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. Bibliographic data that uniquely identifies a scientific article, book or other published material. - bioinformatics - data Moby:GCP_SimpleCitation + + + @@ -3008,12 +2870,11 @@ - data A body of scientific text, typically a full text article from a scientific journal. beta12orEarlier - edam - data - bioinformatics + + + @@ -3025,11 +2886,10 @@ A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. beta12orEarlier - data - data - bioinformatics An abstract of the results of text mining. - edam + + + @@ -3040,15 +2900,11 @@ Entity identifier An identifier of a biological entity or phenomenon. - identifier beta12orEarlier - beta12orEarlier - data true - bioinformatics - edam - identifiers + beta12orEarlier + @@ -3059,15 +2915,11 @@ Data resource identifier beta12orEarlier - An identifier of a data resource. - edam - identifier - identifiers beta12orEarlier - bioinformatics + An identifier of a data resource. true - data + @@ -3077,14 +2929,13 @@ Identifier (typed) - identifiers - edam - data - bioinformatics 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'. - identifier beta12orEarlier + + + + @@ -3094,13 +2945,12 @@ Tool identifier - data beta12orEarlier An identifier of a bioinformatics tool, e.g. an application or web service. - bioinformatics - identifier - identifiers - edam + + + + @@ -3110,16 +2960,12 @@ Discrete entity identifier - identifier - bioinformatics - identifiers - data - true - beta12orEarlier Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). beta12orEarlier - edam + true + beta12orEarlier + @@ -3129,16 +2975,12 @@ Entity feature identifier - identifiers - identifier - data - edam beta12orEarlier 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). - bioinformatics - true beta12orEarlier + true + @@ -3148,16 +2990,12 @@ Entity collection identifier - edam Name or other identifier of a collection of discrete biological entities. - true - data - identifier - identifiers - bioinformatics beta12orEarlier + true beta12orEarlier + @@ -3167,16 +3005,12 @@ Phenomenon identifier - data - identifiers - edam - true - beta12orEarlier Name or other identifier of a physical, observable biological occurrence or event. + true beta12orEarlier - bioinformatics - identifier + beta12orEarlier + @@ -3192,13 +3026,12 @@ - identifier - edam - identifiers beta12orEarlier - data - bioinformatics Name or other identifier of a molecule. + + + + @@ -3209,13 +3042,12 @@ Atom ID beta12orEarlier - data Identifier (e.g. character symbol) of a specific atom. - identifier Atom identifier - bioinformatics - identifiers - edam + + + + @@ -3226,13 +3058,12 @@ Molecule name - identifiers beta12orEarlier - edam - identifier - bioinformatics - data Name of a specific molecule. + + + + @@ -3243,13 +3074,12 @@ Molecule type Protein|DNA|RNA - bioinformatics beta12orEarlier A label (text token) describing the type a molecule. - data - edam - data For example, 'Protein', 'DNA', 'RNA' etc. + + + @@ -3259,16 +3089,12 @@ Chemical identifier - bioinformatics - edam + Unique identifier of a chemical compound. beta12orEarlier beta12orEarlier - Unique identifier of a chemical compound. - identifiers - identifier - data true + @@ -3285,13 +3111,12 @@ - identifier - beta12orEarlier - edam Name of a chromosome. - identifiers - bioinformatics - data + beta12orEarlier + + + + @@ -3302,12 +3127,11 @@ Peptide identifier beta12orEarlier - identifier Identifier of a peptide chain. - data - bioinformatics - identifiers - edam + + + + @@ -3323,13 +3147,12 @@ - identifiers - bioinformatics - edam - identifier - data Identifier of a protein. beta12orEarlier + + + + @@ -3340,14 +3163,13 @@ Compound name - identifier beta12orEarlier - bioinformatics - edam - identifiers Chemical name Unique name of a chemical compound. - data + + + + @@ -3357,13 +3179,12 @@ Chemical registry number - identifiers - edam - identifier Unique registry number of a chemical compound. - bioinformatics beta12orEarlier - data + + + + @@ -3375,14 +3196,10 @@ beta12orEarlier Code word for a ligand, for example from a PDB file. - identifier - true - edam - data - identifiers beta12orEarlier - bioinformatics + true + @@ -3398,13 +3215,12 @@ - edam - data Identifier of a drug. - identifier beta12orEarlier - bioinformatics - identifiers + + + + @@ -3420,14 +3236,13 @@ - bioinformatics - identifier Residue identifier beta12orEarlier Identifier of an amino acid. - data - identifiers - edam + + + + @@ -3437,13 +3252,12 @@ Nucleotide identifier - identifier Name or other identifier of a nucleotide. - bioinformatics - data beta12orEarlier - identifiers - edam + + + + @@ -3454,12 +3268,11 @@ Monosaccharide identifier Identifier of a monosaccharide. - bioinformatics beta12orEarlier - identifiers - edam - data - identifier + + + + @@ -3470,14 +3283,13 @@ Chemical name (ChEBI) This is the recommended chemical name for use for example in database annotation. - edam - Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. - identifier - identifiers - bioinformatics - data beta12orEarlier + Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. ChEBI chemical name + + + + @@ -3487,14 +3299,13 @@ Chemical name (IUPAC) - bioinformatics beta12orEarlier - edam - identifiers IUPAC chemical name - data - identifier IUPAC recommended name of a chemical compound. + + + + @@ -3504,14 +3315,13 @@ Chemical name (INN) - edam - identifier - data International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). - bioinformatics - identifiers beta12orEarlier INN chemical name + + + + @@ -3521,14 +3331,13 @@ Chemical name (brand) - data - identifiers - edam - bioinformatics Brand chemical name beta12orEarlier - identifier Brand name of a chemical compound. + + + + @@ -3538,14 +3347,13 @@ Chemical name (synonymous) - identifiers Synonymous name of a chemical compound. - edam - data - bioinformatics - identifier Synonymous chemical name beta12orEarlier + + + + @@ -3555,14 +3363,13 @@ Chemical registry number (CAS) - identifiers - bioinformatics - identifier - edam - data beta12orEarlier CAS registry number of a chemical compound. CAS chemical registry number + + + + @@ -3572,14 +3379,13 @@ Chemical registry number (Beilstein) - data - identifiers Beilstein registry number of a chemical compound. - bioinformatics - identifier Beilstein chemical registry number beta12orEarlier - edam + + + + @@ -3589,14 +3395,13 @@ Chemical registry number (Gmelin) - bioinformatics Gmelin registry number of a chemical compound. - identifier beta12orEarlier - identifiers - edam - data Gmelin chemical registry number + + + + @@ -3608,13 +3413,12 @@ beta12orEarlier Component identifier code - bioinformatics Short ligand name - identifier - data 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. - identifiers - edam + + + + @@ -3624,13 +3428,12 @@ Amino acid name - identifier - edam - data - bioinformatics - identifiers String of one or more ASCII characters representing an amino acid. beta12orEarlier + + + + @@ -3641,13 +3444,12 @@ Nucleotide code - data - bioinformatics - edam String of one or more ASCII characters representing a nucleotide. - identifier - identifiers beta12orEarlier + + + + @@ -3669,15 +3471,14 @@ Protein chain identifier PDB strand id PDBML:pdbx_PDB_strand_id - edam Identifier of a polypeptide chain from a protein. - data - identifiers Chain identifier - bioinformatics - identifier WHATIF: chain beta12orEarlier + + + + @@ -3688,13 +3489,12 @@ Protein name - identifiers - bioinformatics beta12orEarlier - edam - data - identifier Name of a protein. + + + + @@ -3710,13 +3510,12 @@ - data Name or other identifier of an enzyme or record from a database of enzymes. - bioinformatics - identifiers beta12orEarlier - edam - identifier + + + + @@ -3726,19 +3525,18 @@ EC number - bioinformatics Enzyme Commission number beta12orEarlier - data Moby:Annotated_EC_Number - edam EC An Enzyme Commission (EC) number of an enzyme. EC code Moby:EC_Number [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ - identifier - identifiers + + + + @@ -3751,11 +3549,10 @@ beta12orEarlier Name of an enzyme. - data - identifier - identifiers - bioinformatics - edam + + + + @@ -3771,13 +3568,12 @@ - identifier - data beta12orEarlier - edam Name of a restriction enzyme. - bioinformatics - identifiers + + + + @@ -3789,10 +3585,9 @@ beta12orEarlier A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. - data - data - bioinformatics - edam + + + @@ -3804,12 +3599,11 @@ beta12orEarlier - edam - bioinformatics A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. - identifier - data - identifiers + + + + @@ -3821,14 +3615,13 @@ PDBML:_atom_site.id beta12orEarlier - data WHATIF: number SO:0000735 - data A position of a single point (base or residue) in a sequence, or part of such a specification. - bioinformatics - edam WHATIF: PDBx_atom_site + + + @@ -3838,12 +3631,11 @@ Sequence range - edam - data - data Specification of range(s) of sequence positions. - bioinformatics beta12orEarlier + + + @@ -3853,16 +3645,12 @@ Nucleic acid feature identifier - bioinformatics + true Name or other identifier of an nucleic acid feature. beta12orEarlier beta12orEarlier - data - true - identifiers - identifier - edam + @@ -3872,16 +3660,12 @@ Protein feature identifier - bioinformatics - edam - identifier - Name or other identifier of a protein feature. beta12orEarlier - data beta12orEarlier - identifiers true + Name or other identifier of a protein feature. + @@ -3892,14 +3676,13 @@ Sequence feature key A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. - data - bioinformatics beta12orEarlier - 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 type - edam - data + 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 + + + @@ -3910,12 +3693,11 @@ Sequence feature qualifier Feature qualifiers hold information about a feature beyond that provided by the feature key and location. - data - edam - bioinformatics - data Typically one of the EMBL or Swiss-Prot feature qualifiers. beta12orEarlier + + + @@ -3927,12 +3709,11 @@ 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. beta12orEarlier - bioinformatics Typically an EMBL or Swiss-Prot feature label. - data Sequence feature name - edam - data + + + @@ -3944,12 +3725,11 @@ The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. - bioinformatics - data beta12orEarlier UFO - edam - data + + + @@ -3959,16 +3739,12 @@ Codon name - bioinformatics - beta12orEarlier - beta12orEarlier - identifier - data String of one or more ASCII characters representing a codon. true - identifiers - edam + beta12orEarlier + beta12orEarlier + @@ -3984,14 +3760,13 @@ - edam beta12orEarlier An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. - data - bioinformatics - identifier - identifiers Moby:GeneAccessionList + + + + @@ -4001,15 +3776,14 @@ Gene symbol - edam - data The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. Moby_namespace:Global_GeneCommonName - identifier - identifiers beta12orEarlier Moby_namespace:Global_GeneSymbol - bioinformatics + + + + @@ -4020,20 +3794,19 @@ Gene ID (NCBI) - bioinformatics beta12orEarlier NCBI gene ID - identifiers An NCBI unique identifier of a gene. - edam http://www.geneontology.org/doc/GO.xrf_abbs:LocusID - data Gene identifier (Entrez) http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene Entrez gene ID - identifier Gene identifier (NCBI) NCBI geneid + + + + @@ -4043,16 +3816,12 @@ Gene identifier (NCBI RefSeq) - An NCBI RefSeq unique identifier of a gene. beta12orEarlier - edam - bioinformatics - data + An NCBI RefSeq unique identifier of a gene. true - identifier - identifiers beta12orEarlier + @@ -4062,16 +3831,12 @@ Gene identifier (NCBI UniGene) - edam - identifiers - An NCBI UniGene unique identifier of a gene. - bioinformatics - identifier - data true beta12orEarlier + An NCBI UniGene unique identifier of a gene. beta12orEarlier + @@ -4081,17 +3846,13 @@ Gene identifier (Entrez) - data + beta12orEarlier [0-9]+ - edam beta12orEarlier - beta12orEarlier - identifier true An Entrez unique identifier of a gene. - bioinformatics - identifiers + @@ -4103,12 +3864,11 @@ beta12orEarlier Identifier of a gene or feature from the CGD database. - data - edam CGD ID - identifiers - bioinformatics - identifier + + + + @@ -4118,13 +3878,12 @@ Gene ID (DictyBase) - identifiers - bioinformatics Identifier of a gene from DictyBase. - data - identifier beta12orEarlier - edam + + + + @@ -4135,14 +3894,13 @@ Ensembl gene ID - Gene ID (Ensembl) - bioinformatics - data - edam Unique identifier for a gene (or other feature) from the Ensembl database. + Gene ID (Ensembl) beta12orEarlier - identifier - identifiers + + + + @@ -4153,15 +3911,14 @@ Gene ID (SGD) - identifiers - data - identifier - edam - bioinformatics beta12orEarlier SGD identifier S[0-9]+ Identifier of an entry from the SGD database. + + + + @@ -4171,16 +3928,15 @@ Gene ID (GeneDB) - data [a-zA-Z_0-9\.-]* - bioinformatics - edam Moby_namespace:GeneDB Identifier of a gene from the GeneDB database. - identifier beta12orEarlier - identifiers GeneDB identifier + + + + @@ -4191,13 +3947,12 @@ TIGR identifier - bioinformatics - identifiers - identifier - data - edam Identifier of an entry from the TIGR database. beta12orEarlier + + + + @@ -4210,12 +3965,11 @@ Identifier of an gene from the TAIR database. beta12orEarlier - edam - data - identifiers - bioinformatics - identifier Gene:[0-9]{7} + + + + @@ -4232,14 +3986,13 @@ - bioinformatics - identifier - identifiers This is typically a character or string concatenated with a PDB identifier and a chain identifier. - edam - data Identifier of a protein structural domain. beta12orEarlier + + + + @@ -4255,13 +4008,12 @@ - identifier - bioinformatics beta12orEarlier - identifiers - edam - data Identifier of a protein domain (or other node) from the SCOP database. + + + + @@ -4271,15 +4023,14 @@ CATH domain ID - identifiers - bioinformatics - CATH domain identifier - 1nr3A00 - data - identifier - edam Identifier of a protein domain from CATH. + CATH domain identifier beta12orEarlier + 1nr3A00 + + + + @@ -4289,14 +4040,13 @@ SCOP concise classification string (sccs) - edam - identifiers An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. - data beta12orEarlier - identifier - bioinformatics A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. + + + + @@ -4308,15 +4058,14 @@ 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. - identifier - edam - bioinformatics - data SCOP unique identifier sunid - identifiers Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. beta12orEarlier + + + + @@ -4329,13 +4078,12 @@ beta12orEarlier CATH node identifier A code number identifying a node from the CATH database. - identifiers - bioinformatics CATH code - data - identifier 3.30.1190.10.1.1.1.1.1 - edam + + + + @@ -4345,13 +4093,12 @@ Kingdom name - identifier beta12orEarlier - identifiers The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). - bioinformatics - data - edam + + + + @@ -4362,13 +4109,12 @@ Species name beta12orEarlier - identifier Organism species The name of a species (typically a taxonomic group) of organism. - identifiers - bioinformatics - edam - data + + + + @@ -4381,11 +4127,10 @@ The name of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier - identifier - identifiers - bioinformatics - edam - data + + + + @@ -4395,12 +4140,11 @@ URI - edam - bioinformatics beta12orEarlier A string of characters that name or otherwise identify a resource on the Internet. - data - data + + + @@ -4416,14 +4160,13 @@ - An identifier of a biological or bioinformatics database. - bioinformatics - identifiers - edam - identifier - data beta12orEarlier Database identifier + An identifier of a biological or bioinformatics database. + + + + @@ -4433,13 +4176,12 @@ Directory name - identifiers - bioinformatics - data - edam The name of a directory. beta12orEarlier - identifier + + + + @@ -4450,12 +4192,11 @@ File name beta12orEarlier - data - edam The name (or part of a name) of a file (of any type). - bioinformatics - identifier - identifiers + + + + @@ -4472,13 +4213,12 @@ - identifiers - bioinformatics - data Name of an ontology of biological or bioinformatics concepts and relations. - identifier - edam beta12orEarlier + + + + @@ -4490,12 +4230,11 @@ Moby:Link beta12orEarlier - data Moby:URL A Uniform Resource Locator (URL). - bioinformatics - edam - data + + + @@ -4505,12 +4244,11 @@ URN - edam - data - data beta12orEarlier A Uniform Resource Name (URN). - bioinformatics + + + @@ -4521,13 +4259,12 @@ LSID A Life Science Identifier (LSID) - a unique identifier of some data. - data Life Science Identifier 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:<Authority>:<Namespace>:<ObjectID>[:<Version>] - data beta12orEarlier - bioinformatics - edam + + + @@ -4538,13 +4275,12 @@ Database name - edam - identifiers - bioinformatics beta12orEarlier The name of a biological or bioinformatics database. - data - identifier + + + + @@ -4554,16 +4290,13 @@ Sequence database name + beta12orEarlier beta13 - edam true - bioinformatics The name of a molecular sequence database. - identifier - beta12orEarlier - identifiers - data + + @@ -4573,13 +4306,12 @@ Enumerated file name - edam The name of a file (of any type) with restricted possible values. - data beta12orEarlier - bioinformatics - identifier - identifiers + + + + @@ -4590,13 +4322,12 @@ File name extension beta12orEarlier - data - bioinformatics - identifier A file extension is the characters appearing after the final '.' in the file name. - identifiers - edam The extension of a file name. + + + + @@ -4607,13 +4338,12 @@ File base name A file base name is the file name stripped of its directory specification and extension. - edam - data - identifier The base name of a file. beta12orEarlier - bioinformatics - identifiers + + + + @@ -4630,13 +4360,12 @@ - bioinformatics Name of a QSAR descriptor. beta12orEarlier - data - identifiers - identifier - edam + + + + @@ -4647,16 +4376,12 @@ Database entry identifier beta12orEarlier - edam - identifier + An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. + beta12orEarlier This concept is required for completeness. It should never have child concepts. true - identifiers - beta12orEarlier - An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. - bioinformatics - data + @@ -4673,12 +4398,11 @@ beta12orEarlier - identifier - identifiers An identifier of molecular sequence(s) or entries from a molecular sequence database. - bioinformatics - edam - data + + + + @@ -4696,12 +4420,11 @@ beta12orEarlier - identifiers - edam - data - bioinformatics An identifier of a set of molecular sequence(s). - identifier + + + + @@ -4712,16 +4435,12 @@ Sequence signature identifier Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. - identifiers - bioinformatics - data - edam - beta12orEarlier true beta12orEarlier - identifier + beta12orEarlier + @@ -4738,13 +4457,12 @@ - bioinformatics - identifier beta12orEarlier - identifiers - edam Identifier of a molecular sequence alignment, for example a record from an alignment database. - data + + + + @@ -4754,16 +4472,12 @@ Phylogenetic distance matrix identifier - identifiers - data - Identifier of a phylogenetic distance matrix. + beta12orEarlier true + Identifier of a phylogenetic distance matrix. beta12orEarlier - beta12orEarlier - identifier - edam - bioinformatics + @@ -4780,13 +4494,12 @@ - identifier - beta12orEarlier - identifiers Identifier of a phylogenetic tree for example from a phylogenetic tree database. - bioinformatics - edam - data + beta12orEarlier + + + + @@ -4802,14 +4515,13 @@ - identifiers beta12orEarlier - data - Substitution matrix identifier - bioinformatics - edam - identifier An identifier of a comparison matrix. + Substitution matrix identifier + + + + @@ -4820,13 +4532,12 @@ Structure ID - bioinformatics A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. - identifiers - identifier - data - edam beta12orEarlier + + + + @@ -4843,14 +4554,13 @@ - bioinformatics beta12orEarlier - identifiers - edam - identifier Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). Structural profile identifier - data + + + + @@ -4867,13 +4577,12 @@ - data - identifier - edam Identifier of an entry from a database of tertiary structure alignments. beta12orEarlier - bioinformatics - identifiers + + + + @@ -4890,13 +4599,12 @@ - data beta12orEarlier - identifiers - bioinformatics - edam - identifier Identifier of an index of amino acid physicochemical and biochemical property data. + + + + @@ -4906,13 +4614,12 @@ Protein interaction ID - identifiers - data Identifier of a report of protein interactions from a protein interaction database (typically). - edam - bioinformatics - identifier beta12orEarlier + + + + @@ -4928,14 +4635,13 @@ - identifier beta12orEarlier - bioinformatics - identifiers Identifier of a protein family. - edam Protein secondary database record identifier - data + + + + @@ -4949,22 +4655,21 @@ - + - + - identifiers Unique name of a codon usage table. - bioinformatics - data - identifier - edam beta12orEarlier + + + + @@ -4981,13 +4686,12 @@ - edam - Identifier of a transcription factor (or a TF binding site). - data - identifier beta12orEarlier - bioinformatics - identifiers + Identifier of a transcription factor (or a TF binding site). + + + + @@ -5003,13 +4707,12 @@ - identifiers Identifier of an entry from a database of microarray data. - edam - data beta12orEarlier - bioinformatics - identifier + + + + @@ -5026,13 +4729,12 @@ - edam beta12orEarlier Identifier of an entry from a database of electron microscopy data. - identifier - bioinformatics - identifiers - data + + + + @@ -5050,13 +4752,12 @@ Gene expression profile identifier - edam - identifier - identifiers - data beta12orEarlier Accession of a report of gene expression (e.g. a gene expression profile) from a database. - bioinformatics + + + + @@ -5073,13 +4774,12 @@ - data beta12orEarlier - edam - identifier - bioinformatics - identifiers Identifier of an entry from a database of genotypes and phenotypes. + + + + @@ -5095,13 +4795,12 @@ - data - edam - identifiers - bioinformatics beta12orEarlier - identifier Identifier of an entry from a database of biological pathways or networks. + + + + @@ -5118,13 +4817,12 @@ - bioinformatics - identifiers - data - beta12orEarlier - edam Identifier of a biological or biomedical workflow, typically from a database of workflows. - identifier + beta12orEarlier + + + + @@ -5135,13 +4833,12 @@ Data resource definition ID Data resource definition identifier - identifier Identifier of a data type definition from some provider. - identifiers - bioinformatics - data beta12orEarlier - edam + + + + @@ -5158,13 +4855,12 @@ beta12orEarlier - edam Identifier of a mathematical model, typically an entry from a database. - bioinformatics - identifiers Biological model identifier - data - identifier + + + + @@ -5181,14 +4877,13 @@ beta12orEarlier - identifier Small molecule identifier Identifier of an entry from a database of chemicals. - edam - bioinformatics Chemical compound identifier - data - identifiers + + + + @@ -5199,14 +4894,13 @@ Ontology concept ID - A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - identifier - bioinformatics Ontology concept ID - edam beta12orEarlier - data - identifiers + A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. + + + + @@ -5223,14 +4917,13 @@ - identifier Unique identifier of a scientific article. - bioinformatics - data - identifiers beta12orEarlier Article identifier - edam + + + + @@ -5241,14 +4934,13 @@ FlyBase ID - edam - identifier - data - identifiers - bioinformatics FB[a-zA-Z_0-9]{2}[0-9]{7} beta12orEarlier Identifier of an object from the FlyBase database. + + + + @@ -5259,13 +4951,12 @@ WormBase name - edam - data - identifier - identifiers beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. - bioinformatics + + + + @@ -5275,14 +4966,13 @@ WormBase class - data A WormBase class describes the type of object such as 'sequence' or 'protein'. - edam - bioinformatics Class of an object from the WormBase database. - identifier - identifiers beta12orEarlier + + + + @@ -5294,13 +4984,12 @@ Sequence accession number - data - identifiers - bioinformatics - identifier A persistent, unique identifier of a molecular sequence database entry. beta12orEarlier - edam + + + + @@ -5312,12 +5001,11 @@ beta12orEarlier - bioinformatics - data - edam - data 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). + + + @@ -5328,14 +5016,13 @@ EMBOSS Uniform Sequence Address - bioinformatics - beta12orEarlier - data - identifiers - edam The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. + beta12orEarlier EMBOSS USA - identifier + + + + @@ -5352,13 +5039,12 @@ beta12orEarlier - identifiers Protein sequence accession number - data - bioinformatics - edam Accession number of a protein sequence database entry. - identifier + + + + @@ -5374,14 +5060,13 @@ + Nucleotide sequence accession number beta12orEarlier Accession number of a nucleotide sequence database entry. - bioinformatics - data - Nucleotide sequence accession number - identifier - identifiers - edam + + + + @@ -5391,15 +5076,14 @@ RefSeq accession + (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ RefSeq ID - identifiers beta12orEarlier - identifier Accession number of a RefSeq database entry. - (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ - data - edam - bioinformatics + + + + @@ -5409,18 +5093,14 @@ UniProt accession (extended) - bioinformatics - 1.0 - Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. - [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]+ - data - edam - identifiers Q7M1G0|P43353-2|P01012.107 + 1.0 beta12orEarlier + [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]+ + Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. true - identifier + @@ -5436,15 +5116,14 @@ - edam PIR ID beta12orEarlier - identifiers An identifier of PIR sequence database entry. PIR accession number - data - bioinformatics - identifier + + + + @@ -5454,16 +5133,12 @@ TREMBL accession - data - identifier - bioinformatics - identifiers 1.2 - edam true Identifier of a TREMBL sequence database entry. beta12orEarlier + @@ -5474,13 +5149,12 @@ Gramene primary identifier Primary identifier of a Gramene database entry. - data - identifiers Gramene primary ID - edam - identifier - bioinformatics beta12orEarlier + + + + @@ -5491,12 +5165,11 @@ EMBL/GenBank/DDBJ ID beta12orEarlier - identifiers Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. - data - identifier - bioinformatics - edam + + + + @@ -5508,15 +5181,14 @@ A unique identifier of an entry (gene cluster) from the NCBI UniGene database. UniGene cluster ID - bioinformatics UniGene identifier - edam - identifiers beta12orEarlier - identifier UniGene ID UniGene cluster id - data + + + + @@ -5528,13 +5200,12 @@ beta12orEarlier - identifier - data - dbEST ID - edam Identifier of a dbEST database entry. - identifiers - bioinformatics + dbEST ID + + + + @@ -5545,13 +5216,12 @@ dbSNP ID Identifier of a dbSNP database entry. - data - edam dbSNP identifier - bioinformatics beta12orEarlier - identifier - identifiers + + + + @@ -5561,17 +5231,13 @@ EMBOSS sequence type - edam - true - identifiers - bioinformatics - data The EMBOSS type of a molecular sequence. beta12orEarlier - identifier See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. + true beta12orEarlier + @@ -5581,12 +5247,11 @@ EMBOSS listfile - bioinformatics - data beta12orEarlier List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). - edam - data + + + @@ -5602,13 +5267,12 @@ - identifier beta12orEarlier - edam - identifiers - data An identifier of a cluster of molecular sequence(s). - bioinformatics + + + + @@ -5618,14 +5282,13 @@ Sequence cluster ID (COG) - identifier - identifiers - bioinformatics - edam Unique identifier of an entry from the COG database. beta12orEarlier - data COG ID + + + + @@ -5641,13 +5304,12 @@ - identifier beta12orEarlier - edam - identifiers - bioinformatics - data Identifier of a sequence motif, for example an entry from a motif database. + + + + @@ -5665,13 +5327,12 @@ A sequence profile typically represents a sequence alignment. - edam Identifier of a sequence profile. - identifier - data - bioinformatics - identifiers beta12orEarlier + + + + @@ -5681,13 +5342,12 @@ ELM ID - bioinformatics beta12orEarlier - data Identifier of an entry from the ELMdb database of protein functional sites. - edam - identifier - identifiers + + + + @@ -5697,15 +5357,14 @@ Prosite accession number - Prosite ID - edam PS[0-9]{5} - data + Prosite ID Accession number of an entry from the Prosite database. - bioinformatics - identifiers - identifier beta12orEarlier + + + + @@ -5721,13 +5380,12 @@ - identifiers - edam beta12orEarlier - data Unique identifier or name of a HMMER hidden Markov model. - identifier - bioinformatics + + + + @@ -5738,12 +5396,11 @@ JASPAR profile ID Unique identifier or name of a profile from the JASPAR database. - bioinformatics - data - identifier beta12orEarlier - identifiers - edam + + + + @@ -5754,13 +5411,12 @@ Sequence alignment type - bioinformatics - data 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. - data - edam beta12orEarlier + + + @@ -5771,15 +5427,11 @@ BLAST sequence alignment type The type of a BLAST sequence alignment. - identifiers - bioinformatics - edam - beta12orEarlier - data beta12orEarlier - identifier + beta12orEarlier true + @@ -5790,13 +5442,12 @@ Phylogenetic tree type nj|upgmp - data - edam - data A label (text token) describing the type of a phylogenetic tree. beta12orEarlier - bioinformatics For example 'nj', 'upgmp' etc. + + + @@ -5806,13 +5457,12 @@ TreeBASE study accession number - bioinformatics - identifier - identifiers beta12orEarlier - data - edam Accession number of an entry from the TreeBASE database. + + + + @@ -5822,13 +5472,12 @@ TreeFam accession number - identifiers - edam - data Accession number of an entry from the TreeFam database. - bioinformatics - identifier beta12orEarlier + + + + @@ -5840,14 +5489,13 @@ For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. - A label (text token) describing the type of a comparison matrix. Substitution matrix type + A label (text token) describing the type of a comparison matrix. beta12orEarlier - bioinformatics blosum|pam|gonnet|id - data - edam - data + + + @@ -5865,14 +5513,13 @@ Unique name or identifier of a comparison matrix. - identifiers - identifier Substitution matrix name - bioinformatics - edam See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. - data beta12orEarlier + + + + @@ -5882,16 +5529,15 @@ PDB ID - edam - identifier [a-zA-Z_0-9]{4} - identifiers beta12orEarlier PDB identifier - bioinformatics - data PDBID An identifier of an entry from the PDB database. + + + + @@ -5901,13 +5547,12 @@ AAindex ID - data - edam Identifier of an entry from the AAindex database. - bioinformatics - identifier beta12orEarlier - identifiers + + + + @@ -5917,13 +5562,12 @@ BIND accession number - data beta12orEarlier Accession number of an entry from the BIND database. - identifier - edam - bioinformatics - identifiers + + + + @@ -5933,14 +5577,13 @@ IntAct accession number - data - identifier Accession number of an entry from the IntAct database. - edam beta12orEarlier - bioinformatics - identifiers EBI\-[0-9]+ + + + + @@ -5952,12 +5595,11 @@ Name of a protein family. - identifiers - identifier beta12orEarlier - data - edam - bioinformatics + + + + @@ -5973,13 +5615,12 @@ - identifier - edam - identifiers - data Name of an InterPro entry, usually indicating the type of protein matches for that entry. beta12orEarlier - bioinformatics + + + + @@ -5996,17 +5637,16 @@ IPR[0-9]{6} - bioinformatics IPR015590 - edam - identifier InterPro primary accession number beta12orEarlier Every InterPro entry has a unique accession number to provide a persistent citation of database records. - data InterPro primary accession - identifiers Primary accession number of an InterPro entry. + + + + @@ -6022,14 +5662,13 @@ - identifiers - Secondary accession number of an InterPro entry. - identifier InterPro secondary accession number - bioinformatics - data beta12orEarlier - edam + Secondary accession number of an InterPro entry. + + + + @@ -6039,13 +5678,12 @@ Gene3D ID - identifiers - bioinformatics Unique identifier of an entry from the Gene3D database. - identifier - edam beta12orEarlier - data + + + + @@ -6056,13 +5694,12 @@ PIRSF ID Unique identifier of an entry from the PIRSF database. - identifiers - edam beta12orEarlier - identifier - bioinformatics PIRSF[0-9]{6} - data + + + + @@ -6073,13 +5710,12 @@ PRINTS code The unique identifier of an entry in the PRINTS database. - edam PR[0-9]{5} - data - identifier - identifiers beta12orEarlier - bioinformatics + + + + @@ -6090,13 +5726,12 @@ Pfam accession number beta12orEarlier - data - edam - identifier - bioinformatics Accession number of a Pfam entry. PF[0-9]{5} - identifiers + + + + @@ -6106,14 +5741,13 @@ SMART accession number - data SM[0-9]{5} beta12orEarlier - identifier - bioinformatics - identifiers Accession number of an entry from the SMART database. - edam + + + + @@ -6123,13 +5757,12 @@ Superfamily hidden Markov model number - identifiers beta12orEarlier - data Unique identifier (number) of a hidden Markov model from the Superfamily database. - identifier - bioinformatics - edam + + + + @@ -6139,14 +5772,13 @@ TIGRFam ID - identifier beta12orEarlier Accession number of an entry (family) from the TIGRFam database. - identifiers - edam TIGRFam accession number - data - bioinformatics + + + + @@ -6156,15 +5788,14 @@ ProDom accession number - beta12orEarlier - identifiers - bioinformatics - data ProDom is a protein domain family database. + beta12orEarlier PD[0-9]+ - edam - identifier A ProDom domain family accession number. + + + + @@ -6174,13 +5805,12 @@ TRANSFAC accession number - edam - identifiers Identifier of an entry from the TRANSFAC database. - identifier beta12orEarlier - bioinformatics - data + + + + @@ -6190,15 +5820,14 @@ ArrayExpress accession number - [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ - bioinformatics - identifiers - edam ArrayExpress experiment ID + [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ beta12orEarlier - identifier - data Accession number of an entry from the ArrayExpress database. + + + + @@ -6208,14 +5837,13 @@ PRIDE experiment accession number - identifier PRIDE experiment accession number. beta12orEarlier - identifiers [0-9]+ - bioinformatics - edam - data + + + + @@ -6225,13 +5853,12 @@ EMDB ID - bioinformatics - edam - data Identifier of an entry from the EMDB electron microscopy database. - identifiers beta12orEarlier - identifier + + + + @@ -6242,13 +5869,12 @@ GEO accession number beta12orEarlier - data - edam o^GDS[0-9]+ - bioinformatics - identifiers - identifier Accession number of an entry from the GEO database. + + + + @@ -6258,13 +5884,12 @@ GermOnline ID - bioinformatics - identifier - data beta12orEarlier Identifier of an entry from the GermOnline database. - edam - identifiers + + + + @@ -6274,13 +5899,12 @@ EMAGE ID - data - identifiers - identifier beta12orEarlier - bioinformatics - edam Identifier of an entry from the EMAGE database. + + + + @@ -6297,13 +5921,12 @@ - bioinformatics beta12orEarlier Identifier of an entry from a database of disease. - edam - data - identifier - identifiers + + + + @@ -6313,13 +5936,12 @@ HGVbase ID - data beta12orEarlier - identifiers Identifier of an entry from the HGVbase database. - identifier - bioinformatics - edam + + + + @@ -6329,16 +5951,12 @@ HIVDB identifier + beta12orEarlier Identifier of an entry from the HIVDB database. beta12orEarlier - bioinformatics - identifier true - beta12orEarlier - identifiers - data - edam + @@ -6350,12 +5968,11 @@ Identifier of an entry from the OMIM database. [*#+%^]?[0-9]{6} - identifiers - bioinformatics - edam beta12orEarlier - identifier - data + + + + @@ -6366,13 +5983,12 @@ KEGG object identifier - bioinformatics - data Unique identifier of an object from one of the KEGG databases (excluding the GENES division). - identifier - edam beta12orEarlier - identifiers + + + + @@ -6382,15 +5998,14 @@ Pathway ID (reactome) - identifier - identifiers - bioinformatics - data - Reactome ID - edam beta12orEarlier REACT_[0-9]+(\.[0-9]+)? Identifier of an entry from the Reactome database. + Reactome ID + + + + @@ -6400,17 +6015,13 @@ Pathway ID (aMAZE) - identifier Identifier of an entry from the aMAZE database. - bioinformatics beta12orEarlier - identifiers + true aMAZE ID beta12orEarlier - data - edam - true + @@ -6421,14 +6032,13 @@ Pathway ID (BioCyc) - edam - identifiers - data Identifier of an pathway from the BioCyc biological pathways database. - identifier beta12orEarlier - bioinformatics BioCyc pathway ID + + + + @@ -6438,14 +6048,13 @@ Pathway ID (INOH) - bioinformatics - identifiers Identifier of an entry from the INOH database. INOH identifier - identifier - edam beta12orEarlier - data + + + + @@ -6455,14 +6064,13 @@ Pathway ID (PATIKA) - edam beta12orEarlier - identifiers - identifier - bioinformatics PATIKA ID Identifier of an entry from the PATIKA database. - data + + + + @@ -6473,14 +6081,13 @@ Pathway ID (CPDB) beta12orEarlier - identifiers - data - bioinformatics + Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. CPDB ID This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. - edam - identifier - Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. + + + + @@ -6490,15 +6097,14 @@ Pathway ID (Panther) - beta12orEarlier - data - Identifier of a biological pathway from the Panther Pathways database. - identifier - bioinformatics - edam Panther Pathways ID PTHR[0-9]{5} - identifiers + beta12orEarlier + Identifier of a biological pathway from the Panther Pathways database. + + + + @@ -6515,15 +6121,14 @@ MIR:[0-9]{8} - identifier MIR:00100005 - edam Unique identifier of a MIRIAM data resource. This is the identifier used internally by MIRIAM for a data type. beta12orEarlier - data - bioinformatics - identifiers + + + + @@ -6539,13 +6144,12 @@ - identifier The name of a data type from the MIRIAM database. - data - identifiers beta12orEarlier - edam - bioinformatics + + + + @@ -6562,16 +6166,15 @@ - identifier urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 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. identifiers.org synonym - data - identifiers The URI (URL or URN) of a data entity from the MIRIAM database. - bioinformatics beta12orEarlier - edam + + + + @@ -6581,19 +6184,18 @@ MIRIAM data type primary name - bioinformatics - identifiers + 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. UniProt|Enzyme Nomenclature - data - edam - The primary name of a data type from the MIRIAM database. beta12orEarlier - identifier + + + + - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -6605,14 +6207,13 @@ MIRIAM data type synonymous name - identifiers - bioinformatics - data beta12orEarlier - identifier - edam A synonymous name for a MIRIAM data type taken from a controlled vocabulary. A synonymous name of a data type from the MIRIAM database. + + + + @@ -6622,13 +6223,12 @@ Taverna workflow ID - identifier - identifiers - bioinformatics Unique identifier of a Taverna workflow. - edam - data beta12orEarlier + + + + @@ -6639,13 +6239,12 @@ Biological model name - data - identifiers - identifier Name of a biological (mathematical) model. - bioinformatics beta12orEarlier - edam + + + + @@ -6656,13 +6255,12 @@ BioModel ID (BIOMD|MODEL)[0-9]{10} - data - identifier - bioinformatics - edam beta12orEarlier Unique identifier of an entry from the BioModel database. - identifiers + + + + @@ -6673,15 +6271,14 @@ PubChem CID - identifier beta12orEarlier - edam Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. - bioinformatics PubChem compound accession identifier [0-9]+ - identifiers - data + + + + @@ -6691,14 +6288,13 @@ ChemSpider ID - identifier - bioinformatics - edam [0-9]+ beta12orEarlier - data Identifier of an entry from the ChemSpider database. - identifiers + + + + @@ -6709,14 +6305,13 @@ ChEBI ID beta12orEarlier - identifiers - edam - bioinformatics CHEBI:[0-9]+ - identifier - data ChEBI identifier Identifier of an entry from the ChEBI database. + + + + @@ -6726,13 +6321,12 @@ BioPax concept ID - identifier An identifier of a concept from the BioPax ontology. beta12orEarlier - bioinformatics - identifiers - data - edam + + + + @@ -6742,15 +6336,14 @@ GO concept ID - data - [0-9]{7}|GO:[0-9]{7} - identifiers - edam An identifier of a concept from The Gene Ontology. beta12orEarlier - bioinformatics - identifier + [0-9]{7}|GO:[0-9]{7} GO concept identifier + + + + @@ -6760,13 +6353,12 @@ MeSH concept ID - identifiers - identifier - edam - data - bioinformatics An identifier of a concept from the MeSH vocabulary. beta12orEarlier + + + + @@ -6776,13 +6368,12 @@ HGNC concept ID - identifier An identifier of a concept from the HGNC controlled vocabulary. beta12orEarlier - data - edam - bioinformatics - identifiers + + + + @@ -6794,16 +6385,15 @@ beta12orEarlier - identifier 9662|3483|182682 A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. NCBI tax ID - edam [1-9][0-9]{0,8} - data - identifiers NCBI taxonomy identifier - bioinformatics + + + + @@ -6813,13 +6403,12 @@ Plant Ontology concept ID - data beta12orEarlier - identifier - bioinformatics - edam An identifier of a concept from the Plant Ontology (PO). - identifiers + + + + @@ -6829,13 +6418,12 @@ UMLS concept ID - identifier beta12orEarlier - identifiers An identifier of a concept from the UMLS vocabulary. - bioinformatics - edam - data + + + + @@ -6845,15 +6433,14 @@ FMA concept ID - identifier + beta12orEarlier 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. An identifier of a concept from Foundational Model of Anatomy. FMA:[0-9]+ - beta12orEarlier - bioinformatics - edam - data - identifiers + + + + @@ -6863,13 +6450,12 @@ EMAP concept ID - identifier - identifiers - edam An identifier of a concept from the EMAP mouse ontology. - data beta12orEarlier - bioinformatics + + + + @@ -6879,13 +6465,12 @@ ChEBI concept ID - bioinformatics - edam - data An identifier of a concept from the ChEBI ontology. - identifiers - identifier beta12orEarlier + + + + @@ -6895,13 +6480,12 @@ MGED concept ID - data - bioinformatics - identifiers - edam - identifier An identifier of a concept from the MGED ontology. beta12orEarlier + + + + @@ -6913,12 +6497,11 @@ 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. - edam beta12orEarlier - data - identifier - identifiers - bioinformatics + + + + @@ -6930,14 +6513,13 @@ 4963447 beta12orEarlier - edam PubMed unique identifier of an article. - data [1-9][0-9]{0,8} - bioinformatics - identifier PMID - identifiers + + + + @@ -6947,15 +6529,14 @@ DOI - bioinformatics Digital Object Identifier (DOI) of a published article. Digital Object Identifier - beta12orEarlier - data - identifier (doi\:)?[0-9]{2}\.[0-9]{4}/.* - identifiers - edam + beta12orEarlier + + + + @@ -6965,15 +6546,14 @@ Medline UI - identifier + Medline unique identifier The use of Medline UI has been replaced by the PubMed unique identifier. Medline UI (unique identifier) of an article. beta12orEarlier - edam - Medline unique identifier - identifiers - data - bioinformatics + + + + @@ -6983,13 +6563,12 @@ Tool name - identifier - bioinformatics - data beta12orEarlier The name of a computer package, application, method or function. - identifiers - edam + + + + @@ -7000,13 +6579,12 @@ Tool name (signature) 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. - edam - bioinformatics The unique name of a signature (sequence classifier) method. - identifiers - identifier - data beta12orEarlier + + + + @@ -7019,12 +6597,11 @@ BLAST name beta12orEarlier The name of a BLAST tool. - identifiers - edam - data - bioinformatics - identifier This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + + + + @@ -7034,14 +6611,13 @@ Tool name (FASTA) - identifiers This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. - identifier - edam - data - bioinformatics The name of a FASTA tool. beta12orEarlier + + + + @@ -7051,13 +6627,12 @@ Tool name (EMBOSS) - bioinformatics - edam - identifier beta12orEarlier - data - identifiers The name of an EMBOSS application. + + + + @@ -7069,11 +6644,10 @@ beta12orEarlier The name of an EMBASSY package. - bioinformatics - identifier - identifiers - edam - data + + + + @@ -7084,12 +6658,11 @@ QSAR descriptor (constitutional) QSAR constitutional descriptor - bioinformatics - edam - data beta12orEarlier - data A QSAR constitutional descriptor. + + + @@ -7099,13 +6672,12 @@ QSAR descriptor (electronic) - data QSAR electronic descriptor - bioinformatics - data A QSAR electronic descriptor. - edam beta12orEarlier + + + @@ -7115,13 +6687,12 @@ QSAR descriptor (geometrical) - bioinformatics beta12orEarlier - edam A QSAR geometrical descriptor. - data - data QSAR geometrical descriptor + + + @@ -7131,13 +6702,12 @@ QSAR descriptor (topological) - edam A QSAR topological descriptor. QSAR topological descriptor - data - bioinformatics - data beta12orEarlier + + + @@ -7147,13 +6717,12 @@ QSAR descriptor (molecular) - data - edam QSAR molecular descriptor beta12orEarlier - data A QSAR molecular descriptor. - bioinformatics + + + @@ -7164,11 +6733,10 @@ Sequence set (protein) beta12orEarlier - data - bioinformatics - edam - data Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. + + + @@ -7179,12 +6747,11 @@ Sequence set (nucleic acid) - data - data - edam Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. beta12orEarlier - bioinformatics + + + @@ -7208,11 +6775,10 @@ beta12orEarlier The cluster might include sequences identifiers, short descriptions, alignment and summary information. - bioinformatics - edam - data - data A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. + + + @@ -7223,15 +6789,12 @@ Psiblast checkpoint file A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. - bioinformatics true beta12orEarlier A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. beta12orEarlier - edam - data - data + @@ -7241,15 +6804,12 @@ HMMER synthetic sequences set - data - beta12orEarlier true beta12orEarlier + beta12orEarlier Sequences generated by HMMER package in FASTA-style format. - bioinformatics - edam - data + @@ -7265,12 +6825,11 @@ - edam - data A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. beta12orEarlier - data - bioinformatics + + + @@ -7281,12 +6840,11 @@ Restriction digest beta12orEarlier - data - data - edam SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. - bioinformatics + + + @@ -7296,12 +6854,11 @@ PCR primers - bioinformatics - edam - data Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. - data beta12orEarlier + + + @@ -7311,15 +6868,12 @@ vectorstrip cloning vector definition file - File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. - edam - bioinformatics beta12orEarlier - data - data + File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. true beta12orEarlier + @@ -7330,14 +6884,11 @@ Primer3 internal oligo mishybridizing library beta12orEarlier - bioinformatics - edam - data A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. - data beta12orEarlier true + @@ -7347,15 +6898,12 @@ Primer3 mispriming library file - data - data - 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 - edam beta12orEarlier beta12orEarlier - bioinformatics + 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 + @@ -7365,15 +6913,12 @@ primersearch primer pairs sequence record - data + File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. beta12orEarlier beta12orEarlier - data true - edam - File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. - bioinformatics + @@ -7385,13 +6930,12 @@ beta12orEarlier - Protein sequence cluster - bioinformatics A cluster of protein sequences. - data The sequences are typically related, for example a family of sequences. - edam - data + Protein sequence cluster + + + @@ -7402,14 +6946,13 @@ Sequence cluster (nucleic acid) - bioinformatics beta12orEarlier - Nucleotide sequence cluster - data - data The sequences are typically related, for example a family of sequences. + Nucleotide sequence cluster A cluster of nucleotide sequences. - edam + + + @@ -7419,12 +6962,11 @@ Sequence length - edam - data - data beta12orEarlier The size (length) of a sequence, subsequence or region in a sequence. - bioinformatics + + + @@ -7434,14 +6976,13 @@ Word size - data - data - edam beta12orEarlier Size of a sequence word. - bioinformatics Word length Word size is used for example in word-based sequence database search methods. + + + @@ -7451,13 +6992,12 @@ Window size - edam Size of a sequence window. - data beta12orEarlier 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. - data - bioinformatics + + + @@ -7467,12 +7007,11 @@ Sequence length range - data Specification of range(s) of length of sequences. beta12orEarlier - data - bioinformatics - edam + + + @@ -7483,15 +7022,12 @@ Sequence information report true - edam - bioinformatics - Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. beta12orEarlier beta12orEarlier - data - data + Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. + @@ -7502,12 +7038,11 @@ Sequence property Sequence properties report - edam An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. - data - bioinformatics - data beta12orEarlier + + + @@ -7520,16 +7055,15 @@ Sequence features Features Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. - data - edam - data General sequence features This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. SO:0000110 - bioinformatics beta12orEarlier Sequence features report + + + @@ -7539,16 +7073,13 @@ Sequence features (comparative) - bioinformatics beta12orEarlier - data - edam + true 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. beta13 Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. - data - true + @@ -7558,15 +7089,12 @@ Sequence property (protein) - edam - A report of general sequence properties derived from protein sequence data. - true - data beta12orEarlier - data - bioinformatics beta12orEarlier + A report of general sequence properties derived from protein sequence data. + true + @@ -7576,15 +7104,12 @@ Sequence property (nucleic acid) - beta12orEarlier - data beta12orEarlier true - edam - data A report of general sequence properties derived from nucleotide sequence data. - bioinformatics + beta12orEarlier + @@ -7594,13 +7119,12 @@ Sequence complexity - bioinformatics Sequence property (complexity) - data - edam beta12orEarlier - data A report on sequence complexity, for example low-complexity or repeat regions in sequences. + + + @@ -7611,12 +7135,11 @@ Sequence ambiguity beta12orEarlier - bioinformatics Sequence property (ambiguity) A report on ambiguity in molecular sequence(s). - edam - data - data + + + @@ -7627,12 +7150,11 @@ Sequence composition Sequence property (composition) - edam - data - bioinformatics - data A report (typically a table) on character or word composition / frequency of a molecular sequence(s). beta12orEarlier + + + @@ -7642,12 +7164,11 @@ Peptide molecular weight hits - edam - data beta12orEarlier - data - bioinformatics A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. + + + @@ -7657,12 +7178,11 @@ Sequence composition (base position variability) - data - edam - data - bioinformatics Report on or plot of third base position variability in a nucleotide sequence. beta12orEarlier + + + @@ -7676,11 +7196,8 @@ true beta12orEarlier A table of character or word composition / frequency of a molecular sequence. - data - data - edam - bioinformatics + @@ -7690,12 +7207,11 @@ Sequence composition (base frequencies) - bioinformatics - data - edam A table of base frequencies of a nucleotide sequence. - data beta12orEarlier + + + @@ -7705,12 +7221,11 @@ Sequence composition (base words) - data - edam - data A table of word composition of a nucleotide sequence. beta12orEarlier - bioinformatics + + + @@ -7720,13 +7235,12 @@ Amino acid frequencies - data - data A table of amino acid frequencies of a protein sequence. beta12orEarlier - bioinformatics Sequence composition (amino acid frequencies) - edam + + + @@ -7736,13 +7250,12 @@ Amino acid word frequencies - data - edam beta12orEarlier Sequence composition (amino acid words) - bioinformatics - data A table of amino acid word composition of a protein sequence. + + + @@ -7752,15 +7265,12 @@ DAS sequence feature annotation - edam - data true - bioinformatics + beta12orEarlier Annotation of a molecular sequence in DAS format. beta12orEarlier - beta12orEarlier - data + @@ -7772,11 +7282,10 @@ Feature table Annotation of positional sequence features, organized into a standard feature table. - data beta12orEarlier - edam - bioinformatics - data + + + @@ -7792,13 +7301,12 @@ - bioinformatics A map of (typically one) DNA sequence annotated with positional or non-positional features. - data beta12orEarlier DNA map - edam - data + + + @@ -7809,15 +7317,14 @@ Nucleic acid features - edam - bioinformatics Feature table (nucleic acid) Nucleic acid feature table Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence). - data This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. - data beta12orEarlier + + + @@ -7830,13 +7337,12 @@ Protein feature table This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. - edam - data Feature table (protein) - bioinformatics - data Protein sequence-specific feature annotation (positional features of a protein sequence). beta12orEarlier + + + @@ -7848,13 +7354,12 @@ Moby:GeneticMap Linkage map - beta12orEarlier - data - edam 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. - bioinformatics - data + beta12orEarlier 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. + + + @@ -7865,12 +7370,11 @@ Sequence map A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. - data - data beta12orEarlier - bioinformatics - edam 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. + + + @@ -7880,13 +7384,12 @@ Physical map - data beta12orEarlier - bioinformatics 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. - edam - data 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. + + + @@ -7896,15 +7399,12 @@ Sequence signature map - bioinformatics - edam + beta12orEarlier beta12orEarlier - data - data Image of a sequence with matches to signatures, motifs or profiles. true - beta12orEarlier + @@ -7914,16 +7414,15 @@ Cytogenetic map - bioinformatics 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. Cytogenic map - data Chromosome map - edam Cytologic map A map showing banding patterns derived from direct observation of a stained chromosome. - data beta12orEarlier + + + @@ -7934,11 +7433,10 @@ DNA transduction map A gene map showing distances between loci based on relative cotransduction frequencies. - data - data - bioinformatics beta12orEarlier - edam + + + @@ -7949,11 +7447,10 @@ Gene map beta12orEarlier - data - edam - data 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. - bioinformatics + + + @@ -7965,10 +7462,9 @@ beta12orEarlier Sequence map of a plasmid (circular DNA). - bioinformatics - data - data - edam + + + @@ -7978,12 +7474,11 @@ Genome map - edam - bioinformatics - data - data Sequence map of a whole genome. beta12orEarlier + + + @@ -7995,12 +7490,11 @@ - data - data beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. - bioinformatics - edam + + + @@ -8010,16 +7504,13 @@ InterPro compact match image - edam - data - data true - bioinformatics beta12orEarlier 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. Image showing matches between protein sequence(s) and InterPro Entries. beta12orEarlier + @@ -8033,12 +7524,9 @@ The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Image showing detailed information on matches between protein sequence(s) and InterPro Entries. beta12orEarlier - data - edam - bioinformatics - data beta12orEarlier + @@ -8048,16 +7536,13 @@ InterPro architecture image - true - bioinformatics - beta12orEarlier - data 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. - edam - data + true + beta12orEarlier beta12orEarlier + @@ -8067,15 +7552,12 @@ SMART protein schematic + SMART protein schematic in PNG format. beta12orEarlier beta12orEarlier true - data - SMART protein schematic in PNG format. - edam - data - bioinformatics + @@ -8085,15 +7567,12 @@ GlobPlot domain image - bioinformatics - beta12orEarlier - data - edam Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. true beta12orEarlier - data + beta12orEarlier + @@ -8103,13 +7582,12 @@ Sequence features (motifs) - data Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. beta12orEarlier Use this concept if another, more specific concept is not available. - bioinformatics - data - edam + + + @@ -8119,14 +7597,13 @@ Sequence features (repeats) - data - data Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. The report might include derived data map such as classification, annotation, organization, periodicity etc. Repeat sequence map - edam beta12orEarlier - bioinformatics + + + @@ -8137,13 +7614,12 @@ Nucleic acid features (gene and transcript structure) - edam - bioinformatics - data A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. beta12orEarlier - data Gene annotation (structure) + + + @@ -8153,14 +7629,13 @@ Nucleic acid features (mobile genetic elements) - data - data - edam beta12orEarlier A report on a region of a nucleic acid sequence containin mobile genetic elements. Nucleic acid features (transposons) This includes transposons, Plasmids, Bacteriophage elements and Group II introns. - bioinformatics + + + @@ -8171,14 +7646,13 @@ Nucleic acid features (PolyA signal or site) beta12orEarlier - 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. - bioinformatics - data A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - data + 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. PolyA site PolyA signal - edam + + + @@ -8189,11 +7663,10 @@ Nucleic acid features (quadruplexes) beta12orEarlier - data - bioinformatics - data A report on quadruplex-forming motifs in a nucleotide sequence. - edam + + + @@ -8203,12 +7676,11 @@ Nucleic acid features (CpG island and isochore) - data A report or plot of CpG rich regions (isochores) in a nucleotide sequence. - bioinformatics beta12orEarlier - edam - data + + + @@ -8218,12 +7690,11 @@ Nucleic acid features (restriction sites) - bioinformatics - data Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - edam - data beta12orEarlier + + + @@ -8234,11 +7705,10 @@ Nucleic acid features (nucleosome exclusion sequences) A report on nucleosome formation potential or exclusion sequence(s). - data beta12orEarlier - edam - bioinformatics - data + + + @@ -8250,12 +7720,11 @@ Nucleic acid report (RNA splicing) Nucleic acid report (RNA splice model) - bioinformatics - data - data beta12orEarlier A report on splice sites in a nucleotide sequence or alternative RNA splicing events. - edam + + + @@ -8265,12 +7734,11 @@ Nucleic acid features (matrix/scaffold attachment sites) - edam - data beta12orEarlier - bioinformatics A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - data + + + @@ -8280,15 +7748,12 @@ Gene features (exonic splicing enhancer) + A report on exonic splicing enhancers (ESE) in an exon. true - edam - bioinformatics beta13 - data - A report on exonic splicing enhancers (ESE) in an exon. beta12orEarlier - data + @@ -8304,12 +7769,11 @@ - data A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. - edam - data beta12orEarlier - bioinformatics + + + @@ -8319,14 +7783,13 @@ Nucleic acid features (operon) - data beta12orEarlier A report on operons (operators, promoters and genes) from a bacterial genome. - edam - bioinformatics The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. Gene features (operon) - data + + + @@ -8337,11 +7800,10 @@ Gene features (promoter) beta12orEarlier - data - data A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. - edam - bioinformatics + + + @@ -8352,14 +7814,13 @@ Nucleic acid features (coding sequence) Gene features (coding sequence) + Gene annotation (translation) beta12orEarlier Gene features (coding region) A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. - Gene annotation (translation) - bioinformatics - data - edam - data + + + @@ -8369,15 +7830,12 @@ Gene features (SECIS element) - beta12orEarlier true - data - data beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. - edam - bioinformatics + beta12orEarlier + @@ -8394,12 +7852,11 @@ - data A report on the transcription factor binding sites (TFBS) in a DNA sequence. - bioinformatics - data - edam beta12orEarlier + + + @@ -8410,15 +7867,12 @@ Protein features (sites) A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. - bioinformatics beta12orEarlier - beta12orEarlier - data Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. - edam + beta12orEarlier true - data + @@ -8429,11 +7883,10 @@ Protein features (signal peptides) beta12orEarlier - edam A report on the location of signal peptides or signal peptide cleavage sites in protein sequences. - data - bioinformatics - data + + + @@ -8449,12 +7902,11 @@ - data - bioinformatics - edam beta12orEarlier A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - data + + + @@ -8463,15 +7915,14 @@ Protein features (post-translation modifications) - - data - data + Post-translation modification beta12orEarlier - bioinformatics A report on post-translation modifications in a protein sequence, typically describing the specific sites involved. - edam Protein features (post-translation modification sites) + + + @@ -8481,13 +7932,12 @@ Protein features (active sites) - data beta12orEarlier Enzyme active site A report on catalytic residues (active site) of an enzyme. - data - edam - bioinformatics + + + @@ -8497,12 +7947,11 @@ Protein features (binding sites) - bioinformatics A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. beta12orEarlier - data - data - edam + + + @@ -8513,15 +7962,12 @@ Protein features (epitopes) true - beta13 - A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. - data Epitope mapping is commonly done during vaccine design. beta12orEarlier - bioinformatics - edam - data + A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. + beta13 + @@ -8531,12 +7977,11 @@ Protein features (nucleic acid binding sites) - bioinformatics beta12orEarlier - edam - data - data A report on RNA and DNA-binding proteins and binding sites in protein sequences. + + + @@ -8546,15 +7991,12 @@ MHC Class I epitopes report - edam true A report on epitopes that bind to MHC class I molecules. - bioinformatics - beta12orEarlier - data beta12orEarlier - data + beta12orEarlier + @@ -8564,15 +8006,12 @@ MHC Class II epitopes report - data - beta12orEarlier - beta12orEarlier A report on predicted epitopes that bind to MHC class II molecules. - data true - edam - bioinformatics + beta12orEarlier + beta12orEarlier + @@ -8582,16 +8021,13 @@ Protein features (PEST sites) - data - bioinformatics - 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. - beta13 true - data - edam + beta13 + 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. A report or plot of PEST sites in a protein sequence. beta12orEarlier + @@ -8601,15 +8037,12 @@ Sequence database hits scores list - data beta12orEarlier - Scores from a sequence database search (for example a BLAST search). - data - bioinformatics true - edam beta12orEarlier + Scores from a sequence database search (for example a BLAST search). + @@ -8621,13 +8054,10 @@ true beta12orEarlier - data Alignments from a sequence database search (for example a BLAST search). beta12orEarlier - edam - bioinformatics - data + @@ -8637,15 +8067,12 @@ Sequence database hits evaluation data - data - data - edam - beta12orEarlier - beta12orEarlier true - bioinformatics + beta12orEarlier A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). + beta12orEarlier + @@ -8655,15 +8082,12 @@ MEME motif alphabet - bioinformatics - beta12orEarlier - data true - data beta12orEarlier + beta12orEarlier Alphabet for the motifs (patterns) that MEME will search for. - edam + @@ -8673,15 +8097,12 @@ MEME background frequencies file - data - edam - true - data beta12orEarlier beta12orEarlier - bioinformatics + true MEME background frequencies file. + @@ -8691,15 +8112,12 @@ MEME motifs directive file + beta12orEarlier File of directives for ordering and spacing of MEME motifs. true - data - data - beta12orEarlier - edam beta12orEarlier - bioinformatics + @@ -8709,12 +8127,11 @@ Dirichlet distribution - data - data - edam - bioinformatics beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. + + + @@ -8723,13 +8140,14 @@ HMM emission and transition counts - - bioinformatics + beta12orEarlier - data + 1.4 + true 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. - data - edam + + + @@ -8739,12 +8157,11 @@ Regular expression - bioinformatics beta12orEarlier - data Regular expression pattern. - data - edam + + + @@ -8760,12 +8177,11 @@ - edam - bioinformatics Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. - data beta12orEarlier - data + + + @@ -8781,12 +8197,11 @@ - edam - bioinformatics - data - data beta12orEarlier Some type of statistical model representing a (typically multiple) sequence alignment. + + + @@ -8797,13 +8212,12 @@ Protein signature - data - edam beta12orEarlier InterPro entry - data An entry (sequence classifier and associated data) from the InterPro database. - bioinformatics + + + @@ -8813,15 +8227,12 @@ Prosite nucleotide pattern - beta12orEarlier - bioinformatics beta12orEarlier true - data A nucleotide regular expression pattern from the Prosite database. - data - edam + beta12orEarlier + @@ -8831,15 +8242,12 @@ Prosite protein pattern - data - edam - beta12orEarlier - bioinformatics true beta12orEarlier - data + beta12orEarlier A protein regular expression pattern from the Prosite database. + @@ -8851,11 +8259,10 @@ PFM A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. - bioinformatics beta12orEarlier - edam - data - data + + + @@ -8866,13 +8273,12 @@ Position weight matrix Contributions of individual sequences to the matrix might be uneven (weighted). - data A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. - data - edam beta12orEarlier PWM - bioinformatics + + + @@ -8882,13 +8288,12 @@ Information content matrix - edam 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. - data ICM - bioinformatics - data beta12orEarlier + + + @@ -8898,13 +8303,12 @@ Hidden Markov model - edam - data - data A hidden Markov model representation of a set or alignment of sequences. beta12orEarlier - bioinformatics HMM + + + @@ -8914,12 +8318,11 @@ Fingerprint - bioinformatics One or more fingerprints (sequence classifiers) as used in the PRINTS database. - data - edam - data beta12orEarlier + + + @@ -8929,15 +8332,12 @@ Domainatrix signature - data beta12orEarlier beta12orEarlier - bioinformatics true - data - edam A protein signature of the type used in the EMBASSY Signature package. + @@ -8947,15 +8347,12 @@ HMMER NULL hidden Markov model - bioinformatics - true - data - edam NULL hidden Markov model representation used by the HMMER package. - data + true beta12orEarlier beta12orEarlier + @@ -8966,12 +8363,11 @@ Protein family signature A protein family signature (sequence classifier) from the InterPro database. - data - data - bioinformatics - edam beta12orEarlier 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. + + + @@ -8982,12 +8378,11 @@ Protein domain signature Protein domain signatures identify structural or functional domains or other units with defined boundaries. - bioinformatics A protein domain signature (sequence classifier) from the InterPro database. - edam - data beta12orEarlier - data + + + @@ -8998,12 +8393,11 @@ Protein region signature A protein region signature defines a region which cannot be described as a protein family or domain signature. - bioinformatics - data beta12orEarlier A protein region signature (sequence classifier) from the InterPro database. - edam - data + + + @@ -9015,11 +8409,10 @@ A protein repeat signature (sequence classifier) from the InterPro database. beta12orEarlier - data - edam A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. - data - bioinformatics + + + @@ -9029,13 +8422,12 @@ Protein site signature - edam - data - bioinformatics A protein site signature (sequence classifier) from the InterPro database. - data beta12orEarlier A protein site signature is a classifier for a specific site in a protein. + + + @@ -9044,14 +8436,14 @@ Protein conserved site signature - + beta12orEarlier - edam A protein conserved site signature (sequence classifier) from the InterPro database. - bioinformatics 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. - data - data + true + 1.4 + + @@ -9060,14 +8452,14 @@ Protein active site signature - + beta12orEarlier - edam - data - bioinformatics - data + 1.4 + true 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. + + @@ -9076,14 +8468,14 @@ Protein binding site signature - - data + beta12orEarlier 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. - data - bioinformatics + true A protein binding site signature (sequence classifier) from the InterPro database. - edam + 1.4 + + @@ -9092,14 +8484,14 @@ Protein post-translational modification signature - + + true beta12orEarlier + 1.4 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. A protein post-translational modification signature (sequence classifier) from the InterPro database. - data - bioinformatics - edam - data + + @@ -9109,12 +8501,11 @@ Sequence alignment (pair) - data Alignment of exactly two molecular sequences. - bioinformatics beta12orEarlier - data - edam + + + @@ -9125,15 +8516,12 @@ Sequence alignment (multiple) - data true - edam - beta12orEarlier - bioinformatics Alignment of more than two molecular sequences. + beta12orEarlier beta12orEarlier - data + @@ -9144,12 +8532,11 @@ Sequence alignment (nucleic acid) - data Alignment of multiple nucleotide sequences. - edam - bioinformatics - data beta12orEarlier + + + @@ -9160,12 +8547,11 @@ Sequence alignment (protein) - bioinformatics beta12orEarlier - data - edam - data Alignment of multiple protein sequences. + + + @@ -9175,13 +8561,12 @@ Sequence alignment (hybrid) - data - bioinformatics beta12orEarlier Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. - data Alignment of multiple molecular sequences of different types. - edam + + + @@ -9192,12 +8577,11 @@ Sequence alignment (nucleic acid pair) - bioinformatics Alignment of exactly two nucleotide sequences. beta12orEarlier - data - edam - data + + + @@ -9210,10 +8594,9 @@ beta12orEarlier Alignment of exactly two protein sequences. - data - edam - bioinformatics - data + + + @@ -9224,14 +8607,11 @@ Hybrid sequence alignment (pair) Alignment of exactly two molecular sequences of different types. - data - beta12orEarlier - edam - bioinformatics beta12orEarlier - data + beta12orEarlier true + @@ -9243,13 +8623,10 @@ beta12orEarlier true - data - bioinformatics - data - beta12orEarlier - edam Alignment of more than two nucleotide sequences. + beta12orEarlier + @@ -9259,15 +8636,12 @@ Multiple protein sequence alignment - bioinformatics - data - edam Alignment of more than two protein sequences. beta12orEarlier - data beta12orEarlier true + @@ -9279,11 +8653,10 @@ A simple floating point number defining the penalty for opening or extending a gap in an alignment. - data - edam - bioinformatics - data beta12orEarlier + + + @@ -9293,15 +8666,12 @@ Score end gaps control - bioinformatics - Whether end gaps are scored or not. - beta12orEarlier - data true - edam + Whether end gaps are scored or not. beta12orEarlier - data + beta12orEarlier + @@ -9312,14 +8682,11 @@ Aligned sequence order Controls the order of sequences in an output sequence alignment. - data - data - bioinformatics true - edam beta12orEarlier beta12orEarlier + @@ -9329,12 +8696,11 @@ Gap opening penalty - bioinformatics beta12orEarlier - data - edam A penalty for opening a gap in an alignment. - data + + + @@ -9344,12 +8710,11 @@ Gap extension penalty - edam beta12orEarlier - data A penalty for extending a gap in an alignment. - bioinformatics - data + + + @@ -9359,12 +8724,11 @@ Gap separation penalty - data - edam - bioinformatics A penalty for gaps that are close together in an alignment. - data beta12orEarlier + + + @@ -9376,14 +8740,11 @@ beta12orEarlier true - data - bioinformatics 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. - data - edam beta12orEarlier + @@ -9393,12 +8754,11 @@ Match reward score - data The score for a 'match' used in various sequence database search applications with simple scoring schemes. - edam beta12orEarlier - data - bioinformatics + + + @@ -9410,10 +8770,9 @@ The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. beta12orEarlier - bioinformatics - data - edam - data + + + @@ -9424,11 +8783,10 @@ Drop off score beta12orEarlier - data - bioinformatics - data This is the threshold drop in score at which extension of word alignment is halted. - edam + + + @@ -9439,14 +8797,11 @@ Gap opening penalty (integer) beta12orEarlier - true - data - data A simple floating point number defining the penalty for opening a gap in an alignment. + true beta12orEarlier - bioinformatics - edam + @@ -9456,15 +8811,12 @@ Gap opening penalty (float) + true A simple floating point number defining the penalty for opening a gap in an alignment. beta12orEarlier - bioinformatics beta12orEarlier - edam - true - data - data + @@ -9474,15 +8826,12 @@ Gap extension penalty (integer) - edam beta12orEarlier - A simple floating point number defining the penalty for extending a gap in an alignment. - data beta12orEarlier - bioinformatics + A simple floating point number defining the penalty for extending a gap in an alignment. true - data + @@ -9492,15 +8841,12 @@ Gap extension penalty (float) - data - beta12orEarlier - bioinformatics beta12orEarlier - edam - data A simple floating point number defining the penalty for extending a gap in an alignment. true + beta12orEarlier + @@ -9510,15 +8856,12 @@ Gap separation penalty (integer) - true - data - bioinformatics - A simple floating point number defining the penalty for gaps that are close together in an alignment. - edam beta12orEarlier - data + true beta12orEarlier + A simple floating point number defining the penalty for gaps that are close together in an alignment. + @@ -9528,15 +8871,12 @@ Gap separation penalty (float) - data - bioinformatics - true - edam A simple floating point number defining the penalty for gaps that are close together in an alignment. beta12orEarlier - data + true beta12orEarlier + @@ -9546,12 +8886,11 @@ Terminal gap opening penalty - data A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - edam - data beta12orEarlier - bioinformatics + + + @@ -9561,12 +8900,11 @@ Terminal gap extension penalty - bioinformatics - data - data - edam beta12orEarlier 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. + + + @@ -9577,11 +8915,10 @@ Sequence identity beta12orEarlier - data - edam - bioinformatics - data Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. + + + @@ -9592,12 +8929,11 @@ Sequence similarity Data Type is float probably. - edam 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 - data - bioinformatics beta12orEarlier + + + @@ -9607,15 +8943,12 @@ Sequence alignment metadata (quality report) - edam - data - bioinformatics - true - data - beta12orEarlier Data on molecular sequence alignment quality (estimated accuracy). beta12orEarlier + true + beta12orEarlier + @@ -9624,14 +8957,14 @@ Sequence alignment report (site conservation) - + 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. - data - data + true Data on character conservation in a molecular sequence alignment. + 1.4 beta12orEarlier - edam - bioinformatics + + @@ -9640,13 +8973,13 @@ Sequence alignment report (site correlation) - + + true 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. - data beta12orEarlier - bioinformatics - edam - data + 1.4 + + @@ -9656,15 +8989,12 @@ Sequence-profile alignment (Domainatrix signature) + true beta12orEarlier Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). beta12orEarlier - bioinformatics - true - data - edam - data + @@ -9674,12 +9004,11 @@ Sequence-profile alignment (HMM) - bioinformatics - data Alignment of molecular sequence(s) to a hidden Markov model(s). - edam - data beta12orEarlier + + + @@ -9689,12 +9018,11 @@ Sequence-profile alignment (fingerprint) - edam beta12orEarlier - bioinformatics - data - data Alignment of molecular sequences to a protein fingerprint from the PRINTS database. + + + @@ -9705,13 +9033,12 @@ Phylogenetic continuous quantitative data Continuous quantitative data that may be read during phylogenetic tree calculation. - edam Quantitative traits Phylogenetic continuous quantitative characters beta12orEarlier - data - bioinformatics - data + + + @@ -9722,14 +9049,13 @@ Phylogenetic discrete data Discretely coded characters - data - bioinformatics beta12orEarlier Phylogenetic discrete states - edam - data Character data with discrete states that may be read during phylogenetic tree calculation. Discrete characters + + + @@ -9739,13 +9065,12 @@ Phylogenetic character cliques - data beta12orEarlier - edam Phylogenetic report (cliques) - data 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. - bioinformatics + + + @@ -9761,13 +9086,12 @@ - bioinformatics Phylogenetic report (invariants) - data - data beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. - edam + + + @@ -9777,14 +9101,13 @@ Phylogenetic tree report - data - data 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 a placeholder for other, more specific types. - bioinformatics beta12orEarlier + 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. Phylogenetic tree-derived report - edam + + + @@ -9793,17 +9116,15 @@ DNA substitution model - - + A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. beta12orEarlier Sequence alignment report (DNA substitution model) - edam - data - A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. - data - bioinformatics Phylogenetic tree report (DNA substitution model) + Substitution model + + + @@ -9812,13 +9133,13 @@ Phylogenetic tree report (tree shape) - - data + Data about the shape of a phylogenetic tree. - data - edam + 1.4 + true beta12orEarlier - bioinformatics + + @@ -9827,13 +9148,13 @@ Phylogenetic tree report (tree evaluation) - - bioinformatics + Data on the confidence of a phylogenetic tree. - edam - data - data + 1.4 + true beta12orEarlier + + @@ -9841,14 +9162,14 @@ - Phylogenetic tree report (tree distances) + Phylogenetic tree distances Distances, such as Branch Score distance, between two or more phylogenetic trees. - data - edam - data + Phylogenetic tree report (tree distances) beta12orEarlier - bioinformatics + + + @@ -9857,13 +9178,13 @@ Phylogenetic tree report (tree stratigraphic) - - bioinformatics - data - edam + Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. - data + true + 1.4 beta12orEarlier + + @@ -9874,12 +9195,11 @@ Phylogenetic character contrasts beta12orEarlier - edam - data Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. - bioinformatics Phylogenetic report (character contrasts) - data + + + @@ -9889,16 +9209,13 @@ Comparison matrix (integers) - bioinformatics - Matrix of integer numbers for sequence comparison. - beta12orEarlier - data true - edam - data + beta12orEarlier + Matrix of integer numbers for sequence comparison. Substitution matrix (integers) beta12orEarlier + @@ -9908,16 +9225,13 @@ Comparison matrix (floats) - data - beta12orEarlier - bioinformatics Substitution matrix (floats) - edam - data Matrix of floating point numbers for sequence comparison. true beta12orEarlier + beta12orEarlier + @@ -9927,13 +9241,12 @@ Comparison matrix (nucleotide) - data - data - bioinformatics Nucleotide substitution matrix beta12orEarlier - edam Matrix of integer or floating point numbers for nucleotide comparison. + + + @@ -9945,12 +9258,11 @@ Amino acid substitution matrix - edam - data - data Matrix of integer or floating point numbers for amino acid comparison. beta12orEarlier - bioinformatics + + + @@ -9960,16 +9272,13 @@ Nucleotide comparison matrix (integers) + beta12orEarlier true Matrix of integer numbers for nucleotide comparison. - beta12orEarlier beta12orEarlier - data Nucleotide substitution matrix (integers) - edam - data - bioinformatics + @@ -9979,16 +9288,13 @@ Nucleotide comparison matrix (floats) - edam Nucleotide substitution matrix (floats) + Matrix of floating point numbers for nucleotide comparison. beta12orEarlier true - data - bioinformatics - Matrix of floating point numbers for nucleotide comparison. - data beta12orEarlier + @@ -9998,16 +9304,13 @@ Amino acid comparison matrix (integers) - data - data beta12orEarlier true - beta12orEarlier - bioinformatics Amino acid substitution matrix (integers) - edam Matrix of integer numbers for amino acid comparison. + beta12orEarlier + @@ -10017,16 +9320,13 @@ Amino acid comparison matrix (floats) - data - beta12orEarlier - data - Amino acid substitution matrix (floats) - bioinformatics - edam Matrix of floating point numbers for amino acid comparison. true + beta12orEarlier + Amino acid substitution matrix (floats) beta12orEarlier + @@ -10036,16 +9336,15 @@ Protein features (membrane regions) - bioinformatics An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. beta12orEarlier Intramembrane region report - data - edam - data Transmembrane region report Protein report (membrane protein) + + + @@ -10061,12 +9360,11 @@ - data - edam - bioinformatics beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. - data + + + @@ -10079,21 +9377,20 @@ - + - + beta12orEarlier - data - edam 3D coordinate and associated data for a protein tertiary (3D) structure. - bioinformatics - data + + + @@ -10104,12 +9401,11 @@ Protein-ligand complex 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. - data - bioinformatics - edam beta12orEarlier 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. - data + + + @@ -10122,21 +9418,20 @@ - + - + - bioinformatics 3D coordinate and associated data for a carbohydrate (3D) structure. beta12orEarlier - edam - data - data + + + @@ -10152,13 +9447,12 @@ - data beta12orEarlier - bioinformatics CHEBI:23367 - edam - data 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. + + + @@ -10168,12 +9462,11 @@ DNA structure - data - data - bioinformatics 3D coordinate and associated data for a DNA tertiary (3D) structure. beta12orEarlier - edam + + + @@ -10189,12 +9482,11 @@ - edam 3D coordinate and associated data for an RNA tertiary (3D) structure. - bioinformatics beta12orEarlier - data - data + + + @@ -10204,12 +9496,11 @@ tRNA structure record - data beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. - data - edam - bioinformatics + + + @@ -10219,12 +9510,11 @@ Protein chain - bioinformatics 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. - data beta12orEarlier - edam - data + + + @@ -10240,12 +9530,11 @@ - data - data beta12orEarlier - bioinformatics - edam 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. + + + @@ -10256,11 +9545,10 @@ Protein structure (all atoms) 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). - data - bioinformatics - data - edam beta12orEarlier + + + @@ -10270,13 +9558,12 @@ Protein structure (C-alpha atoms) - data beta12orEarlier - data - bioinformatics - edam C-beta atoms from amino acid side-chains may be included. 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). + + + @@ -10287,15 +9574,12 @@ Protein chain (all atoms) true - edam - data + beta12orEarlier beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). - data - beta12orEarlier - bioinformatics + @@ -10305,17 +9589,14 @@ Protein chain (C-alpha atoms) - data - edam - beta12orEarlier - 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). - data - bioinformatics C-beta atoms from amino acid side-chains may be included. beta12orEarlier + beta12orEarlier + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). true + @@ -10325,16 +9606,13 @@ Protein domain (all atoms) - data + beta12orEarlier true - data beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). - beta12orEarlier - bioinformatics - edam + @@ -10346,15 +9624,12 @@ beta12orEarlier beta12orEarlier - bioinformatics - data - C-beta atoms from amino acid side-chains may be included. - edam - data 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). true + C-beta atoms from amino acid side-chains may be included. + @@ -10364,12 +9639,11 @@ Structure alignment (pair) - data - data beta12orEarlier - edam - bioinformatics Alignment (superimposition) of exactly two molecular tertiary (3D) structures. + + + @@ -10379,15 +9653,12 @@ Structure alignment (multiple) - data Alignment (superimposition) of more than two molecular tertiary (3D) structures. - bioinformatics - beta12orEarlier - edam - data true beta12orEarlier + beta12orEarlier + @@ -10398,12 +9669,11 @@ Structure alignment (protein) - data - edam - bioinformatics - data Alignment (superimposition) of protein tertiary (3D) structures. beta12orEarlier + + + @@ -10414,12 +9684,11 @@ Structure alignment (nucleic acid) - bioinformatics - data Alignment (superimposition) of nucleic acid tertiary (3D) structures. beta12orEarlier - edam - data + + + @@ -10432,10 +9701,10 @@ Alignment (superimposition) of exactly two protein tertiary (3D) structures. beta12orEarlier - data - bioinformatics - data - edam + Pairwise protein structural alignment + + + @@ -10448,12 +9717,9 @@ beta12orEarlier true beta12orEarlier - data - bioinformatics Alignment (superimposition) of more than two protein tertiary (3D) structures. - edam - data + @@ -10463,12 +9729,11 @@ Structure alignment (protein all atoms) - data beta12orEarlier Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). - edam - bioinformatics - data + + + @@ -10479,12 +9744,12 @@ Structure alignment (protein C-alpha atoms) beta12orEarlier - bioinformatics - edam - data + C-alpha trace C-beta atoms from amino acid side-chains may be considered. - data Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). + + + @@ -10494,15 +9759,12 @@ Pairwise protein tertiary structure alignment (all atoms) - edam - data - true - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). beta12orEarlier beta12orEarlier - data - bioinformatics + true + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + @@ -10512,16 +9774,13 @@ Pairwise protein tertiary structure alignment (C-alpha atoms) - beta12orEarlier - edam - true - data - data beta12orEarlier - bioinformatics Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + beta12orEarlier + true C-beta atoms from amino acid side-chains may be included. + @@ -10531,15 +9790,12 @@ Multiple protein tertiary structure alignment (all atoms) - data - bioinformatics - edam beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - data true beta12orEarlier + @@ -10549,16 +9805,13 @@ Multiple protein tertiary structure alignment (C-alpha atoms) - data - data + C-beta atoms from amino acid side-chains may be included. beta12orEarlier - bioinformatics true - beta12orEarlier - C-beta atoms from amino acid side-chains may be included. - edam Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + beta12orEarlier + @@ -10570,11 +9823,10 @@ Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - data - data - bioinformatics beta12orEarlier - edam + + + @@ -10587,12 +9839,9 @@ beta12orEarlier true Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. - edam beta12orEarlier - bioinformatics - data - data + @@ -10604,10 +9853,9 @@ beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. - edam - data - bioinformatics - data + + + @@ -10618,11 +9866,10 @@ Structural transformation matrix beta12orEarlier - edam Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. - data - data - bioinformatics + + + @@ -10632,16 +9879,13 @@ DaliLite hit table - data - data - beta12orEarlier - DaliLite hit table of protein chain tertiary structure alignment data. beta12orEarlier true - bioinformatics + beta12orEarlier 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. - edam + DaliLite hit table of protein chain tertiary structure alignment data. + @@ -10651,15 +9895,12 @@ Molecular similarity score - true - edam - data beta12orEarlier - bioinformatics + true A score reflecting structural similarities of two molecules. - data beta12orEarlier + @@ -10670,12 +9911,11 @@ Root-mean-square deviation Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. - bioinformatics - edam beta12orEarlier - data - data RMSD + + + @@ -10685,13 +9925,12 @@ Tanimoto similarity score - bioinformatics 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. - edam - data A measure of the similarity between two ligand fingerprints. - data beta12orEarlier + + + @@ -10701,12 +9940,11 @@ 3D-1D scoring matrix - data beta12orEarlier - data A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. - bioinformatics - edam + + + @@ -10717,12 +9955,11 @@ Amino acid index - edam A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. - bioinformatics - data - data beta12orEarlier + + + @@ -10732,12 +9969,11 @@ Amino acid index (chemical classes) - data beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. - bioinformatics - data - edam + + + @@ -10748,11 +9984,10 @@ Amino acid pair-wise contact potentials beta12orEarlier - edam - bioinformatics - data - data Statistical protein contact potentials. + + + @@ -10762,12 +9997,11 @@ Amino acid index (molecular weight) - edam - bioinformatics beta12orEarlier - data Molecular weights of amino acids. - data + + + @@ -10778,11 +10012,10 @@ Amino acid index (hydropathy) beta12orEarlier - data Hydrophobic, hydrophilic or charge properties of amino acids. - edam - data - bioinformatics + + + @@ -10792,12 +10025,11 @@ Amino acid index (White-Wimley data) - edam - data Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. - data - bioinformatics beta12orEarlier + + + @@ -10808,11 +10040,10 @@ Amino acid index (van der Waals radii) beta12orEarlier - data - data - edam Van der Waals radii of atoms for different amino acid residues. - bioinformatics + + + @@ -10829,13 +10060,12 @@ An informative report on a specific enzyme. - bioinformatics - data - data Enzyme report - edam beta12orEarlier Protein report (enzyme) + + + @@ -10845,16 +10075,15 @@ Restriction enzyme property - edam - data - data Restriction enzyme report Protein report (restriction enzyme) 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. beta12orEarlier - bioinformatics Restriction enzyme pattern data An informative report on a specific restriction enzyme such as enzyme reference data. + + + @@ -10865,12 +10094,11 @@ Peptide molecular weights The report might include associated data such as frequency of peptide fragment molecular weights. - data List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. beta12orEarlier - bioinformatics - edam - data + + + @@ -10880,13 +10108,12 @@ Peptide hydrophobic moment - data Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. Report on the hydrophobic moment of a polypeptide sequence. - bioinformatics - data beta12orEarlier - edam + + + @@ -10899,10 +10126,9 @@ The aliphatic index is the relative protein volume occupied by aliphatic side chains. beta12orEarlier The aliphatic index of a protein. - bioinformatics - data - edam - data + + + @@ -10912,13 +10138,12 @@ Protein sequence hydropathy plot - edam beta12orEarlier 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. - data - data - bioinformatics + + + @@ -10928,12 +10153,11 @@ Protein charge plot - data 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. - data - edam - bioinformatics beta12orEarlier + + + @@ -10944,12 +10168,11 @@ Protein solubility Protein solubility data - edam - data - data The solubility or atomic solvation energy of a protein sequence or structure. - bioinformatics beta12orEarlier + + + @@ -10959,13 +10182,12 @@ Protein crystallizability - data - data - edam Data on the crystallizability of a protein sequence. Protein crystallizability data - bioinformatics beta12orEarlier + + + @@ -10975,13 +10197,12 @@ Protein globularity - data - edam Data on the stability, intrinsic disorder or globularity of a protein sequence. beta12orEarlier - data Protein globularity data - bioinformatics + + + @@ -10991,12 +10212,11 @@ Protein titration curve - data - bioinformatics beta12orEarlier - data The titration curve of a protein. - edam + + + @@ -11007,11 +10227,10 @@ Protein isoelectric point The isoelectric point of one proteins. - data - bioinformatics - data - edam beta12orEarlier + + + @@ -11021,12 +10240,11 @@ Protein pKa value - data - bioinformatics beta12orEarlier The pKa value of a protein. - data - edam + + + @@ -11036,12 +10254,11 @@ Protein hydrogen exchange rate - data - data The hydrogen exchange rate of a protein. - bioinformatics - edam beta12orEarlier + + + @@ -11052,11 +10269,10 @@ Protein extinction coefficient beta12orEarlier - data - edam The extinction coefficient of a protein. - data - bioinformatics + + + @@ -11066,12 +10282,11 @@ Protein optical density - bioinformatics beta12orEarlier - data - edam - data The optical density of a protein. + + + @@ -11082,15 +10297,12 @@ Protein subcellular localization beta13 + beta12orEarlier + true An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). - data Protein report (subcellular localization) - data - true - beta12orEarlier - edam - bioinformatics + @@ -11101,14 +10313,13 @@ Peptide immunogenicity data 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. + Peptide immunogenicity beta12orEarlier Peptide immunogenicity report - data - bioinformatics - data - edam - Peptide immunogenicity An report on allergenicity / immunogenicity of peptides and proteins. + + + @@ -11118,15 +10329,12 @@ MHC peptide immunogenicity report - edam - data - bioinformatics beta12orEarlier true - data A report on the immunogenicity of MHC class I or class II binding peptides. beta13 + @@ -11142,12 +10350,12 @@ Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. beta12orEarlier Protein property (structural) - edam - data - bioinformatics - data + 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). Protein structure-derived report Protein structural property + + + @@ -11160,14 +10368,14 @@ beta12orEarlier Protein report (structural quality) - data - edam Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. - data Protein property (structural quality) Protein structure report (quality evaluation) - bioinformatics + Protein structure validation report Report on the quality of a protein three-dimensional model. + + + @@ -11184,14 +10392,13 @@ - bioinformatics 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. - data - edam Atom interaction data beta12orEarlier Residue interaction data - data + + + @@ -11200,18 +10407,17 @@ Protein flexibility or motion report - - + Protein structure report (flexibility or motion) + 1.4 + true beta12orEarlier Protein flexibility or motion - edam - data Informative report on flexibility or motion of a protein structure. Protein property (flexibility or motion) - bioinformatics 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. - data + + @@ -11221,13 +10427,12 @@ Protein solvent accessibility - data - data Data on the solvent accessible or buried surface area of a protein structure. beta12orEarlier - edam - bioinformatics 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. + + + @@ -11236,16 +10441,15 @@ Protein surface report - - - Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. - data + beta12orEarlier - bioinformatics - edam + true + Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. + 1.4 Protein structure report (surface) 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. - data + + @@ -11255,12 +10459,11 @@ Ramachandran plot - bioinformatics - edam Phi/psi angle data or a Ramachandran plot of a protein structure. beta12orEarlier - data - data + + + @@ -11270,12 +10473,11 @@ Protein dipole moment - edam beta12orEarlier - bioinformatics Data on the net charge distribution (dipole moment) of a protein structure. - data - data + + + @@ -11285,12 +10487,11 @@ Protein distance matrix - data - edam A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. - data beta12orEarlier - bioinformatics + + + @@ -11300,12 +10501,11 @@ Protein contact map - data - bioinformatics - edam - data beta12orEarlier An amino acid residue contact map for a protein structure. + + + @@ -11315,12 +10515,11 @@ Protein residue 3D cluster - data - data - edam Report on clusters of contacting residues in protein structures such as a key structural residue network. - bioinformatics beta12orEarlier + + + @@ -11330,12 +10529,11 @@ Protein hydrogen bonds - edam - data - bioinformatics - data beta12orEarlier Patterns of hydrogen bonding in protein structures. + + + @@ -11344,15 +10542,14 @@ Protein non-canonical interactions - - - data + beta12orEarlier - edam + 1.4 Non-canonical atomic interactions in protein structures. - data + true Protein non-canonical interactions report - bioinformatics + + @@ -11362,14 +10559,13 @@ CATH node - data CATH classification node report beta12orEarlier - bioinformatics - edam - data 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. + + + @@ -11379,13 +10575,12 @@ SCOP node - bioinformatics - edam beta12orEarlier - data Information on a node from the SCOP database. SCOP classification node - data + + + @@ -11395,15 +10590,12 @@ EMBASSY domain classification - true - edam - data - beta12orEarlier An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. - bioinformatics + true beta12orEarlier - data + beta12orEarlier + @@ -11413,12 +10605,11 @@ CATH class - bioinformatics - edam - data - data Information on a protein 'class' node from the CATH database. beta12orEarlier + + + @@ -11428,12 +10619,11 @@ CATH architecture - data - bioinformatics Information on a protein 'architecture' node from the CATH database. - edam beta12orEarlier - data + + + @@ -11444,11 +10634,10 @@ CATH topology beta12orEarlier - bioinformatics Information on a protein 'topology' node from the CATH database. - edam - data - data + + + @@ -11459,11 +10648,10 @@ CATH homologous superfamily Information on a protein 'homologous superfamily' node from the CATH database. - data beta12orEarlier - data - bioinformatics - edam + + + @@ -11473,12 +10661,11 @@ CATH structurally similar group - edam Information on a protein 'structurally similar group' node from the CATH database. - bioinformatics beta12orEarlier - data - data + + + @@ -11488,12 +10675,11 @@ CATH functional category - data beta12orEarlier - edam - bioinformatics Information on a protein 'functional category' node from the CATH database. - data + + + @@ -11504,15 +10690,12 @@ Protein fold recognition report beta12orEarlier - edam true - data - 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. - bioinformatics A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). beta12orEarlier - data + 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. + @@ -11528,14 +10711,13 @@ - data - data - edam - Data on protein-protein interaction(s). - bioinformatics For example, an informative report about a specific protein complex (of multiple polypeptide chains). Protein structure report (protein complex) beta12orEarlier + Data on protein-protein interaction(s). + + + @@ -11551,12 +10733,11 @@ - data - data - bioinformatics beta12orEarlier Data on protein-ligand (small molecule) interaction(s). - edam + + + @@ -11574,10 +10755,9 @@ Data on protein-DNA/RNA interaction(s). beta12orEarlier - data - data - bioinformatics - edam + + + @@ -11587,14 +10767,13 @@ Nucleic acid melting profile - data - edam beta12orEarlier - bioinformatics - data 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. Nucleic acid stability profile + + + @@ -11604,12 +10783,11 @@ Nucleic acid enthalpy - data Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - data - edam beta12orEarlier - bioinformatics + + + @@ -11619,12 +10797,11 @@ Nucleic acid entropy - data beta12orEarlier - data Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - edam - bioinformatics + + + @@ -11635,14 +10812,11 @@ Nucleic acid melting temperature true - Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - data - edam - bioinformatics beta12orEarlier beta12orEarlier - data + Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + @@ -11653,12 +10827,11 @@ Nucleic acid stitch profile 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. - bioinformatics Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - data - data beta12orEarlier - edam + + + @@ -11668,12 +10841,11 @@ DNA base pair stacking energies data - edam - data - data beta12orEarlier - bioinformatics DNA base pair stacking energies data. + + + @@ -11683,12 +10855,11 @@ DNA base pair twist angle data - edam - bioinformatics DNA base pair twist angle data. - data beta12orEarlier - data + + + @@ -11698,12 +10869,11 @@ DNA base trimer roll angles data - data - data - edam DNA base trimer roll angles data. beta12orEarlier - bioinformatics + + + @@ -11713,15 +10883,12 @@ Vienna RNA parameters - bioinformatics - data + beta12orEarlier true beta12orEarlier RNA parameters used by the Vienna package. - edam - beta12orEarlier - data + @@ -11731,15 +10898,12 @@ Vienna RNA structure constraints + beta12orEarlier beta12orEarlier - data - bioinformatics Structure constraints used by the Vienna package. - edam true - beta12orEarlier - data + @@ -11751,13 +10915,10 @@ beta12orEarlier true - edam - data - data - bioinformatics RNA concentration data used by the Vienna package. beta12orEarlier + @@ -11767,15 +10928,12 @@ Vienna RNA calculated energy - edam + RNA calculated energy data generated by the Vienna package. true beta12orEarlier beta12orEarlier - bioinformatics - data - RNA calculated energy data generated by the Vienna package. - data + @@ -11785,13 +10943,12 @@ Base pairing probability matrix dotplot - data - data Dotplot of RNA base pairing probability matrix. Such as generated by the Vienna package. beta12orEarlier - edam - bioinformatics + + + @@ -11802,14 +10959,13 @@ Nucleic acid folding report 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. - bioinformatics Nucleic acid report (folding model) A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. beta12orEarlier - data - data Nucleic acid report (folding) - edam + + + @@ -11826,12 +10982,11 @@ beta12orEarlier - data 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. Table of codon usage data calculated from one or more nucleic acid sequences. - bioinformatics - data - edam + + + @@ -11841,13 +10996,12 @@ Genetic code - bioinformatics - edam - data A genetic code need not include detailed codon usage information. - data A genetic code for an organism. beta12orEarlier + + + @@ -11857,16 +11011,13 @@ Codon adaptation index - edam - data beta12orEarlier - data - bioinformatics beta12orEarlier CAI A simple measure of synonymous codon usage bias often used to predict gene expression levels. true + @@ -11875,14 +11026,13 @@ Codon usage bias plot - - bioinformatics - data - edam + A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. - data beta12orEarlier Synonymous codon usage statistic plot + + + @@ -11892,15 +11042,12 @@ Nc statistic - data beta12orEarlier The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. - edam - data - bioinformatics beta12orEarlier true + @@ -11911,11 +11058,10 @@ Codon usage fraction difference beta12orEarlier - edam The differences in codon usage fractions between two codon usage tables. - data - data - bioinformatics + + + @@ -11927,11 +11073,10 @@ Data on the influence of genotype on drug response. The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. - bioinformatics beta12orEarlier - data - edam - data + + + @@ -11939,7 +11084,7 @@ - Disease annotation + Disease report @@ -11947,12 +11092,13 @@ - data + Disease report beta12orEarlier - bioinformatics - data + 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. An informative report on a specific disease. - edam + + + @@ -11962,12 +11108,11 @@ Gene annotation (linkage disequilibrium) - data beta12orEarlier - bioinformatics - data - edam A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + + + @@ -11978,12 +11123,11 @@ Heat map 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. - data - bioinformatics - edam - data beta12orEarlier A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. + + + @@ -11993,16 +11137,13 @@ Affymetrix probe sets library file - bioinformatics - edam - data - true beta12orEarlier - data beta12orEarlier CDF file Affymetrix library file of information about which probes belong to which probe set. + true + @@ -12012,16 +11153,13 @@ Affymetrix probe sets information library file + beta12orEarlier beta12orEarlier GIN file - bioinformatics - data - data - beta12orEarlier Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. true - edam + @@ -12032,11 +11170,10 @@ Molecular weights standard fingerprint Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. - bioinformatics - data - data - edam beta12orEarlier + + + @@ -12046,13 +11183,12 @@ Pathway or network (metabolic) - data - bioinformatics - edam - data A report typically including a map (diagram) of a metabolic pathway. beta12orEarlier This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. + + + @@ -12062,12 +11198,11 @@ Pathway or network (genetic information processing) - data A report typically including a map (diagram) of a genetic information processing pathway. - bioinformatics - data - edam beta12orEarlier + + + @@ -12078,11 +11213,10 @@ Pathway or network (environmental information processing) beta12orEarlier - bioinformatics - edam A report typically including a map (diagram) of an environmental information processing pathway. - data - data + + + @@ -12093,11 +11227,10 @@ Pathway or network (signal transduction) beta12orEarlier - edam - data - data - bioinformatics A report typically including a map (diagram) of a signal transduction pathway. + + + @@ -12108,11 +11241,10 @@ Pathway or network (cellular process) beta12orEarlier - data - edam - data A report typically including a map (diagram) of a cellular process pathway. - bioinformatics + + + @@ -12122,12 +11254,11 @@ Pathway or network (disease) - data - edam A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease. - bioinformatics - data beta12orEarlier + + + @@ -12137,12 +11268,11 @@ Pathway or network (drug structure relationship) - edam - data beta12orEarlier - bioinformatics - data A report typically including a map (diagram) of drug structure relationships. + + + @@ -12152,12 +11282,11 @@ Pathway or network (protein-protein interaction) - data beta12orEarlier - data A report typically including a map (diagram) of a network of protein interactions. - edam - bioinformatics + + + @@ -12168,12 +11297,11 @@ MIRIAM datatype beta12orEarlier - bioinformatics An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. - edam 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. - data - data + + + @@ -12186,11 +11314,10 @@ Expectation value A simple floating point number defining the lower or upper limit of an expectation value (E-value). beta12orEarlier - data - edam - bioinformatics - data 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. + + + @@ -12202,11 +11329,10 @@ A z-value might be specified as a threshold for reporting hits from database searches. The z-value is the number of standard deviations a data value is above or below a mean value. - bioinformatics - data - edam beta12orEarlier - data + + + @@ -12218,11 +11344,10 @@ 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. - data - data beta12orEarlier - bioinformatics - edam + + + @@ -12235,11 +11360,10 @@ beta12orEarlier Information on a database (or ontology) version, for example name, version number and release date. - edam - bioinformatics Ontology version information - data - data + + + @@ -12250,12 +11374,11 @@ Tool version information - data - data - edam beta12orEarlier Information on an application version, for example name, version number and release date. - bioinformatics + + + @@ -12265,15 +11388,12 @@ CATH version information - edam + Information on a version of the CATH database. true beta12orEarlier - bioinformatics beta12orEarlier - Information on a version of the CATH database. - data - data + @@ -12283,15 +11403,12 @@ Swiss-Prot to PDB mapping - data beta12orEarlier - beta12orEarlier - edam true - data - bioinformatics + beta12orEarlier Cross-mapping of Swiss-Prot codes to PDB identifiers. + @@ -12301,15 +11418,12 @@ Sequence database cross-references - data - beta12orEarlier - Cross-references from a sequence record to other databases. - bioinformatics - edam beta12orEarlier - data true + beta12orEarlier + Cross-references from a sequence record to other databases. + @@ -12319,13 +11433,12 @@ Job status - data 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). - bioinformatics - data - edam beta12orEarlier Metadata on the status of a submitted job. + + + @@ -12335,16 +11448,12 @@ Job ID - beta12orEarlier - 1.0 - edam - bioinformatics true + beta12orEarlier The (typically numeric) unique identifier of a submitted job. - identifiers - data - identifier + 1.0 + @@ -12356,10 +11465,9 @@ A label (text token) describing the type of job, for example interactive or non-interactive. beta12orEarlier - bioinformatics - data - data - edam + + + @@ -12370,11 +11478,10 @@ Tool log beta12orEarlier - edam - data - bioinformatics A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. - data + + + @@ -12384,15 +11491,12 @@ DaliLite log file - bioinformatics - data - true beta12orEarlier - data - edam DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. + true beta12orEarlier + @@ -12403,14 +11507,11 @@ STRIDE log file beta12orEarlier - true - data - edam beta12orEarlier - data + true STRIDE log file. - bioinformatics + @@ -12420,15 +11521,12 @@ NACCESS log file - data - data - bioinformatics - beta12orEarlier NACCESS log file. true + beta12orEarlier beta12orEarlier - edam + @@ -12439,14 +11537,11 @@ EMBOSS wordfinder log file true - edam beta12orEarlier - bioinformatics - EMBOSS wordfinder log file. - data beta12orEarlier - data + EMBOSS wordfinder log file. + @@ -12456,15 +11551,12 @@ EMBOSS domainatrix log file - edam - data - bioinformatics true beta12orEarlier - data EMBOSS (EMBASSY) domainatrix application log file. beta12orEarlier + @@ -12475,14 +11567,11 @@ EMBOSS sites log file EMBOSS (EMBASSY) sites application log file. - edam + beta12orEarlier beta12orEarlier true - data - beta12orEarlier - data - bioinformatics + @@ -12492,15 +11581,12 @@ EMBOSS supermatcher error file - bioinformatics - beta12orEarlier - data true - edam beta12orEarlier + beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. - data + @@ -12511,14 +11597,11 @@ EMBOSS megamerger log file true - data EMBOSS megamerger log file. beta12orEarlier beta12orEarlier - edam - bioinformatics - data + @@ -12529,14 +11612,11 @@ EMBOSS whichdb log file beta12orEarlier - data + EMBOSS megamerger log file. true - data beta12orEarlier - EMBOSS megamerger log file. - bioinformatics - edam + @@ -12546,15 +11626,12 @@ EMBOSS vectorstrip log file - data - beta12orEarlier - true EMBOSS vectorstrip log file. - bioinformatics - data - edam + beta12orEarlier beta12orEarlier + true + @@ -12565,12 +11642,11 @@ Username beta12orEarlier - identifiers - edam - data - identifier - bioinformatics A username on a computer system. + + + + @@ -12580,13 +11656,12 @@ Password - identifier - bioinformatics - data - edam - identifiers A password on a computer system. beta12orEarlier + + + + @@ -12596,15 +11671,14 @@ Email address - identifiers Moby:EmailAddress A valid email address of an end-user. Moby:Email - bioinformatics - identifier - edam - data beta12orEarlier + + + + @@ -12614,13 +11688,12 @@ Person name - bioinformatics - data The name of a person. - identifiers - identifier beta12orEarlier - edam + + + + @@ -12630,12 +11703,11 @@ Number of iterations - edam beta12orEarlier - bioinformatics - data Number of iterations of an algorithm. - data + + + @@ -12645,12 +11717,11 @@ Number of output entities - data - data beta12orEarlier - edam Number of entities (for example database hits, sequences, alignments etc) to write to an output file. - bioinformatics + + + @@ -12660,15 +11731,12 @@ Hit sort order - data true beta12orEarlier - Controls the order of hits (reported matches) in an output file from a database search. - bioinformatics - data - edam beta12orEarlier + Controls the order of hits (reported matches) in an output file from a database search. + @@ -12676,7 +11744,7 @@ - Drug annotation + Drug report @@ -12684,12 +11752,13 @@ - data + Drug annotation beta12orEarlier - bioinformatics An informative report on a specific drug. - data - edam + + + + @@ -12701,12 +11770,11 @@ See also 'Phylogenetic tree' - bioinformatics beta12orEarlier 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. - data - edam - data + + + @@ -12715,13 +11783,12 @@ RNA secondary structure image - + beta12orEarlier Image of RNA secondary structure, knots, pseudoknots etc. - data - bioinformatics - edam - data + + + @@ -12730,14 +11797,12 @@ Protein secondary structure image - beta12orEarlier Image of protein secondary structure. - data - data - edam - bioinformatics + + + @@ -12749,11 +11814,10 @@ Image of one or more molecular tertiary (3D) structures. - data - data - bioinformatics beta12orEarlier - edam + + + @@ -12764,12 +11828,11 @@ Sequence alignment image - edam - bioinformatics Image of two or more aligned molecular sequences possibly annotated with alignment features. - data beta12orEarlier - data + + + @@ -12780,15 +11843,14 @@ Structure image (small molecule) - edam beta12orEarlier Small molecule structure image The molecular identifier and formula are typically included. An image of the structure of a small chemical compound. - data - data Chemical structure image - bioinformatics + + + @@ -12799,11 +11861,10 @@ Fate map beta12orEarlier - edam A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. - data - data - bioinformatics + + + @@ -12814,12 +11875,11 @@ Microarray spots image - data - edam - data An image of spots from a microarray experiment. beta12orEarlier - bioinformatics + + + @@ -12829,15 +11889,12 @@ BioPax - data - bioinformatics - beta12orEarlier - edam true - data beta12orEarlier A term from the BioPax ontology. + beta12orEarlier + @@ -12847,20 +11904,17 @@ GO - Moby:GO_Term Moby:GOTerm + Moby:GO_Term beta12orEarlier A term definition from The Gene Ontology (GO). true Moby:Annotated_GO_Term_With_Probability - data Moby:Annotated_GO_Term Gene Ontology term beta12orEarlier - bioinformatics - data - edam + @@ -12870,15 +11924,12 @@ MeSH - A term from the MeSH vocabulary. - edam beta12orEarlier beta12orEarlier - bioinformatics - data + A term from the MeSH vocabulary. true - data + @@ -12888,15 +11939,12 @@ HGNC - data - bioinformatics beta12orEarlier - edam A term from the HGNC controlled vocabulary. true beta12orEarlier - data + @@ -12906,15 +11954,12 @@ NCBI taxonomy vocabulary - beta12orEarlier - bioinformatics - data A term from the NCBI taxonomy vocabulary. - edam true + beta12orEarlier beta12orEarlier - data + @@ -12924,15 +11969,12 @@ Plant ontology term - bioinformatics + A term from the Plant Ontology (PO). beta12orEarlier beta12orEarlier true - data - edam - A term from the Plant Ontology (PO). - data + @@ -12942,15 +11984,12 @@ UMLS - data + true A term from the UMLS vocabulary. beta12orEarlier beta12orEarlier - bioinformatics - data - true - edam + @@ -12960,16 +11999,13 @@ FMA - edam true - data - beta12orEarlier - bioinformatics A term from Foundational Model of Anatomy. beta12orEarlier - data 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. + beta12orEarlier + @@ -12979,15 +12015,12 @@ EMAP - edam - beta12orEarlier beta12orEarlier - data + beta12orEarlier true - bioinformatics A term from the EMAP mouse ontology. - data + @@ -12997,15 +12030,12 @@ ChEBI - edam - beta12orEarlier - A term from the ChEBI ontology. beta12orEarlier - data - data - bioinformatics true + beta12orEarlier + A term from the ChEBI ontology. + @@ -13015,15 +12045,12 @@ MGED - data A term from the MGED ontology. - beta12orEarlier beta12orEarlier - data true - bioinformatics - edam + beta12orEarlier + @@ -13033,16 +12060,13 @@ myGrid - bioinformatics beta12orEarlier A term from the myGrid ontology. - data true - data - edam beta12orEarlier 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. + @@ -13052,16 +12076,13 @@ GO (biological process) + A term definition for a biological process from the Gene Ontology (GO). Data Type is an enumerated string. beta12orEarlier - data true - A term definition for a biological process from the Gene Ontology (GO). - edam - data - bioinformatics beta12orEarlier + @@ -13072,15 +12093,12 @@ GO (molecular function) beta12orEarlier - bioinformatics - Data Type is an enumerated string. - data true + Data Type is an enumerated string. beta12orEarlier - edam - data A term definition for a molecular function from the Gene Ontology (GO). + @@ -13090,16 +12108,13 @@ GO (cellular component) - A term definition for a cellular component from the Gene Ontology (GO). - beta12orEarlier - true - data - data Data Type is an enumerated string. beta12orEarlier - bioinformatics - edam + A term definition for a cellular component from the Gene Ontology (GO). + true + beta12orEarlier + @@ -13109,12 +12124,11 @@ Ontology relation type - bioinformatics A relation type defined in an ontology. - data - edam beta12orEarlier - data + + + @@ -13125,11 +12139,11 @@ Ontology concept definition The definition of a concept from an ontology. - data - data - bioinformatics + Ontology class definition beta12orEarlier - edam + + + @@ -13138,13 +12152,13 @@ Ontology concept comment - - bioinformatics - edam + A comment on a concept from an ontology. - data + true + 1.4 beta12orEarlier - data + + @@ -13154,15 +12168,12 @@ Ontology concept reference - data - edam beta12orEarlier - data + Reference for a concept from an ontology. true beta12orEarlier - bioinformatics - Reference for a concept from an ontology. + @@ -13173,15 +12184,12 @@ doc2loc document information Information on a published article provided by the doc2loc program. + beta12orEarlier The doc2loc output includes the url, format, type and availability code of a document for every service provider. - data - edam true beta12orEarlier - data - beta12orEarlier - bioinformatics + @@ -13192,13 +12200,12 @@ PDB residue number A residue identifier (a string) from a PDB file. - edam - data - data - bioinformatics beta12orEarlier PDBML:PDB_residue_no WHATIF: pdb_number + + + @@ -13209,12 +12216,11 @@ Atomic coordinate Cartesian coordinate - edam - data - bioinformatics beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). - data + + + @@ -13225,14 +12231,13 @@ Atomic x coordinate Cartesian x coordinate of an atom (in a molecular structure). - beta12orEarlier - WHATIF: PDBx_Cartn_x - edam - data - bioinformatics - data PDBML:_atom_site.Cartn_x in PDBML + beta12orEarlier Cartesian x coordinate + WHATIF: PDBx_Cartn_x + + + @@ -13242,15 +12247,14 @@ Atomic y coordinate - data - data - WHATIF: PDBx_Cartn_y - edam Cartesian y coordinate of an atom (in a molecular structure). PDBML:_atom_site.Cartn_y in PDBML beta12orEarlier - bioinformatics Cartesian y coordinate + WHATIF: PDBx_Cartn_y + + + @@ -13260,15 +12264,14 @@ Atomic z coordinate - bioinformatics - data Cartesian z coordinate - data - edam beta12orEarlier Cartesian z coordinate of an atom (in a molecular structure). WHATIF: PDBx_Cartn_z PDBML:_atom_site.Cartn_z + + + @@ -13279,17 +12282,16 @@ PDB atom name Identifier (a string) of a specific atom from a PDB file for a molecular structure. - bioinformatics - identifier WHATIF: atom_type PDBML:pdbx_PDB_atom_name - identifiers WHATIF: alternate_atom WHATIF: PDBx_auth_atom_id beta12orEarlier - edam WHATIF: PDBx_type_symbol - data + + + + @@ -13300,14 +12302,13 @@ Protein atom beta12orEarlier - data - 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. - data - bioinformatics 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. CHEBI:33250 Atom data - edam + + + @@ -13319,12 +12320,11 @@ Residue 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. - edam Data on a single amino acid residue position in a protein structure. - bioinformatics - data beta12orEarlier - data + + + @@ -13335,13 +12335,12 @@ Atom name - data beta12orEarlier - identifier - edam Name of an atom. - bioinformatics - identifiers + + + + @@ -13351,14 +12350,13 @@ PDB residue name - identifiers beta12orEarlier - bioinformatics WHATIF: type - edam - identifier - data Three-letter amino acid residue names as used in PDB files. + + + + @@ -13368,16 +12366,15 @@ PDB model number - identifiers WHATIF: model_number - edam beta12orEarlier - bioinformatics - identifier Identifier of a model structure from a PDB file. Model number PDBML:pdbx_PDB_model_num - data + + + + @@ -13387,16 +12384,13 @@ CATH domain report - edam - bioinformatics - true - beta12orEarlier - data - 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. + Summary of domain classification information for a CATH domain. + true beta13 - data + beta12orEarlier + @@ -13406,15 +12400,12 @@ CATH representative domain sequences (ATOM) - data true FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). - data - bioinformatics beta12orEarlier beta12orEarlier - edam + @@ -13425,14 +12416,11 @@ CATH representative domain sequences (COMBS) beta12orEarlier - FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). - edam beta12orEarlier - bioinformatics - data + FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). true - data + @@ -13442,15 +12430,12 @@ CATH domain sequences (ATOM) - edam - FASTA sequence database for all CATH domains (based on PDB ATOM records). - bioinformatics - data beta12orEarlier - data beta12orEarlier + FASTA sequence database for all CATH domains (based on PDB ATOM records). true + @@ -13460,15 +12445,12 @@ CATH domain sequences (COMBS) - data beta12orEarlier - edam + true beta12orEarlier FASTA sequence database for all CATH domains (based on COMBS sequence data). - data - true - bioinformatics + @@ -13479,12 +12461,11 @@ Sequence version information - edam - bioinformatics - data Information on an molecular sequence version. beta12orEarlier - data + + + @@ -13496,10 +12477,9 @@ A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty). beta12orEarlier - edam - bioinformatics - data - data + + + @@ -13510,15 +12490,12 @@ Protein report (function) beta12orEarlier - bioinformatics - edam Report on general functional properties of specific protein(s). beta13 For properties that can be mapped to a sequence, use 'Sequence report' instead. - data - data true + @@ -13528,17 +12505,13 @@ Gene name (ASPGD) - edam - true - 1.3 http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS - identifier - identifiers - data Name of a gene from Aspergillus Genome Database. + true beta12orEarlier - bioinformatics + 1.3 + @@ -13548,17 +12521,13 @@ Gene name (CGD) - data - http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS + 1.3 beta12orEarlier - identifier + http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS true - edam Name of a gene from Candida Genome Database. - identifiers - 1.3 - bioinformatics + @@ -13569,16 +12538,12 @@ Gene name (dictyBase) Name of a gene from dictyBase database. + true 1.3 beta12orEarlier - edam - identifiers - true - data - bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase - identifier + @@ -13588,18 +12553,14 @@ Gene name (EcoGene primary) - identifier - 1.3 + beta12orEarlier true + 1.3 EcoGene primary gene name - data - identifiers - Primary name of a gene from EcoGene Database. - edam - beta12orEarlier - bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G + Primary name of a gene from EcoGene Database. + @@ -13609,17 +12570,13 @@ Gene name (MaizeGDB) - identifier - bioinformatics - identifiers - edam - 1.3 - data beta12orEarlier true Name of a gene from MaizeGDB (maize genes) database. + 1.3 http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus + @@ -13629,17 +12586,13 @@ Gene name (SGD) - data - bioinformatics - beta12orEarlier - 1.3 - identifier - edam Name of a gene from Saccharomyces Genome Database. - identifiers http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS + beta12orEarlier + 1.3 true + @@ -13649,17 +12602,13 @@ Gene name (TGD) - data - true - identifiers - edam - identifier - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS - 1.3 + true Name of a gene from Tetrahymena Genome Database. - bioinformatics + 1.3 + beta12orEarlier + @@ -13670,16 +12619,12 @@ Gene name (CGSC) Symbol of a gene from E.coli Genetic Stock Center. - identifiers http://www.geneontology.org/doc/GO.xrf_abbs: CGSC + true 1.3 beta12orEarlier - bioinformatics - data - identifier - true - edam + @@ -13695,20 +12640,16 @@ HGNC:[0-9]{1,5} HUGO gene symbol HGNC gene name - edam - identifier http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene HUGO gene name - identifiers Official gene name - bioinformatics HGNC symbol true 1.3 HUGO symbol beta12orEarlier - data + @@ -13718,18 +12659,14 @@ Gene name (MGD) - identifier beta12orEarlier true 1.3 http://www.geneontology.org/doc/GO.xrf_abbs: MGD - MGI:[0-9]+ - bioinformatics - edam - identifiers - data Symbol of a gene from the Mouse Genome Database. + MGI:[0-9]+ + @@ -13739,17 +12676,13 @@ Gene name (Bacillus subtilis) - data - 1.3 true - edam - bioinformatics + 1.3 beta12orEarlier - identifier Symbol of a gene from Bacillus subtilis Genome Sequence Project. - identifiers http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG + @@ -13759,14 +12692,13 @@ Gene ID (PlasmoDB) - identifier http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB beta12orEarlier - bioinformatics Identifier of a gene from PlasmoDB Plasmodium Genome Resource. - identifiers - data - edam + + + + @@ -13776,15 +12708,14 @@ Gene ID (EcoGene) - data - EcoGene Accession - edam - identifiers - Identifier of a gene from EcoGene Database. - identifier beta12orEarlier EcoGene ID - bioinformatics + EcoGene Accession + Identifier of a gene from EcoGene Database. + + + + @@ -13795,14 +12726,13 @@ Gene ID (FlyBase) http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase - data http://www.geneontology.org/doc/GO.xrf_abbs: FB Gene identifier from FlyBase database. - bioinformatics beta12orEarlier - identifier - identifiers - edam + + + + @@ -13816,13 +12746,9 @@ Gene identifier from Glossina morsitans GeneDB database. beta13 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans - identifier true - bioinformatics - identifiers - data - edam + @@ -13832,17 +12758,13 @@ Gene ID (GeneDB Leishmania major) - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor + beta12orEarlier + beta13 true - bioinformatics - identifiers Gene identifier from Leishmania major GeneDB database. - data - beta13 - identifier - edam + @@ -13853,16 +12775,12 @@ Gene ID (GeneDB Plasmodium falciparum) beta12orEarlier - identifiers - edam - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum - Gene identifier from Plasmodium falciparum GeneDB database. - identifier beta13 - data + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum true - bioinformatics + Gene identifier from Plasmodium falciparum GeneDB database. + @@ -13872,17 +12790,13 @@ Gene ID (GeneDB Schizosaccharomyces pombe) - bioinformatics - identifier - edam + Gene identifier from Schizosaccharomyces pombe GeneDB database. + beta13 true http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe beta12orEarlier - Gene identifier from Schizosaccharomyces pombe GeneDB database. - beta13 - data - identifiers + @@ -13894,15 +12808,11 @@ http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei beta12orEarlier - identifier - true - edam - data - bioinformatics beta13 - identifiers + true Gene identifier from Trypanosoma brucei GeneDB database. + @@ -13915,12 +12825,11 @@ Gene identifier from Gramene database. http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE beta12orEarlier - bioinformatics - data - identifiers - identifier - edam http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene + + + + @@ -13930,15 +12839,14 @@ Gene ID (Virginia microbial) - bioinformatics - Gene identifier from Virginia Bioinformatics Institute microbial database. - identifiers - data - edam http://www.geneontology.org/doc/GO.xrf_abbs: VMD - identifier + Gene identifier from Virginia Bioinformatics Institute microbial database. http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD beta12orEarlier + + + + @@ -13949,13 +12857,12 @@ Gene ID (SGN) beta12orEarlier - identifiers - identifier Gene identifier from Sol Genomics Network. - edam - data - bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs: SGN + + + + @@ -13966,16 +12873,15 @@ Gene ID (WormBase) - identifier http://www.geneontology.org/doc/GO.xrf_abbs: WormBase Gene identifier used by WormBase database. beta12orEarlier - bioinformatics - edam http://www.geneontology.org/doc/GO.xrf_abbs: WB WBGene[0-9]{8} - data - identifiers + + + + @@ -13985,17 +12891,13 @@ Gene synonym - identifier - Any name (other than the recommended one) for a gene. - Gene name synonym - data - identifiers - bioinformatics beta12orEarlier beta12orEarlier - edam + Any name (other than the recommended one) for a gene. true + Gene name synonym + @@ -14007,12 +12909,11 @@ The name of an open reading frame attributed by a sequencing project. - identifier - edam - bioinformatics - identifiers beta12orEarlier - data + + + + @@ -14022,15 +12923,12 @@ Sequence assembly component - data - beta12orEarlier - edam - data beta12orEarlier - bioinformatics + beta12orEarlier true A component of a larger sequence assembly. + @@ -14041,14 +12939,11 @@ Chromosome annotation (aberration) A report on a chromosome aberration such as abnormalities in chromosome structure. + true beta12orEarlier beta12orEarlier - bioinformatics - edam - true - data - data + @@ -14058,13 +12953,12 @@ Clone ID - data - identifiers An identifier of a clone (cloned molecular sequence) from a database. - identifier - bioinformatics beta12orEarlier - edam + + + + @@ -14074,14 +12968,13 @@ PDB insertion code - edam An insertion code (part of the residue number) for an amino acid residue from a PDB file. - data - data PDBML:pdbx_PDB_ins_code WHATIF: insertion_code - bioinformatics beta12orEarlier + + + @@ -14093,12 +12986,11 @@ The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. beta12orEarlier - data The fraction of an atom type present at a site in a molecular structure. - bioinformatics - edam - data WHATIF: PDBx_occupancy + + + @@ -14108,13 +13000,12 @@ Isotropic B factor - bioinformatics beta12orEarlier WHATIF: PDBx_B_iso_or_equiv - data - edam - data Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. + + + @@ -14125,13 +13016,12 @@ Deletion map Deletion-based cytogenetic map - bioinformatics - edam A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. - data beta12orEarlier 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. - data + + + @@ -14142,12 +13032,11 @@ QTL map Quantitative trait locus map - bioinformatics - data beta12orEarlier - data A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. - edam + + + @@ -14157,13 +13046,12 @@ Haplotype map - data A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. - bioinformatics Moby:Haplotyping_Study_obj - data - edam beta12orEarlier + + + @@ -14173,14 +13061,13 @@ Map set - data - data Moby:GCP_CorrelatedMapSet - bioinformatics - edam Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. Moby:GCP_CorrelatedLinkageMapSet beta12orEarlier + + + @@ -14192,17 +13079,14 @@ Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. beta12orEarlier - edam Moby:MapFeature A feature which may mapped (positioned) on a genetic or other type of map. true - data beta12orEarlier - bioinformatics - data + @@ -14214,12 +13098,11 @@ beta12orEarlier - data - data - edam Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. A designation of the type of map (genetic map, physical map, sequence map etc) or map set. - bioinformatics + + + @@ -14229,13 +13112,12 @@ Protein fold name - bioinformatics beta12orEarlier - identifiers - edam - data The name of a protein fold. - identifier + + + + @@ -14247,16 +13129,15 @@ Moby:BriefTaxonConcept The name of a group of organisms belonging to the same taxonomic rank. - data For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - edam Taxonomic rank Taxonomy rank beta12orEarlier - identifiers Moby:PotentialTaxon - identifier - bioinformatics + + + + @@ -14272,13 +13153,12 @@ - edam - data - bioinformatics - identifier A unique identifier of a (group of) organisms. beta12orEarlier - identifiers + + + + @@ -14288,13 +13168,12 @@ Genus name - identifier The name of a genus of organism. - edam - identifiers - bioinformatics - data beta12orEarlier + + + + @@ -14305,20 +13184,19 @@ Taxonomic classification Moby:TaxonTCS - identifiers Moby:TaxonScientificName - identifier Taxonomic information - bioinformatics 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. Taxonomic name Moby:iANT_organism-xml - data The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. - edam beta12orEarlier Moby:GCP_Taxon Moby:TaxonName + + + + @@ -14328,14 +13206,13 @@ iHOP organism ID - identifier - data A unique identifier for an organism used in the iHOP database. Moby_namespace:iHOPorganism beta12orEarlier - edam - bioinformatics - identifiers + + + + @@ -14346,12 +13223,11 @@ Genbank common name beta12orEarlier - identifier Common name for an organism as used in the GenBank database. - edam - bioinformatics - data - identifiers + + + + @@ -14362,12 +13238,11 @@ NCBI taxon beta12orEarlier - identifier - data - edam - bioinformatics The name of a taxon from the NCBI taxonomy database. - identifiers + + + + @@ -14379,14 +13254,11 @@ An alternative for a word. true - data - edam - data beta12orEarlier - bioinformatics Alternative name beta12orEarlier + @@ -14396,15 +13268,12 @@ Misspelling - bioinformatics - edam - beta12orEarlier - data - data beta12orEarlier true + beta12orEarlier A common misspelling of a word. + @@ -14415,14 +13284,11 @@ Acronym beta12orEarlier - edam - data - bioinformatics + An abbreviation of a phrase or word. beta12orEarlier true - data - An abbreviation of a phrase or word. + @@ -14432,15 +13298,12 @@ Misnomer - bioinformatics - edam + true beta12orEarlier beta12orEarlier - data - true A term which is likely to be misleading of its meaning. - data + @@ -14452,12 +13315,11 @@ beta12orEarlier Moby:Author - identifiers - edam - data - identifier Information on the authors of a published work. - bioinformatics + + + + @@ -14467,13 +13329,12 @@ DragonDB author identifier - data - edam - identifiers - bioinformatics beta12orEarlier - identifier An identifier representing an author in the DragonDB database. + + + + @@ -14485,12 +13346,11 @@ Moby:DescribedLink - data - data - bioinformatics A URI along with annotation describing the data found at the address. - edam beta12orEarlier + + + @@ -14500,15 +13360,12 @@ UniProt keywords - bioinformatics - data - beta12orEarlier - data A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. + beta12orEarlier beta12orEarlier true - edam + @@ -14518,14 +13375,13 @@ Gene ID (GeneFarm) - edam beta12orEarlier Identifier of a gene from the GeneFarm database. - identifiers - bioinformatics - identifier Moby_namespace:GENEFARM_GeneID - data + + + + @@ -14535,14 +13391,13 @@ Blattner number - edam - data The blattner identifier for a gene. Moby_namespace:Blattner_number - identifiers - identifier - bioinformatics beta12orEarlier + + + + @@ -14552,18 +13407,14 @@ Gene ID (MIPS Maize) - bioinformatics - edam - identifiers - data true - identifier beta13 Moby_namespace:MIPS_GE_Maize beta12orEarlier Identifier for genetic elements in MIPS Maize database. MIPS genetic element identifier (Maize) + @@ -14573,18 +13424,14 @@ Gene ID (MIPS Medicago) - bioinformatics - beta13 - identifier - beta12orEarlier - MIPS genetic element identifier (Medicago) Identifier for genetic elements in MIPS Medicago database. Moby_namespace:MIPS_GE_Medicago true - data - edam - identifiers + beta13 + beta12orEarlier + MIPS genetic element identifier (Medicago) + @@ -14594,17 +13441,13 @@ Gene name (DragonDB) - beta12orEarlier - edam - true - Moby_namespace:DragonDB_Gene 1.3 - bioinformatics - identifiers - data + Moby_namespace:DragonDB_Gene + beta12orEarlier The name of an Antirrhinum Gene from the DragonDB database. - identifier + true + @@ -14615,16 +13458,12 @@ Gene name (Arabidopsis) 1.3 - edam - true - bioinformatics - data beta12orEarlier - identifier A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. - identifiers + true Moby_namespace:ArabidopsisGeneSymbol + @@ -14637,13 +13476,12 @@ beta12orEarlier - identifiers - bioinformatics - edam Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. - identifier - data + + + + @@ -14653,18 +13491,14 @@ Gene name (GeneFarm) - identifiers - edam + beta12orEarlier GeneFarm gene ID Moby_namespace:GENEFARM_GeneName - bioinformatics - beta12orEarlier - identifier - data + Name of a gene from the GeneFarm database. 1.3 true - Name of a gene from the GeneFarm database. + @@ -14681,15 +13515,14 @@ - edam beta12orEarlier - identifiers 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. - data - identifier - bioinformatics Locus identifier Locus name + + + + @@ -14700,18 +13533,17 @@ Locus ID (AGI) AGI identifier - identifiers - identifier beta12orEarlier AGI locus code Arabidopsis gene loci number - edam - bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) AGI ID - data AT[1-5]G[0-9]{5} + + + + @@ -14723,13 +13555,12 @@ Identifier for loci from ASPGD (Aspergillus Genome Database). http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID - data beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD - bioinformatics - identifier - identifiers - edam + + + + @@ -14739,14 +13570,13 @@ Locus ID (MGG) - edam - identifiers http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG beta12orEarlier - identifier - bioinformatics Identifier for loci from Magnaporthe grisea Database at the Broad Institute. - data + + + + @@ -14757,16 +13587,15 @@ Locus ID (CGD) http://www.geneontology.org/doc/GO.xrf_abbs: CGD - data CGDID - bioinformatics beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: CGDID CGD locus identifier - edam - identifiers - identifier Identifier for loci from CGD (Candida Genome Database). + + + + @@ -14776,15 +13605,14 @@ Locus ID (CMR) + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. - data - edam http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR - bioinformatics - beta12orEarlier - identifiers - identifier + + + + @@ -14794,16 +13622,15 @@ NCBI locus tag - identifier - data - bioinformatics Identifier for loci from NCBI database. http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag - identifiers - edam Locus ID (NCBI) Moby_namespace:LocusID beta12orEarlier + + + + @@ -14815,15 +13642,14 @@ SGDID - bioinformatics - identifier Identifier for loci from SGD (Saccharomyces Genome Database). - identifiers - data http://www.geneontology.org/doc/GO.xrf_abbs: SGD beta12orEarlier - edam http://www.geneontology.org/doc/GO.xrf_abbs: SGDID + + + + @@ -14833,14 +13659,13 @@ Locus ID (MMP) - bioinformatics beta12orEarlier - identifiers Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. - identifier - edam - data + + + + @@ -14850,14 +13675,13 @@ Locus ID (DictyBase) - identifier - bioinformatics - identifiers - data Identifier of locus from DictyBase (Dictyostelium discoideum). beta12orEarlier - edam Moby_namespace:DDB_gene + + + + @@ -14868,14 +13692,13 @@ Locus ID (EntrezGene) Moby_namespace:EntrezGene_EntrezGeneID - identifiers - beta12orEarlier - edam - identifier Moby_namespace:EntrezGene_ID - data + beta12orEarlier Identifier of a locus from EntrezGene database. - bioinformatics + + + + @@ -14885,14 +13708,13 @@ Locus ID (MaizeGDB) - identifier - edam - identifiers beta12orEarlier Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). - bioinformatics - data + + + + @@ -14903,17 +13725,14 @@ Quantitative trait locus Moby:SO_QTL - edam true A QTL sometimes but does not necessarily correspond to a gene. - data 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). - data beta12orEarlier beta12orEarlier QTL - bioinformatics + @@ -14923,14 +13742,13 @@ Gene ID (KOME) - data - bioinformatics - edam Moby_namespace:GeneId beta12orEarlier - identifier - identifiers Identifier of a gene from the KOME database. + + + + @@ -14940,14 +13758,13 @@ Locus ID (Tropgene) - data - identifiers - edam beta12orEarlier Moby:Tropgene_locus Identifier of a locus from the Tropgene database. - identifier - bioinformatics + + + + @@ -14957,12 +13774,11 @@ Alignment - bioinformatics - data - data beta12orEarlier - edam An alignment of molecular sequences, structures or profiles derived from them. + + + @@ -14972,13 +13788,12 @@ Atomic property - bioinformatics - data beta12orEarlier - edam Data for an atom (in a molecular structure). - data General atomic property + + + @@ -14990,12 +13805,11 @@ http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW Moby_namespace:SP_KW - data A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. - data - bioinformatics - edam beta12orEarlier + + + @@ -15005,16 +13819,12 @@ Ordered locus name - edam beta12orEarlier 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. - bioinformatics true - identifiers - data - identifier beta12orEarlier + @@ -15026,25 +13836,24 @@ - Moby:GCP_MapInterval - beta12orEarlier - Moby:HitPosition - bioinformatics - Moby:Position - Map position PDBML:_atom_site.id Moby:GCP_MapPoint Moby:GCP_MapPosition + Moby:GCP_MapInterval + beta12orEarlier Moby:Locus Moby:MapPosition + Moby:HitPosition 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. Moby:GenePosition - data A position in a map (for example a genetic map), either a single position (point) or a region / interval. - data - edam Sequence co-ordinates Locus + Moby:Position + Map position + + + @@ -15056,11 +13865,10 @@ Amino acid data beta12orEarlier - data - edam - data - bioinformatics Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. + + + @@ -15071,15 +13879,12 @@ 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. - bioinformatics - beta12orEarlier - data - data - This is a broad data type and is used a placeholder for other, more specific types. beta13 - edam + This is a broad data type and is used a placeholder for other, more specific types. true + beta12orEarlier + @@ -15095,12 +13900,11 @@ - bioinformatics beta12orEarlier - data An attribute of a molecular map (genetic or physical). - edam - data + + + @@ -15111,14 +13915,11 @@ Vienna RNA structural data beta12orEarlier - edam beta12orEarlier - bioinformatics Data used by the Vienna RNA analysis package. true - data - data + @@ -15128,12 +13929,11 @@ Sequence mask parameter - data Data used to replace (mask) characters in a molecular sequence. - bioinformatics - edam - data beta12orEarlier + + + @@ -15145,11 +13945,10 @@ This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier - edam Data concerning chemical reaction(s) catalysed by enzyme(s). - data - data - bioinformatics + + + @@ -15159,12 +13958,11 @@ Michaelis Menten plot - edam beta12orEarlier - data 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. - data - bioinformatics + + + @@ -15175,11 +13973,10 @@ 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). - edam - data - bioinformatics beta12orEarlier - data + + + @@ -15190,17 +13987,14 @@ Experimental data Experimental measurement data - edam - data beta13 - bioinformatics beta12orEarlier Raw data from or annotation on laboratory experiments. true 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. - data + @@ -15212,11 +14006,10 @@ Information on a genome version. - data - bioinformatics beta12orEarlier - edam - data + + + @@ -15227,11 +14020,10 @@ Evidence beta12orEarlier - bioinformatics - data - data - edam 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. + + + @@ -15241,12 +14033,11 @@ Sequence record lite - data - edam - bioinformatics A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - data beta12orEarlier + + + @@ -15262,14 +14053,13 @@ - edam - data One or more molecular sequences, possibly with associated annotation. - data - beta12orEarlier 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. - bioinformatics + beta12orEarlier + + + @@ -15281,12 +14071,11 @@ Sequence record lite (nucleic acid) - bioinformatics - edam - data A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - data beta12orEarlier + + + @@ -15298,11 +14087,10 @@ A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - data beta12orEarlier - edam - bioinformatics - data + + + @@ -15313,16 +14101,15 @@ Report beta12orEarlier - data document - data This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. - bioinformatics Document - edam A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself. Text + + + @@ -15333,13 +14120,12 @@ Molecular property (general) - data beta12orEarlier General data for a molecule. - bioinformatics General molecular property - data - edam + + + @@ -15349,17 +14135,14 @@ Structural data - edam beta13 Data concerning molecular structural data. true - data - data beta12orEarlier - bioinformatics This is a broad data type and is used a placeholder for other, more specific types. + @@ -15369,12 +14152,11 @@ Sequence motif (nucleic acid) - bioinformatics beta12orEarlier - data - data - edam A nucleotide sequence motif. + + + @@ -15384,12 +14166,11 @@ Sequence motif (protein) - edam An amino acid sequence motif. - bioinformatics beta12orEarlier - data - data + + + @@ -15399,12 +14180,11 @@ Search parameter - data - data Some simple value controlling a search operation, typically a search of a database. beta12orEarlier - edam - bioinformatics + + + @@ -15414,12 +14194,11 @@ Database hits - edam - data - bioinformatics A report of hits from searching a database of some type. beta12orEarlier - data + + + @@ -15431,10 +14210,9 @@ The secondary structure assignment (predicted or real) of a nucleic acid or protein. beta12orEarlier - data - data - edam - bioinformatics + + + @@ -15445,12 +14223,11 @@ Matrix An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences. - bioinformatics - data This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier - data - edam + + + @@ -15461,12 +14238,11 @@ Alignment report This is a broad data type and is used a placeholder for other, more specific types. - edam - data An informative report about a molecular alignment of some type, including alignment-derived data or metadata. - bioinformatics beta12orEarlier - data + + + @@ -15476,12 +14252,11 @@ Nucleic acid report - data - bioinformatics beta12orEarlier - data - edam An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. + + + @@ -15492,12 +14267,11 @@ Structure report Structure-derived report - data beta12orEarlier - bioinformatics An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. - data - edam + + + @@ -15509,14 +14283,13 @@ 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). - data beta12orEarlier Nucleic acid property (structural) - bioinformatics Nucleic acid structural property This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. - edam - data + + + @@ -15526,14 +14299,13 @@ Molecular property - bioinformatics - data Physicochemical property - data - edam A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. SO:0000400 beta12orEarlier + + + @@ -15544,12 +14316,11 @@ DNA base structural data - data - edam beta12orEarlier - data Structural data for DNA base pairs or runs of bases, such as energy or angle data. - bioinformatics + + + @@ -15560,12 +14331,11 @@ Database entry version information - edam - data 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. - data beta12orEarlier - bioinformatics + + + @@ -15575,13 +14345,12 @@ Accession - identifier - data - bioinformatics A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. beta12orEarlier - edam - identifiers + + + + @@ -15593,15 +14362,14 @@ Nucleic acid features (SNP) - An SNP is an individual point mutation or substitution of a single nucleotide. - beta12orEarlier - data - edam - data SNP annotation + An SNP is an individual point mutation or substitution of a single nucleotide. Single nucleotide polymorphism Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence. - bioinformatics + beta12orEarlier + + + @@ -15612,12 +14380,11 @@ Data reference beta12orEarlier - data Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. - edam - bioinformatics A list of database accessions or identifiers are usually included. - data + + + @@ -15627,13 +14394,12 @@ Job identifier - identifier - identifiers - edam beta12orEarlier - bioinformatics - data An identifier of a submitted job. + + + + @@ -15645,13 +14411,12 @@ Name Symbolic name - identifiers A name of a thing, which need not necessarily uniquely identify it. beta12orEarlier - identifier - edam - data - bioinformatics + + + + @@ -15670,12 +14435,11 @@ Type - data - data beta12orEarlier - edam A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). - bioinformatics + + + @@ -15686,13 +14450,12 @@ User ID - edam - bioinformatics - identifier - data beta12orEarlier An identifier of a software end-user (typically a person). - identifiers + + + + @@ -15703,13 +14466,12 @@ KEGG organism code - edam A three-letter code used in the KEGG databases to uniquely identify organisms. beta12orEarlier - bioinformatics - identifier - identifiers - data + + + + @@ -15719,19 +14481,15 @@ Gene name (KEGG GENES) - identifiers - edam Moby_namespace:GeneId Name of an entry (gene) from the KEGG GENES database. - data 1.3 - bioinformatics true - identifier [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* KEGG GENES entry name beta12orEarlier + @@ -15742,13 +14500,12 @@ BioCyc ID - edam - identifiers - bioinformatics beta12orEarlier Identifier of an object from one of the BioCyc databases. - identifier - data + + + + @@ -15759,15 +14516,14 @@ Compound ID (BioCyc) - edam beta12orEarlier Identifier of a compound from the BioCyc chemical compounds database. - identifier - bioinformatics BioCyc compound identifier - identifiers - data BioCyc compound ID + + + + @@ -15784,13 +14540,12 @@ - identifiers - bioinformatics - beta12orEarlier - edam - data Identifier of a biological reaction from the BioCyc reactions database. - identifier + beta12orEarlier + + + + @@ -15801,14 +14556,13 @@ Enzyme ID (BioCyc) + Identifier of an enzyme from the BioCyc enzymes database. beta12orEarlier BioCyc enzyme ID - edam - identifier - Identifier of an enzyme from the BioCyc enzymes database. - data - identifiers - bioinformatics + + + + @@ -15825,13 +14579,12 @@ - identifier Identifier of a biological reaction from a database. - edam - bioinformatics - identifiers beta12orEarlier - data + + + + @@ -15841,14 +14594,13 @@ Identifier (hybrid) - edam beta12orEarlier 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'. An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). - identifiers - data - bioinformatics - identifier + + + + @@ -15864,13 +14616,12 @@ - identifiers - bioinformatics Identifier of a molecular property. - edam - data beta12orEarlier - identifier + + + + @@ -15893,13 +14644,12 @@ Codon usage table identifier - data - identifier - edam - bioinformatics beta12orEarlier - identifiers Identifier of a codon usage table, for example a genetic code. + + + + @@ -15910,12 +14660,11 @@ FlyBase primary identifier Primary identifier of an object from the FlyBase database. - identifiers - bioinformatics - identifier - edam - data beta12orEarlier + + + + @@ -15925,13 +14674,12 @@ WormBase identifier - identifier - identifiers Identifier of an object from the WormBase database. beta12orEarlier - bioinformatics - data - edam + + + + @@ -15942,14 +14690,13 @@ WormBase wormpep ID - bioinformatics beta12orEarlier CE[0-9]{5} - identifiers Protein identifier used by WormBase database. - edam - identifier - data + + + + @@ -15960,14 +14707,11 @@ Nucleic acid features (codon) beta12orEarlier - data - data - 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. - bioinformatics true + 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. beta12orEarlier - edam + @@ -15983,13 +14727,12 @@ - data - identifiers - identifier - edam - bioinformatics beta12orEarlier An identifier of a map of a molecular sequence. + + + + @@ -15999,13 +14742,12 @@ Person identifier - identifiers beta12orEarlier - bioinformatics - edam - data An identifier of a software end-user (typically a person). - identifier + + + + @@ -16021,13 +14763,12 @@ - identifiers - bioinformatics beta12orEarlier - edam - identifier - data Name or other identifier of a nucleic acid molecule. + + + + @@ -16037,12 +14778,11 @@ Translation frame specification - edam - data Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). - data - bioinformatics beta12orEarlier + + + @@ -16058,13 +14798,12 @@ - bioinformatics - data - identifier - identifiers beta12orEarlier An identifier of a genetic code. - edam + + + + @@ -16075,13 +14814,12 @@ Genetic code name - bioinformatics - identifier - identifiers beta12orEarlier - data Informal name for a genetic code, typically an organism name. - edam + + + + @@ -16091,13 +14829,13 @@ File format name + beta12orEarlier - bioinformatics - identifiers Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. - edam - identifier - data + + + + @@ -16110,10 +14848,9 @@ beta12orEarlier A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. - data - edam - bioinformatics - data + + + @@ -16123,13 +14860,12 @@ Operating system name - bioinformatics Name of a computer operating system such as Linux, PC or Mac. beta12orEarlier - edam - identifier - data - identifiers + + + + @@ -16139,15 +14875,12 @@ Mutation type - bioinformatics - true - data - data - beta12orEarlier A type of point or block mutation, including insertion, deletion, change, duplication and moves. beta12orEarlier - edam + true + beta12orEarlier + @@ -16157,13 +14890,12 @@ Logical operator - data - edam - bioinformatics - identifier A logical operator such as OR, AND, XOR, and NOT. - identifiers beta12orEarlier + + + + @@ -16173,13 +14905,12 @@ Results sort order - bioinformatics A control of the order of data that is output, for example the order of sequences in an alignment. - edam - data - data beta12orEarlier Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. + + + @@ -16189,15 +14920,12 @@ Toggle - edam beta12orEarlier - data - data true - bioinformatics A simple parameter that is a toggle (boolean value), typically a control for a modal tool. beta12orEarlier + @@ -16209,13 +14937,10 @@ The width of an output sequence or alignment. beta12orEarlier - bioinformatics - data - edam - true beta12orEarlier - data + true + @@ -16226,11 +14951,10 @@ Gap penalty A penalty for introducing or extending a gap in an alignment. - data beta12orEarlier - data - edam - bioinformatics + + + @@ -16241,12 +14965,11 @@ Nucleic acid melting temperature Melting temperature - data - data A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. - bioinformatics - edam beta12orEarlier + + + @@ -16256,12 +14979,11 @@ Concentration - data - data The concentration of a chemical compound. beta12orEarlier - bioinformatics - edam + + + @@ -16272,11 +14994,10 @@ Window step size Size of the incremental 'step' a sequence window is moved over a sequence. - bioinformatics - data beta12orEarlier - data - edam + + + @@ -16287,14 +15008,11 @@ EMBOSS graph An image of a graph generated by the EMBOSS suite. + beta12orEarlier true beta12orEarlier - bioinformatics - beta12orEarlier - data - data - edam + @@ -16304,15 +15022,12 @@ EMBOSS report - edam - An application report generated by the EMBOSS suite. - bioinformatics true beta12orEarlier - data beta12orEarlier - data + An application report generated by the EMBOSS suite. + @@ -16324,11 +15039,10 @@ An offset for a single-point sequence position. - data - edam - data beta12orEarlier - bioinformatics + + + @@ -16338,12 +15052,11 @@ Threshold - edam A value that serves as a threshold for a tool (usually to control scoring or output). beta12orEarlier - data - data - bioinformatics + + + @@ -16353,17 +15066,14 @@ Protein report (transcription factor) - data - edam - An informative report on a transcription factor protein. - true - data beta12orEarlier Transcription factor binding site data + 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. - bioinformatics beta13 + true + @@ -16373,16 +15083,12 @@ Database category name - identifiers beta12orEarlier - identifier + beta12orEarlier The name of a category of biological or bioinformatics database. true - edam - bioinformatics - beta12orEarlier - data + @@ -16392,16 +15098,12 @@ Sequence profile name - data - bioinformatics - edam - identifier - Name of a sequence profile. - beta12orEarlier beta12orEarlier - identifiers true + Name of a sequence profile. + beta12orEarlier + @@ -16414,12 +15116,9 @@ beta12orEarlier true beta12orEarlier - data Specification of one or more colors. - data - edam - bioinformatics + @@ -16432,11 +15131,10 @@ Graphics parameter Graphical parameter A parameter that is used to control rendering (drawing) to a device or image. - bioinformatics - data beta12orEarlier - data - edam + + + @@ -16447,13 +15145,12 @@ Sequence name - identifier - data - edam - bioinformatics - identifiers Any arbitrary name of a molecular sequence. beta12orEarlier + + + + @@ -16463,12 +15160,11 @@ Date - edam beta12orEarlier - data A temporal date. - bioinformatics - data + + + @@ -16478,16 +15174,13 @@ Word composition - true - edam - beta12orEarlier beta12orEarlier - data - bioinformatics + true Word composition data for a molecular sequence. - data + beta12orEarlier + @@ -16497,12 +15190,11 @@ Fickett testcode plot - data beta12orEarlier - data A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. - edam - bioinformatics + + + @@ -16510,14 +15202,16 @@ - Sequence similarity plot + Sequence similarity report A plot of sequence similarities identified from word-matching or character comparison. - bioinformatics - data + Sequence similarity plot + Sequence conservation report + 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. beta12orEarlier - edam - data + + + @@ -16528,11 +15222,10 @@ Helical wheel An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. - bioinformatics - edam - data beta12orEarlier - data + + + @@ -16542,13 +15235,12 @@ Helical net - edam 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. - bioinformatics - data Useful for highlighting amphipathicity and other properties. beta12orEarlier - data + + + @@ -16559,14 +15251,11 @@ Protein sequence properties plot A plot of general physicochemical properties of a protein sequence. - data - beta12orEarlier - data - edam beta12orEarlier + beta12orEarlier true - bioinformatics + @@ -16576,12 +15265,11 @@ Protein ionization curve - data A plot of pK versus pH for a protein. - bioinformatics beta12orEarlier - data - edam + + + @@ -16593,10 +15281,9 @@ A plot of character or word composition / frequency of a molecular sequence. beta12orEarlier - data - edam - bioinformatics - data + + + @@ -16606,12 +15293,11 @@ Nucleic acid density plot - edam - data - data Density plot (of base composition) for a nucleotide sequence. beta12orEarlier - bioinformatics + + + @@ -16621,12 +15307,11 @@ Sequence trace image - bioinformatics beta12orEarlier - data - edam Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). - data + + + @@ -16643,11 +15328,10 @@ A report on siRNA duplexes in mRNA. - bioinformatics - data - data beta12orEarlier - edam + + + @@ -16657,16 +15341,13 @@ Sequence set (stream) - data - data - true - This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. - beta12orEarlier - edam - bioinformatics beta12orEarlier 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 + beta12orEarlier + @@ -16677,13 +15358,12 @@ FlyBase secondary identifier beta12orEarlier - identifier - identifiers - bioinformatics Secondary identifier are used to handle entries that were merged with or split from other entries in the database. Secondary identifier of an object from the FlyBase database. - edam - data + + + + @@ -16694,13 +15374,10 @@ Cardinality beta12orEarlier - data true beta12orEarlier - edam - data - bioinformatics The number of a certain thing. + @@ -16711,13 +15388,10 @@ Exactly 1 true - bioinformatics - edam A single thing. - data - data beta12orEarlier beta12orEarlier + @@ -16728,13 +15402,10 @@ 1 or more beta12orEarlier - edam - bioinformatics true beta12orEarlier One or more things. - data - data + @@ -16744,14 +15415,11 @@ Exactly 2 - data beta12orEarlier - edam true beta12orEarlier - bioinformatics Exactly two things. - data + @@ -16761,14 +15429,11 @@ 2 or more - data - edam - data true beta12orEarlier - bioinformatics beta12orEarlier Two or more things. + @@ -16780,15 +15445,14 @@ Hash - edam Hash code A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. - data Hash value - bioinformatics Hash sum - data beta12orEarlier + + + @@ -16798,15 +15462,14 @@ Protein features (chemical modification) + Protein modification annotation GO:0006464 - edam - data MOD:00000 - bioinformatics - Protein modification annotation - Data on a chemical modification of a protein. - data beta12orEarlier + A report on a chemical modification of a protein. + + + @@ -16816,12 +15479,11 @@ Error - data - data - bioinformatics Data on an error generated by computer system or tool. beta12orEarlier - edam + + + @@ -16831,12 +15493,11 @@ Database entry metadata - data - bioinformatics Basic information on any arbitrary database entry. - edam - data beta12orEarlier + + + @@ -16847,14 +15508,11 @@ Gene cluster A cluster of similar genes. - edam + beta12orEarlier true beta13 - bioinformatics - beta12orEarlier - data - data + @@ -16866,12 +15524,11 @@ SO:2000061 A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - data beta12orEarlier - edam - bioinformatics - data + + + @@ -16881,13 +15538,12 @@ Plasmid identifier - data beta12orEarlier - identifier An identifier of a plasmid in a database. - bioinformatics - edam - identifiers + + + + @@ -16900,11 +15556,10 @@ A unique identifier of a specific mutation catalogued in a database. beta12orEarlier - identifier - identifiers - bioinformatics - edam - data + + + + @@ -16914,15 +15569,12 @@ Mutation annotation (basic) - data - beta12orEarlier beta12orEarlier true - edam - data - bioinformatics + beta12orEarlier 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. + @@ -16932,15 +15584,12 @@ Mutation annotation (prevalence) - edam - data beta12orEarlier An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. - data - beta12orEarlier true - bioinformatics + beta12orEarlier + @@ -16950,15 +15599,12 @@ Mutation annotation (prognostic) - data true beta12orEarlier - beta12orEarlier - bioinformatics An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. - edam - data + beta12orEarlier + @@ -16968,15 +15614,12 @@ Mutation annotation (functional) - data - edam - true - 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. beta12orEarlier - data beta12orEarlier - bioinformatics + true + 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. + @@ -16986,12 +15629,11 @@ Codon number - data - data The number of a codon, for instance, at which a mutation is located. - bioinformatics beta12orEarlier - edam + + + @@ -17000,13 +15642,13 @@ Tumor annotation - + beta12orEarlier 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. - bioinformatics - edam - data - data + 1.4 + true + + @@ -17016,12 +15658,11 @@ Server metadata - bioinformatics - edam beta12orEarlier - data Basic information about a server on the web, such as an SRS server. - data + + + @@ -17031,13 +15672,12 @@ Database field name - identifier beta12orEarlier - data - identifiers - bioinformatics The name of a field in a database. - edam + + + + @@ -17047,14 +15687,13 @@ Sequence cluster ID (SYSTERS) - identifier - edam - bioinformatics - data beta12orEarlier - identifiers SYSTERS cluster ID Unique identifier of a sequence cluster from the SYSTERS database. + + + + @@ -17070,12 +15709,11 @@ - bioinformatics - data - edam - data Data concerning a biological ontology. beta12orEarlier + + + @@ -17085,16 +15723,13 @@ Raw SCOP domain classification + These are the parsable data files provided by SCOP. + beta13 Raw SCOP domain classification data files. beta12orEarlier true - These are the parsable data files provided by SCOP. - beta13 - data - data - bioinformatics - edam + @@ -17105,15 +15740,12 @@ Raw CATH domain classification beta12orEarlier - bioinformatics - data - beta13 - Raw CATH domain classification data files. - data true + beta13 These are the parsable data files provided by CATH. - edam + Raw CATH domain classification data files. + @@ -17122,13 +15754,13 @@ Heterogen annotation - - bioinformatics - edam - data + An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. beta12orEarlier - data + true + 1.4 + + @@ -17140,13 +15772,10 @@ beta12orEarlier true - data - data - bioinformatics Phylogenetic property values data. - edam beta12orEarlier + @@ -17157,12 +15786,11 @@ Sequence set (bootstrapped) A collection of sequences output from a bootstrapping (resampling) procedure. - data - bioinformatics - data Bootstrapping is often performed in phylogenetic analysis. beta12orEarlier - edam + + + @@ -17173,14 +15801,11 @@ Phylogenetic consensus tree beta12orEarlier - bioinformatics - data beta12orEarlier A consensus phylogenetic tree derived from comparison of multiple trees. true - edam - data + @@ -17190,12 +15815,11 @@ Schema - edam - data A data schema for organising or transforming data of some type. - data - bioinformatics beta12orEarlier + + + @@ -17205,12 +15829,11 @@ DTD - edam beta12orEarlier - data - bioinformatics A DTD (document type definition). - data + + + @@ -17220,13 +15843,12 @@ XML Schema - edam - data - data An XML Schema. XSD beta12orEarlier - bioinformatics + + + @@ -17236,12 +15858,11 @@ Relax-NG schema - edam - data A relax-NG schema. - bioinformatics - data beta12orEarlier + + + @@ -17251,12 +15872,11 @@ XSLT stylesheet - data - data An XSLT stylesheet. beta12orEarlier - edam - bioinformatics + + + @@ -17268,12 +15888,11 @@ The name of a data type. - identifier beta12orEarlier - identifiers - bioinformatics - data - edam + + + + @@ -17283,13 +15902,12 @@ OBO file format name - bioinformatics beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. - edam - identifiers - identifier - data + + + + @@ -17301,12 +15919,11 @@ MIPS genetic element identifier beta12orEarlier - identifiers - data - bioinformatics Identifier for genetic elements in MIPS database. - identifier - edam + + + + @@ -17317,15 +15934,11 @@ Sequence identifier (protein) true - identifier - data - beta12orEarlier - edam - identifiers beta12orEarlier - bioinformatics + beta12orEarlier An identifier of protein sequence(s) or protein sequence database entries. + @@ -17336,15 +15949,11 @@ Sequence identifier (nucleic acid) beta12orEarlier + beta12orEarlier true - identifiers An identifier of nucleotide sequence(s) or nucleotide sequence database entries. - edam - beta12orEarlier - identifier - data - bioinformatics + @@ -17354,16 +15963,15 @@ EMBL accession - edam - data - An accession number of an entry from the EMBL sequence database. - EMBL accession number EMBL identifier + EMBL accession number + An accession number of an entry from the EMBL sequence database. beta12orEarlier EMBL ID - identifiers - bioinformatics - identifier + + + + @@ -17379,17 +15987,16 @@ - edam UniProt entry name - data UniProt identifier beta12orEarlier - bioinformatics UniProtKB entry name An identifier of a polypeptide in the UniProt database. - identifier UniProtKB identifier - identifiers + + + + @@ -17399,16 +16006,15 @@ GenBank accession - bioinformatics GenBank identifier - identifiers GenBank ID GenBank accession number beta12orEarlier - edam - data Accession number of an entry from the GenBank sequence database. - identifier + + + + @@ -17418,16 +16024,15 @@ Gramene secondary identifier - identifier Gramene secondary ID Secondary (internal) identifier of a Gramene database entry. - identifiers - edam Gramene internal ID - bioinformatics - data Gramene internal identifier beta12orEarlier + + + + @@ -17438,13 +16043,12 @@ Sequence variation ID - bioinformatics - identifier beta12orEarlier - identifiers - data An identifier of an entry from a database of molecular sequence variation. - edam + + + + @@ -17455,15 +16059,14 @@ Gene ID - identifiers - identifier beta12orEarlier Gene accession Gene code - bioinformatics A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. - edam - data + + + + @@ -17473,17 +16076,13 @@ Gene name (AceView) - Name of an entry (gene) from the AceView genes database. - AceView gene name - data beta12orEarlier - edam - identifier + Name of an entry (gene) from the AceView genes database. true - identifiers 1.3 - bioinformatics + AceView gene name + @@ -17495,14 +16094,13 @@ http://www.geneontology.org/doc/GO.xrf_abbs: ECK E. coli K-12 gene identifier - identifier Identifier of an E. coli K-12 gene from EcoGene Database. - data - edam - bioinformatics beta12orEarlier ECK accession - identifiers + + + + @@ -17512,14 +16110,13 @@ Gene ID (HGNC) - bioinformatics - identifier - edam Identifier for a gene approved by the HUGO Gene Nomenclature Committee. beta12orEarlier - data HGNC ID - identifiers + + + + @@ -17531,13 +16128,12 @@ beta12orEarlier - identifiers 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. - bioinformatics - edam - data - identifier + + + + @@ -17547,17 +16143,13 @@ Gene name (NCBI) - edam true Name of an entry (gene) from the NCBI genes database. - bioinformatics 1.3 - data - beta12orEarlier - identifier NCBI gene name - identifiers + beta12orEarlier + @@ -17567,12 +16159,11 @@ SMILES string - edam - data beta12orEarlier A specification of a chemical structure in SMILES format. - bioinformatics - data + + + @@ -17583,12 +16174,11 @@ STRING ID beta12orEarlier - identifier - data - bioinformatics Unique identifier of an entry from the STRING database of protein-protein interactions. - identifiers - edam + + + + @@ -17597,13 +16187,13 @@ Virus annotation - + beta12orEarlier - bioinformatics - data - data - edam + 1.4 + true An informative report on a specific virus. + + @@ -17612,13 +16202,13 @@ Virus annotation (taxonomy) - - edam + + 1.4 + true beta12orEarlier - data - data An informative report on the taxonomy of a specific virus. - bioinformatics + + @@ -17628,14 +16218,13 @@ Reaction ID (SABIO-RK) - bioinformatics - data [0-9]+ - edam beta12orEarlier - identifier Identifier of a biological reaction from the SABIO-RK reactions database. - identifiers + + + + @@ -17645,12 +16234,11 @@ Carbohydrate structure report - data - bioinformatics - edam beta12orEarlier - data Annotation on or information derived from one or more specific carbohydrate 3D structure(s). + + + @@ -17660,16 +16248,15 @@ GI number - edam - identifiers - bioinformatics 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. 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 - data - identifier beta12orEarlier + + + + @@ -17681,14 +16268,13 @@ accession.version 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. - identifier beta12orEarlier 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. - identifiers - bioinformatics - edam NCBI accession.version - data + + + + @@ -17698,13 +16284,12 @@ Cell line name - edam - data The name of a cell line. - bioinformatics - identifier beta12orEarlier - identifiers + + + + @@ -17715,12 +16300,11 @@ Cell line name (exact) The name of a cell line. - data beta12orEarlier - identifier - edam - identifiers - bioinformatics + + + + @@ -17730,13 +16314,12 @@ Cell line name (truncated) - data - identifiers - identifier - edam beta12orEarlier The name of a cell line. - bioinformatics + + + + @@ -17746,13 +16329,12 @@ Cell line name (no punctuation) - identifiers beta12orEarlier - edam - data - bioinformatics - identifier The name of a cell line. + + + + @@ -17762,13 +16344,12 @@ Cell line name (assonant) - edam - bioinformatics beta12orEarlier - data - identifier The name of a cell line. - identifiers + + + + @@ -17780,13 +16361,12 @@ Enzyme accession - beta12orEarlier - identifiers A unique, persistent identifier of an enzyme. - data - identifier - bioinformatics - edam + beta12orEarlier + + + + @@ -17796,13 +16376,12 @@ REBASE enzyme number - edam - data beta12orEarlier - bioinformatics - identifiers Identifier of an enzyme from the REBASE enzymes database. - identifier + + + + @@ -17812,14 +16391,13 @@ DrugBank ID - edam - bioinformatics Unique identifier of a drug from the DrugBank database. DB[0-9]{5} - identifier - identifiers - data beta12orEarlier + + + + @@ -17831,14 +16409,13 @@ 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. - bioinformatics - edam - identifier beta12orEarlier protein gi - identifiers protein gi number - data + + + + @@ -17848,13 +16425,12 @@ Bit score - data beta12orEarlier - data Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. - edam A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. - bioinformatics + + + @@ -17865,13 +16441,12 @@ Translation phase specification - data - bioinformatics Phase Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. - edam beta12orEarlier - data + + + @@ -17882,13 +16457,12 @@ Metadata beta12orEarlier - data - edam Provenance metadata - bioinformatics This is a broad data type and is used a placeholder for other, more specific types. - data Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. + + + @@ -17904,13 +16478,12 @@ - identifiers - edam Any arbitrary identifier of an ontology. - data - identifier beta12orEarlier - bioinformatics + + + + @@ -17922,12 +16495,11 @@ beta12orEarlier - identifiers - identifier - bioinformatics - data The name of a concept in an ontology. - edam + + + + @@ -17937,13 +16509,12 @@ Genome build identifier - data - edam - identifiers An identifier of a build of a particular genome. - bioinformatics beta12orEarlier - identifier + + + + @@ -17953,13 +16524,12 @@ Pathway or network name - edam beta12orEarlier - data - identifiers - bioinformatics - identifier The name of a biological pathway or network. + + + + @@ -17971,14 +16541,13 @@ [a-zA-Z_0-9]{2,3}[0-9]{5} - identifier beta12orEarlier - data - edam - identifiers KEGG pathway ID - bioinformatics Identifier of a pathway from the KEGG pathway database. + + + + @@ -17990,12 +16559,11 @@ Identifier of a pathway from the NCI-Nature pathway database. [a-zA-Z_0-9]+ - data - bioinformatics - identifier - identifiers beta12orEarlier - edam + + + + @@ -18007,12 +16575,11 @@ Identifier of a pathway from the ConsensusPathDB pathway database. - bioinformatics - identifier beta12orEarlier - edam - data - identifiers + + + + @@ -18022,15 +16589,14 @@ Sequence cluster ID (UniRef) - edam - UniRef entry accession - bioinformatics - data - Unique identifier of an entry from the UniRef database. - identifier beta12orEarlier + UniRef entry accession UniRef cluster id - identifiers + Unique identifier of an entry from the UniRef database. + + + + @@ -18042,13 +16608,12 @@ Unique identifier of an entry from the UniRef100 database. UniRef100 entry accession - identifiers - bioinformatics - UniRef100 cluster id - data - identifier - edam beta12orEarlier + UniRef100 cluster id + + + + @@ -18059,14 +16624,13 @@ Sequence cluster ID (UniRef90) Unique identifier of an entry from the UniRef90 database. - edam - bioinformatics - identifier - identifiers - data UniRef90 cluster id beta12orEarlier UniRef90 entry accession + + + + @@ -18076,15 +16640,14 @@ Sequence cluster ID (UniRef50) - identifiers - UniRef50 cluster id - identifier - data Unique identifier of an entry from the UniRef50 database. - edam - bioinformatics + UniRef50 cluster id UniRef50 entry accession beta12orEarlier + + + + @@ -18094,17 +16657,14 @@ Ontological data - beta13 - edam - true Data concerning an ontology. + true This is a broad data type and is used a placeholder for other, more specific types. + beta13 beta12orEarlier - data - data - bioinformatics + @@ -18114,12 +16674,11 @@ RNA family annotation - bioinformatics - data An informative report on a specific RNA family or other group of classified RNA sequences. beta12orEarlier - edam - data + + + @@ -18135,13 +16694,12 @@ - identifiers Identifier of an RNA family, typically an entry from a RNA sequence classification database. - data - bioinformatics - edam - identifier beta12orEarlier + + + + @@ -18152,13 +16710,12 @@ RFAM accession - identifier beta12orEarlier - edam Stable accession number of an entry (RNA family) from the RFAM database. - identifiers - bioinformatics - data + + + + @@ -18169,12 +16726,11 @@ Protein signature type - data - bioinformatics - edam A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. - data beta12orEarlier + + + @@ -18185,11 +16741,10 @@ Domain-nucleic acid interaction beta12orEarlier - data - data - bioinformatics - edam Data on protein domain-DNA/RNA interaction(s). + + + @@ -18199,12 +16754,11 @@ Domain-domain interaction - bioinformatics - data - data beta12orEarlier Data on protein domain-protein domain interaction(s). - edam + + + @@ -18214,15 +16768,12 @@ Domain-domain interaction (indirect) - beta12orEarlier - true - data - data Data on indirect protein domain-protein domain interaction(s). beta12orEarlier - bioinformatics - edam + beta12orEarlier + true + @@ -18238,13 +16789,12 @@ - data beta12orEarlier Accession number of a nucleotide or protein sequence database entry. - edam - bioinformatics - identifiers - identifier + + + + @@ -18254,17 +16804,14 @@ 2D PAGE data + Data concerning two-dimensional polygel electrophoresis. beta12orEarlier - edam + beta13 true - bioinformatics 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. - data - Data concerning two-dimensional polygel electrophoresis. - data - beta13 + @@ -18280,12 +16827,11 @@ - data - edam An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel. - bioinformatics - data beta12orEarlier + + + @@ -18296,13 +16842,12 @@ Pathway or network accession - edam - identifier - identifiers - data beta12orEarlier A persistent, unique identifier of a biological pathway or network (typically a database entry). - bioinformatics + + + + @@ -18313,11 +16858,10 @@ Secondary structure alignment beta12orEarlier - bioinformatics - data Alignment of the (1D representations of) secondary structure of two or more molecules. - edam - data + + + @@ -18329,12 +16873,11 @@ Identifier of an object from the ASTD database. - identifier beta12orEarlier - bioinformatics - identifiers - data - edam + + + + @@ -18345,12 +16888,11 @@ ASTD ID (exon) Identifier of an exon from the ASTD database. - bioinformatics beta12orEarlier - identifier - edam - data - identifiers + + + + @@ -18360,13 +16902,12 @@ ASTD ID (intron) - edam - identifiers Identifier of an intron from the ASTD database. - identifier beta12orEarlier - data - bioinformatics + + + + @@ -18376,13 +16917,12 @@ ASTD ID (polya) - identifier beta12orEarlier - edam - identifiers - data Identifier of a polyA signal from the ASTD database. - bioinformatics + + + + @@ -18392,13 +16932,12 @@ ASTD ID (tss) - edam - identifier - identifiers - data - bioinformatics beta12orEarlier Identifier of a transcription start site from the ASTD database. + + + + @@ -18408,13 +16947,12 @@ 2D PAGE spot (annotated) - bioinformatics - data - edam - data An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. beta12orEarlier 2D PAGE spot annotation + + + @@ -18426,12 +16964,11 @@ Unique identifier of a spot from a two-dimensional (protein) gel. - data - edam - identifiers beta12orEarlier - identifier - bioinformatics + + + + @@ -18442,12 +16979,11 @@ Spot serial number beta12orEarlier - data - edam - bioinformatics - identifiers Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. - identifier + + + + @@ -18458,12 +16994,11 @@ Spot ID (HSC-2DPAGE) beta12orEarlier - identifier - bioinformatics - data - edam - identifiers Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. + + + + @@ -18473,15 +17008,12 @@ Protein-motif interaction - edam - beta13 - data beta12orEarlier Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. true - data - bioinformatics + beta13 + @@ -18491,13 +17023,12 @@ Strain identifier - identifier - data beta12orEarlier - identifiers Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - edam - bioinformatics + + + + @@ -18508,13 +17039,12 @@ CABRI accession - edam beta12orEarlier - data - bioinformatics - identifiers A unique identifier of an item from the CABRI database. - identifier + + + + @@ -18524,12 +17054,11 @@ Experiment annotation (genotype) - data - edam Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. beta12orEarlier - bioinformatics - data + + + @@ -18543,16 +17072,15 @@ - + - data Identifier of an entry from a database of genotype experiment metadata. - edam - identifiers - identifier beta12orEarlier - bioinformatics + + + + @@ -18564,11 +17092,10 @@ Identifier of an entry from the EGA database. beta12orEarlier - bioinformatics - identifiers - identifier - data - edam + + + + @@ -18578,14 +17105,13 @@ IPI protein ID - identifier - bioinformatics beta12orEarlier - identifiers IPI[0-9]{8} - data - edam Identifier of a protein entry catalogued in the International Protein Index (IPI) database. + + + + @@ -18597,12 +17123,11 @@ beta12orEarlier Accession number of a protein from the RefSeq database. - identifier - identifiers - edam - bioinformatics - data RefSeq protein ID + + + + @@ -18612,14 +17137,13 @@ EPD ID - bioinformatics - identifiers EPD identifier - identifier - data Identifier of an entry (promoter) from the EPD database. - edam beta12orEarlier + + + + @@ -18632,11 +17156,10 @@ Identifier of an entry from the TAIR database. beta12orEarlier - edam - data - bioinformatics - identifiers - identifier + + + + @@ -18646,13 +17169,12 @@ TAIR accession (At gene) - edam Identifier of an Arabidopsis thaliana gene from the TAIR database. - identifiers - bioinformatics beta12orEarlier - data - identifier + + + + @@ -18662,13 +17184,12 @@ UniSTS accession - data Identifier of an entry from the UniSTS database. - bioinformatics - edam - identifiers beta12orEarlier - identifier + + + + @@ -18678,13 +17199,12 @@ UNITE accession - edam - identifiers - bioinformatics Identifier of an entry from the UNITE database. - data beta12orEarlier - identifier + + + + @@ -18694,13 +17214,12 @@ UTR accession - bioinformatics - data - edam - identifiers Identifier of an entry from the UTR database. - identifier beta12orEarlier + + + + @@ -18710,16 +17229,15 @@ UniParc accession - data UPI - UniParc ID Accession number of a UniParc (protein sequence) database entry. - identifier + UniParc ID UPI[A-F0-9]{10} - identifiers - edam - bioinformatics beta12orEarlier + + + + @@ -18729,13 +17247,12 @@ mFLJ/mKIAA number - bioinformatics - identifier - data Identifier of an entry from the Rouge or HUGE databases. - identifiers beta12orEarlier - edam + + + + @@ -18744,13 +17261,13 @@ Fungi annotation - + An informative report on a specific fungus. - data - data + 1.4 beta12orEarlier - edam - bioinformatics + true + + @@ -18759,13 +17276,13 @@ Fungi annotation (anamorph) - - bioinformatics - edam + + true + 1.4 An informative report on a specific fungus anamorph. - data beta12orEarlier - data + + @@ -18777,11 +17294,10 @@ Gene features (exon) beta12orEarlier - data - data An informative report on an exon in a nucleotide sequences. - bioinformatics - edam + + + @@ -18792,15 +17308,14 @@ Ensembl protein ID - bioinformatics Unique identifier for a protein from the Ensembl database. - data Protein ID (Ensembl) beta12orEarlier Ensembl ID (protein) - identifier - edam - identifiers + + + + @@ -18811,13 +17326,12 @@ Gene annotation (transcript) An informative report on a specific gene transcript, clone or EST. - edam Gene annotation (clone or EST) Gene transcript annotation beta12orEarlier - bioinformatics - data - data + + + @@ -18826,13 +17340,13 @@ Toxin annotation - - edam - bioinformatics + + true + 1.4 An informative report on a specific toxin. - data - data beta12orEarlier + + @@ -18842,15 +17356,12 @@ Protein report (membrane protein) - bioinformatics - true - data - edam - beta12orEarlier beta12orEarlier - data An informative report on a membrane protein. + true + beta12orEarlier + @@ -18861,11 +17372,10 @@ Protein-drug interaction beta12orEarlier - bioinformatics - edam - data Informative report on protein-drug interaction(s) including binding affinity data. - data + + + @@ -18875,17 +17385,14 @@ Map data - true - edam - bioinformatics Data concerning a map of molecular sequence(s). beta13 + true This is a broad data type and is used a placeholder for other, more specific types. - data beta12orEarlier - data + @@ -18896,13 +17403,12 @@ Phylogenetic raw data beta12orEarlier - bioinformatics - data - edam - data This is a broad data type and is used a placeholder for other, more specific types. Data concerning phylogeny, typically of molecular sequences. Phylogenetic data + + + @@ -18912,16 +17418,13 @@ Protein data - data - data - beta13 - edam beta12orEarlier - bioinformatics - Data concerning one or more protein molecules. true + Data concerning one or more protein molecules. + beta13 This is a broad data type and is used a placeholder for other, more specific types. + @@ -18931,16 +17434,13 @@ Nucleic acid data - bioinformatics This is a broad data type and is used a placeholder for other, more specific types. - data - data - true beta12orEarlier beta13 Data concerning one or more nucleic acid molecules. - edam + true + @@ -18951,15 +17451,12 @@ Article data beta13 - edam - bioinformatics true Data concerning the scientific literature. 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. - data - data beta12orEarlier + @@ -18972,13 +17469,12 @@ Parameter or primitive Tool parameter - bioinformatics Tool-specific parameter - data - data Typically a simple numerical or string value that controls the operation of a tool. beta12orEarlier - edam + + + @@ -19000,13 +17496,10 @@ beta12orEarlier beta13 Data concerning a specific type of molecule. - edam - bioinformatics - data - data true Molecule-specific data + @@ -19016,13 +17509,12 @@ Molecule report - data - data - edam Molecular report beta12orEarlier - bioinformatics An informative report on a specific molecule. + + + @@ -19030,14 +17522,14 @@ - Organism annotation + Organism report - bioinformatics - data - edam + Organism annotation beta12orEarlier - data An informative report on a specific organism. + + + @@ -19047,12 +17539,11 @@ Experiment annotation - edam Annotation on a wet lab experiment, such as experimental conditions. - data - data beta12orEarlier - bioinformatics + + + @@ -19062,13 +17553,12 @@ Nucleic acid features (mutation) - data Annotation on a mutation. - edam Mutation annotation - data beta12orEarlier - bioinformatics + + + @@ -19078,12 +17568,11 @@ Sequence parameter - data - data - bioinformatics beta12orEarlier - edam A parameter concerning calculations on molecular sequences. + + + @@ -19093,14 +17582,13 @@ Sequence tag profile - bioinformatics - data 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 beta12orEarlier - edam 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. - data + + + @@ -19112,10 +17600,9 @@ Data concerning a mass spectrometry measurement. beta12orEarlier - bioinformatics - data - edam - data + + + @@ -19126,12 +17613,11 @@ Protein structure raw data 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. - bioinformatics Raw data from experimental methods for determining protein structure. - data - edam - data beta12orEarlier + + + @@ -19141,13 +17627,12 @@ Mutation identifier - identifier beta12orEarlier - bioinformatics - edam - data - identifiers An identifier of a mutation. + + + + @@ -19157,17 +17642,14 @@ Alignment data - bioinformatics - edam - true - 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. - data - data beta12orEarlier Data concerning an alignment of two or more molecular sequences, structures or derived data. beta13 + true + 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. + @@ -19180,15 +17662,12 @@ This is a broad data type and is used a placeholder for other, more specific types. Database index beta13 - bioinformatics Data concerning an index of data. - data - edam - data beta12orEarlier true + @@ -19198,13 +17677,12 @@ Amino acid name (single letter) - identifier - identifiers - bioinformatics - edam Single letter amino acid identifier, e.g. G. - data beta12orEarlier + + + + @@ -19214,13 +17692,12 @@ Amino acid name (three letter) - identifier - data - edam Three letter amino acid identifier, e.g. GLY. - bioinformatics - identifiers beta12orEarlier + + + + @@ -19231,12 +17708,11 @@ Amino acid name (full name) Full name of an amino acid, e.g. Glycine. - identifiers - bioinformatics beta12orEarlier - edam - data - identifier + + + + @@ -19252,13 +17728,12 @@ - data - identifier - bioinformatics Identifier of a toxin. - identifiers - edam beta12orEarlier + + + + @@ -19269,12 +17744,11 @@ ArachnoServer ID beta12orEarlier - edam - identifier - bioinformatics Unique identifier of a toxin from the ArachnoServer database. - identifiers - data + + + + @@ -19285,12 +17759,11 @@ Expressed gene list A simple summary of expressed genes. - edam Gene annotation (expressed gene list) - data - bioinformatics beta12orEarlier - data + + + @@ -19302,11 +17775,10 @@ Unique identifier of a monomer from the BindingDB database. beta12orEarlier - identifiers - edam - identifier - bioinformatics - data + + + + @@ -19316,16 +17788,12 @@ GO concept name - data The name of a concept from the GO ontology. - edam - true - bioinformatics beta12orEarlier beta12orEarlier - identifiers - identifier + true + @@ -19336,13 +17804,12 @@ GO concept ID (biological process) An identifier of a 'biological process' concept from the the Gene Ontology. - bioinformatics - identifiers - identifier - edam - data beta12orEarlier [0-9]{7}|GO:[0-9]{7} + + + + @@ -19353,13 +17820,12 @@ GO concept ID (molecular function) An identifier of a 'molecular function' concept from the the Gene Ontology. - data - bioinformatics - identifier [0-9]{7}|GO:[0-9]{7} - identifiers beta12orEarlier - edam + + + + @@ -19369,16 +17835,12 @@ GO concept name (cellular component) - identifier - bioinformatics beta12orEarlier - true - identifiers - edam beta12orEarlier + true The name of a concept for a cellular component from the GO ontology. - data + @@ -19389,11 +17851,10 @@ Northern blot image An image arising from a Northern Blot experiment. - data beta12orEarlier - edam - bioinformatics - data + + + @@ -19404,13 +17865,12 @@ Blot ID - identifier - edam - data - identifiers beta12orEarlier Unique identifier of a blot from a Northern Blot. - bioinformatics + + + + @@ -19420,13 +17880,12 @@ BlotBase blot ID - identifiers - bioinformatics - identifier - data Unique identifier of a blot from a Northern Blot from the BlotBase database. beta12orEarlier - edam + + + + @@ -19437,12 +17896,11 @@ Hierarchy Hierarchy annotation - bioinformatics - edam A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation. beta12orEarlier - data - data + + + @@ -19452,16 +17910,12 @@ Hierarchy identifier - bioinformatics - identifier - data true - Identifier of an entry from a database of biological hierarchies. - identifiers - edam beta12orEarlier + Identifier of an entry from a database of biological hierarchies. beta12orEarlier + @@ -19471,13 +17925,12 @@ Brite hierarchy ID - edam - identifier Identifier of an entry from the Brite database of biological hierarchies. - bioinformatics beta12orEarlier - identifiers - data + + + + @@ -19490,12 +17943,9 @@ beta12orEarlier beta12orEarlier A type (represented as a string) of cancer. - data - data - bioinformatics - edam true + @@ -19505,13 +17955,12 @@ BRENDA organism ID - bioinformatics beta12orEarlier - data A unique identifier for an organism used in the BRENDA database. - edam - identifier - identifiers + + + + @@ -19521,14 +17970,13 @@ UniGene taxon - data - identifiers beta12orEarlier - identifier - bioinformatics UniGene organism abbreviation - edam The name of a taxon using the controlled vocabulary of the UniGene database. + + + + @@ -19538,13 +17986,12 @@ UTRdb taxon - bioinformatics - identifier - data - edam The name of a taxon using the controlled vocabulary of the UTRdb database. beta12orEarlier - identifiers + + + + @@ -19557,11 +18004,10 @@ Catalogue identifier An identifier of a catalogue of biological resources. beta12orEarlier - identifier - identifiers - data - edam - bioinformatics + + + + @@ -19572,13 +18018,12 @@ CABRI catalogue name - bioinformatics beta12orEarlier - identifiers - data The name of a catalogue of biological resources from the CABRI database. - edam - identifier + + + + @@ -19588,15 +18033,12 @@ Secondary structure alignment metadata - data true - data - bioinformatics - beta12orEarlier - edam beta12orEarlier + beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. + @@ -19606,13 +18048,12 @@ Molecular interaction - bioinformatics Molecular interaction data - edam beta12orEarlier - data Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). - data + + + @@ -19628,13 +18069,12 @@ - data Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). - edam beta12orEarlier - bioinformatics Network - data + + + @@ -19644,16 +18084,13 @@ Small molecule data - data + Data concerning one or more small molecules. beta13 - edam beta12orEarlier - true - Data concerning one or more small molecules. - data This is a broad data type and is used a placeholder for other, more specific types. - bioinformatics + true + @@ -19664,14 +18101,11 @@ Genotype and phenotype data Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - data - data true - bioinformatics - edam beta13 beta12orEarlier + @@ -19687,14 +18121,13 @@ - edam + This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 Image or hybridisation data for a microarray, typically a study of gene expression. beta12orEarlier - data Gene expression data - bioinformatics - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 - data + + + @@ -19706,15 +18139,14 @@ KEGG compound identifier - identifier beta12orEarlier Unique identifier of a chemical compound from the KEGG database. - edam C[0-9]+ KEGG compound ID - bioinformatics - data - identifiers + + + + @@ -19726,12 +18158,11 @@ beta12orEarlier - identifiers - edam - data Name (not necessarily stable) an entry (RNA family) from the RFAM database. - bioinformatics - identifier + + + + @@ -19742,14 +18173,13 @@ Reaction ID (KEGG) - edam - Identifier of a biological reaction from the KEGG reactions database. beta12orEarlier - data - identifiers R[0-9]+ - identifier - bioinformatics + Identifier of a biological reaction from the KEGG reactions database. + + + + @@ -19760,14 +18190,13 @@ Drug ID (KEGG) - data - identifiers - identifier D[0-9]+ - edam Unique identifier of a drug from the KEGG Drug database. - bioinformatics beta12orEarlier + + + + @@ -19778,14 +18207,13 @@ Ensembl ID - identifier - identifiers - data - beta12orEarlier - edam Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. ENS[A-Z]*[FPTG][0-9]{11} - bioinformatics + beta12orEarlier + + + + @@ -19801,14 +18229,13 @@ - identifier - data - bioinformatics - beta12orEarlier - identifiers - edam [A-Z][0-9]+(\.[-[0-9]+])? + beta12orEarlier An identifier of a disease from the International Classification of Diseases (ICD) database. + + + + @@ -19818,16 +18245,15 @@ Sequence cluster ID (CluSTr) - identifier CluSTr cluster ID - identifiers beta12orEarlier - edam [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? - bioinformatics CluSTr ID Unique identifier of a sequence cluster from the CluSTr database. - data + + + + @@ -19839,13 +18265,12 @@ beta12orEarlier - bioinformatics - edam - data - identifier Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). - identifiers G[0-9]+ + + + + @@ -19855,16 +18280,15 @@ TCDB ID - data A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. - identifier [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ TC number - edam OBO file for regular expression. - bioinformatics beta12orEarlier - identifiers + + + + @@ -19875,13 +18299,12 @@ MINT ID beta12orEarlier - data - edam - identifier Unique identifier of an entry from the MINT database of protein-protein interactions. - identifiers MINT\-[0-9]{1,5} - bioinformatics + + + + @@ -19891,14 +18314,13 @@ DIP ID - data - identifiers - bioinformatics DIP[\:\-][0-9]{3}[EN] beta12orEarlier - edam - identifier Unique identifier of an entry from the DIP database of protein-protein interactions. + + + + @@ -19908,14 +18330,13 @@ Signaling Gateway protein ID - bioinformatics - identifier A[0-9]{6} - data Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. - identifiers - edam beta12orEarlier + + + + @@ -19928,11 +18349,10 @@ Identifier of a protein modification catalogued in a database. beta12orEarlier - bioinformatics - data - identifiers - edam - identifier + + + + @@ -19943,13 +18363,12 @@ RESID ID beta12orEarlier - edam AA[0-9]{4} - identifier Identifier of a protein modification catalogued in the RESID database. - bioinformatics - identifiers - data + + + + @@ -19963,11 +18382,10 @@ Identifier of an entry from the RGD database. beta12orEarlier [0-9]{4,7} - identifiers - edam - bioinformatics - data - identifier + + + + @@ -19986,12 +18404,11 @@ beta12orEarlier Identifier of a protein sequence from the TAIR database. - identifiers AASequence:[0-9]{10} - data - edam - identifier - bioinformatics + + + + @@ -20001,15 +18418,14 @@ Compound ID (HMDB) - identifiers - beta12orEarlier - bioinformatics - data - HMDB[0-9]{5} Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). - identifier HMDB ID - edam + beta12orEarlier + HMDB[0-9]{5} + + + + @@ -20020,14 +18436,13 @@ LIPID MAPS ID LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? - edam - identifiers - data - bioinformatics Identifier of an entry from the LIPID MAPS database. LM ID - identifier beta12orEarlier + + + + @@ -20037,15 +18452,14 @@ PeptideAtlas ID - data PAp[0-9]{8} - identifiers - edam - identifier beta12orEarlier PDBML:pdbx_PDB_strand_id - bioinformatics Identifier of a peptide from the PeptideAtlas peptide databases. + + + + @@ -20062,13 +18476,12 @@ - bioinformatics beta12orEarlier Identifier of a report of molecular interactions from a database (typically). - identifier - data - edam - identifiers + + + + @@ -20079,13 +18492,12 @@ BioGRID interaction ID A unique identifier of an interaction from the BioGRID database. - bioinformatics beta12orEarlier - data [0-9]+ - identifier - identifiers - edam + + + + @@ -20099,11 +18511,10 @@ Unique identifier of a peptidase enzyme from the MEROPS database. beta12orEarlier MEROPS ID - bioinformatics - edam - identifiers - identifier - data + + + + @@ -20115,12 +18526,11 @@ beta12orEarlier - edam - identifier - identifiers - bioinformatics - data An identifier of a mobile genetic element. + + + + @@ -20130,14 +18540,13 @@ ACLAME ID - identifiers An identifier of a mobile genetic element from the Aclame database. mge:[0-9]+ beta12orEarlier - data - edam - bioinformatics - identifier + + + + @@ -20148,14 +18557,13 @@ SGD ID - data - identifier - PWY[a-zA-Z_0-9]{2}\-[0-9]{3} - identifiers Identifier of an entry from the Saccharomyces genome database (SGD). beta12orEarlier - bioinformatics - edam + PWY[a-zA-Z_0-9]{2}\-[0-9]{3} + + + + @@ -20166,13 +18574,12 @@ Book ID - data - bioinformatics - identifiers - identifier - edam Unique identifier of a book. beta12orEarlier + + + + @@ -20182,14 +18589,13 @@ ISBN - identifier - bioinformatics - data - edam - identifiers The International Standard Book Number (ISBN) is for identifying printed books. (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) beta12orEarlier + + + + @@ -20199,15 +18605,14 @@ Compound ID (3DMET) - edam - bioinformatics - identifiers Identifier of a metabolite from the 3DMET database. beta12orEarlier - data - identifier 3DMET ID B[0-9]{5} + + + + @@ -20218,13 +18623,12 @@ MatrixDB interaction ID beta12orEarlier - edam - bioinformatics - identifier - data A unique identifier of an interaction from the MatrixDB database. - identifiers ([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_.*) + + + + @@ -20235,15 +18639,14 @@ cPath ID - edam A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. beta12orEarlier These identifiers are unique within the cPath database, however, they are not stable between releases. - identifiers - identifier [0-9]+ - data - bioinformatics + + + + @@ -20254,14 +18657,13 @@ PubChem bioassay ID - bioinformatics beta12orEarlier - data - identifier - edam [0-9]+ Identifier of an assay from the PubChem database. - identifiers + + + + @@ -20272,14 +18674,13 @@ PubChem ID - bioinformatics + Identifier of an entry from the PubChem database. beta12orEarlier PubChem identifier - identifier - data - identifiers - Identifier of an entry from the PubChem database. - edam + + + + @@ -20290,14 +18691,13 @@ Reaction ID (MACie) Identifier of an enzyme reaction mechanism from the MACie database. - identifier - bioinformatics - edam MACie entry number M[0-9]{4} - identifiers - data beta12orEarlier + + + + @@ -20307,17 +18707,16 @@ Gene ID (miRBase) - identifier miRNA name beta12orEarlier miRNA identifier MI[0-9]{7} Identifier for a gene from the miRBase database. - identifiers miRNA ID - data - edam - bioinformatics + + + + @@ -20328,13 +18727,12 @@ Gene ID (ZFIN) ZDB\-GENE\-[0-9]+\-[0-9]+ - identifier - edam beta12orEarlier - bioinformatics Identifier for a gene from the Zebrafish information network genome (ZFIN) database. - data - identifiers + + + + @@ -20344,14 +18742,13 @@ Reaction ID (Rhea) - edam - data beta12orEarlier - identifier Identifier of an enzyme-catalysed reaction from the Rhea database. [0-9]{5} - bioinformatics - identifiers + + + + @@ -20362,14 +18759,13 @@ Pathway ID (Unipathway) Identifier of a biological pathway from the Unipathway database. - upaid - identifier - bioinformatics - edam beta12orEarlier - data - identifiers + upaid UPA[0-9]{5} + + + + @@ -20379,15 +18775,14 @@ Compound ID (ChEMBL) - identifier - Identifier of a small molecular from the ChEMBL database. - data - identifiers - edam [0-9]+ beta12orEarlier ChEMBL ID - bioinformatics + Identifier of a small molecular from the ChEMBL database. + + + + @@ -20397,14 +18792,13 @@ LGICdb identifier - data [a-zA-Z_0-9]+ - identifier beta12orEarlier - bioinformatics - identifiers Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. - edam + + + + @@ -20414,14 +18808,13 @@ Reaction kinetics ID (SABIO-RK) - edam - identifiers beta12orEarlier - bioinformatics - identifier [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. - data + + + + @@ -20432,14 +18825,13 @@ PharmGKB ID - data - edam - identifier - beta12orEarlier - identifiers PA[0-9]+ - bioinformatics Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + beta12orEarlier + + + + @@ -20450,14 +18842,13 @@ Pathway ID (PharmGKB) + Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier - bioinformatics PA[0-9]+ - Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - edam - identifier - identifiers - data + + + + @@ -20468,14 +18859,13 @@ Disease ID (PharmGKB) - data - edam - Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - identifiers - bioinformatics PA[0-9]+ - identifier beta12orEarlier + Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + + + + @@ -20486,14 +18876,13 @@ Drug ID (PharmGKB) - bioinformatics - identifiers - identifier - Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - data PA[0-9]+ beta12orEarlier - edam + Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + + + + @@ -20504,13 +18893,12 @@ Drug ID (TTD) beta12orEarlier - identifiers Identifier of a drug from the Therapeutic Target Database (TTD). - data - edam - bioinformatics - identifier DAP[0-9]+ + + + + @@ -20520,14 +18908,13 @@ Target ID (TTD) - bioinformatics - identifier beta12orEarlier Identifier of a target protein from the Therapeutic Target Database (TTD). - identifiers TTDS[0-9]+ - edam - data + + + + @@ -20537,14 +18924,13 @@ Cell type identifier - edam A unique identifier of a type or group of cells. Cell type ID - identifier - data - bioinformatics - identifiers beta12orEarlier + + + + @@ -20554,14 +18940,13 @@ NeuronDB ID - edam - identifiers beta12orEarlier - identifier A unique identifier of a neuron from the NeuronDB database. - data [0-9]+ - bioinformatics + + + + @@ -20571,14 +18956,13 @@ NeuroMorpho ID - data - edam - bioinformatics - identifiers - identifier [a-zA-Z_0-9]+ A unique identifier of a neuron from the NeuroMorpho database. beta12orEarlier + + + + @@ -20591,12 +18975,11 @@ beta12orEarlier [0-9]+ ChemIDplus ID - data - edam - identifiers Identifier of a chemical from the ChemIDplus database. - identifier - bioinformatics + + + + @@ -20607,13 +18990,12 @@ Pathway ID (SMPDB) SMP[0-9]{5} - bioinformatics - data - edam - identifier - identifiers Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). beta12orEarlier + + + + @@ -20624,13 +19006,12 @@ BioNumbers ID beta12orEarlier - data - bioinformatics - identifiers - identifier - edam Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. [0-9]+ + + + + @@ -20641,13 +19022,12 @@ T3DB ID Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. - identifier T3D[0-9]+ - data beta12orEarlier - identifiers - bioinformatics - edam + + + + @@ -20660,22 +19040,21 @@ - + - + Identifier of a carbohydrate. - bioinformatics - edam - identifiers beta12orEarlier - data - identifier + + + + @@ -20685,14 +19064,13 @@ GlycomeDB ID - identifier - identifiers - data - edam [0-9]+ beta12orEarlier - bioinformatics Identifier of an entry from the GlycomeDB database. + + + + @@ -20703,13 +19081,12 @@ LipidBank ID Identifier of an entry from the LipidBank database. - identifier - edam - bioinformatics - identifiers [a-zA-Z_0-9]+[0-9]+ - data beta12orEarlier + + + + @@ -20720,13 +19097,12 @@ CDD ID Identifier of a conserved domain from the Conserved Domain Database. - identifier - edam - data cd[0-9]{5} - bioinformatics - identifiers beta12orEarlier + + + + @@ -20736,15 +19112,14 @@ MMDB ID - beta12orEarlier - data - bioinformatics - identifier - identifiers An identifier of an entry from the MMDB database. MMDB accession + beta12orEarlier [0-9]{1,5} - edam + + + + @@ -20755,13 +19130,12 @@ iRefIndex ID [0-9]+ - data beta12orEarlier - bioinformatics Unique identifier of an entry from the iRefIndex database of protein-protein interactions. - identifiers - identifier - edam + + + + @@ -20771,14 +19145,13 @@ ModelDB ID - edam beta12orEarlier - identifiers [0-9]+ - bioinformatics Unique identifier of an entry from the ModelDB database. - identifier - data + + + + @@ -20788,14 +19161,13 @@ Pathway ID (DQCS) - bioinformatics beta12orEarlier - identifiers Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). - data - edam [0-9]+ - identifier + + + + @@ -20805,17 +19177,13 @@ Ensembl ID (Homo sapiens) - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). ENS([EGTP])[0-9]{11} - edam - bioinformatics - true - identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). beta12orEarlier + true beta12orEarlier - data - identifiers + @@ -20827,15 +19195,11 @@ ENSBTA([EGTP])[0-9]{11} beta12orEarlier - identifiers - edam - bioinformatics - identifier true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). - data beta12orEarlier + @@ -20845,17 +19209,13 @@ Ensembl ID ('Canis familiaris') - true - bioinformatics - edam - identifiers - identifier beta12orEarlier ENSCAF([EGTP])[0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). - data + true beta12orEarlier + @@ -20866,16 +19226,12 @@ Ensembl ID ('Cavia porcellus') beta12orEarlier - data beta12orEarlier - identifiers - identifier - ENSCPO([EGTP])[0-9]{11} - bioinformatics Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). true - edam + ENSCPO([EGTP])[0-9]{11} + @@ -20885,17 +19241,13 @@ Ensembl ID ('Ciona intestinalis') - identifier ENSCIN([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). + beta12orEarlier beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). true - data - bioinformatics - edam - identifiers - beta12orEarlier + @@ -20905,17 +19257,13 @@ Ensembl ID ('Ciona savignyi') - identifiers + true beta12orEarlier - edam - identifier beta12orEarlier ENSCSAV([EGTP])[0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). - data - true - bioinformatics + @@ -20928,14 +19276,10 @@ ENSDAR([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier - bioinformatics - identifiers - data true - edam Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). - identifier + @@ -20945,17 +19289,13 @@ Ensembl ID ('Dasypus novemcinctus') - identifier - bioinformatics - data true - beta12orEarlier ENSDNO([EGTP])[0-9]{11} + beta12orEarlier beta12orEarlier - identifiers Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). - edam + @@ -20966,16 +19306,12 @@ Ensembl ID ('Echinops telfairi') Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). - data - edam - beta12orEarlier - identifier - bioinformatics - identifiers beta12orEarlier + beta12orEarlier true ENSETE([EGTP])[0-9]{11} + @@ -20987,15 +19323,11 @@ beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). - data - identifier beta12orEarlier - bioinformatics ENSEEU([EGTP])[0-9]{11} true - edam - identifiers + @@ -21005,17 +19337,13 @@ Ensembl ID ('Felis catus') - data - edam beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). ENSFCA([EGTP])[0-9]{11} - identifier - beta12orEarlier - identifiers true - bioinformatics + beta12orEarlier + @@ -21025,17 +19353,13 @@ Ensembl ID ('Gallus gallus') - bioinformatics - beta12orEarlier - identifier - edam - data beta12orEarlier true - identifiers + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). ENSGAL([EGTP])[0-9]{11} + @@ -21045,17 +19369,13 @@ Ensembl ID ('Gasterosteus aculeatus') - edam - identifier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). - bioinformatics beta12orEarlier true ENSGAC([EGTP])[0-9]{11} - data - identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). beta12orEarlier + @@ -21065,17 +19385,13 @@ Ensembl ID ('Homo sapiens') - identifier true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). beta12orEarlier beta12orEarlier - data - bioinformatics - edam ENSHUM([EGTP])[0-9]{11} - identifiers + @@ -21085,17 +19401,13 @@ Ensembl ID ('Loxodonta africana') - identifiers + beta12orEarlier ENSLAF([EGTP])[0-9]{11} true - identifier - beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). beta12orEarlier - bioinformatics - data - edam + @@ -21105,17 +19417,13 @@ Ensembl ID ('Macaca mulatta') - bioinformatics beta12orEarlier true - beta12orEarlier ENSMMU([EGTP])[0-9]{11} - identifiers + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). - data - identifier - edam + @@ -21125,17 +19433,13 @@ Ensembl ID ('Monodelphis domestica') - ENSMOD([EGTP])[0-9]{11} - bioinformatics - edam beta12orEarlier - identifier + ENSMOD([EGTP])[0-9]{11} true - identifiers Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). beta12orEarlier - data + @@ -21145,17 +19449,13 @@ Ensembl ID ('Mus musculus') - edam - data - identifiers - identifier - beta12orEarlier - ENSMUS([EGTP])[0-9]{11} - true beta12orEarlier - bioinformatics + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). + true + ENSMUS([EGTP])[0-9]{11} + @@ -21165,17 +19465,13 @@ Ensembl ID ('Myotis lucifugus') - data - identifiers - beta12orEarlier - edam - bioinformatics Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). + beta12orEarlier true - identifier - beta12orEarlier ENSMLU([EGTP])[0-9]{11} + beta12orEarlier + @@ -21185,17 +19481,13 @@ Ensembl ID ("Ornithorhynchus anatinus") - identifiers + beta12orEarlier ENSOAN([EGTP])[0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). - edam - bioinformatics - beta12orEarlier - identifier - data true beta12orEarlier + @@ -21205,17 +19497,13 @@ Ensembl ID ('Oryctolagus cuniculus') - edam - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). - bioinformatics - beta12orEarlier - data - identifiers beta12orEarlier - ENSOCU([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). true - identifier + ENSOCU([EGTP])[0-9]{11} + beta12orEarlier + @@ -21225,17 +19513,13 @@ Ensembl ID ('Oryzias latipes') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). - data - identifiers - ENSORL([EGTP])[0-9]{11} - edam - identifier beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). + beta12orEarlier true - bioinformatics + ENSORL([EGTP])[0-9]{11} + @@ -21245,17 +19529,13 @@ Ensembl ID ('Otolemur garnettii') - bioinformatics + beta12orEarlier ENSSAR([EGTP])[0-9]{11} true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). beta12orEarlier - identifiers - edam - beta12orEarlier - data - identifier + @@ -21265,17 +19545,13 @@ Ensembl ID ('Pan troglodytes') - identifier - ENSPTR([EGTP])[0-9]{11} - data - identifiers true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). - edam - bioinformatics + ENSPTR([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier + @@ -21285,17 +19561,13 @@ Ensembl ID ('Rattus norvegicus') - identifier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). - bioinformatics beta12orEarlier - edam - identifiers ENSRNO([EGTP])[0-9]{11} + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). beta12orEarlier - data + @@ -21305,17 +19577,13 @@ Ensembl ID ('Spermophilus tridecemlineatus') - beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). + beta12orEarlier ENSSTO([EGTP])[0-9]{11} - data - identifier - identifiers beta12orEarlier - edam - bioinformatics true + @@ -21325,17 +19593,13 @@ Ensembl ID ('Takifugu rubripes') - edam + true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). + ENSFRU([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier - true - identifier - ENSFRU([EGTP])[0-9]{11} - bioinformatics - identifiers - data + @@ -21345,17 +19609,13 @@ Ensembl ID ('Tupaia belangeri') - beta12orEarlier - bioinformatics - beta12orEarlier - data - edam - identifier - identifiers ENSTBE([EGTP])[0-9]{11} true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + beta12orEarlier + beta12orEarlier + @@ -21365,17 +19625,13 @@ Ensembl ID ('Xenopus tropicalis') - identifiers ENSXET([EGTP])[0-9]{11} - edam - data true - bioinformatics beta12orEarlier - beta12orEarlier - identifier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). + beta12orEarlier + @@ -21391,13 +19647,12 @@ - identifier - edam Identifier of a protein domain (or other node) from the CATH database. - identifiers - data - bioinformatics beta12orEarlier + + + + @@ -21413,14 +19668,13 @@ - data - edam 2.10.10.10 A code number identifying a family from the CATH database. beta12orEarlier - identifiers - identifier - bioinformatics + + + + @@ -21430,14 +19684,13 @@ Enzyme ID (CAZy) - bioinformatics CAZy ID beta12orEarlier Identifier of an enzyme from the CAZy enzymes database. - data - identifiers - identifier - edam + + + + @@ -21447,15 +19700,14 @@ Clone ID (IMAGE) - bioinformatics - identifiers - IMAGE cloneID - I.M.A.G.E. cloneID - edam - data beta12orEarlier - identifier A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). + IMAGE cloneID + I.M.A.G.E. cloneID + + + + @@ -21465,15 +19717,14 @@ GO concept ID (cellular compartment) + GO concept identifier (cellular compartment) beta12orEarlier - data [0-9]{7}|GO:[0-9]{7} - edam - identifier An identifier of a 'cellular compartment' concept from the Gene Ontology. - identifiers - bioinformatics - GO concept identifier (cellular compartment) + + + + @@ -21484,12 +19735,11 @@ Chromosome name (BioCyc) beta12orEarlier - identifier - bioinformatics - identifiers Name of a chromosome as used in the BioCyc database. - data - edam + + + + @@ -21499,13 +19749,12 @@ CleanEx entry name - bioinformatics An identifier of a gene expression profile from the CleanEx database. beta12orEarlier - data - identifier - edam - identifiers + + + + @@ -21515,13 +19764,12 @@ CleanEx dataset code - identifiers An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. beta12orEarlier - edam - bioinformatics - data - identifier + + + + @@ -21532,11 +19780,10 @@ Genome metadata beta12orEarlier - data - data - edam - bioinformatics Provenance metadata or other general information concerning a genome as a whole. + + + @@ -21547,13 +19794,12 @@ Protein ID (CORUM) Unique identifier for a protein complex from the CORUM database. - identifier CORUM complex ID - data beta12orEarlier - identifiers - bioinformatics - edam + + + + @@ -21563,13 +19809,12 @@ CDD PSSM-ID - bioinformatics - identifiers Unique identifier of a position-specific scoring matrix from the CDD database. - identifier - data - edam beta12orEarlier + + + + @@ -21580,13 +19825,12 @@ Protein ID (CuticleDB) Unique identifier for a protein from the CuticleDB database. - identifiers - edam - identifier - bioinformatics beta12orEarlier CuticleDB ID - data + + + + @@ -21597,12 +19841,11 @@ DBD ID beta12orEarlier - data Identifier of a predicted transcription factor from the DBD database. - bioinformatics - identifier - edam - identifiers + + + + @@ -21618,12 +19861,11 @@ - edam - data General annotation on an oligonucleotide probe. - data beta12orEarlier - bioinformatics + + + @@ -21634,13 +19876,12 @@ Oligonucleotide ID - data beta12orEarlier - bioinformatics - edam Identifier of an oligonucleotide from a database. - identifiers - identifier + + + + @@ -21650,13 +19891,12 @@ dbProbe ID - bioinformatics - edam - data - identifiers beta12orEarlier - identifier Identifier of an oligonucleotide probe from the dbProbe database. + + + + @@ -21667,11 +19907,10 @@ Dinucleotide property Physicochemical property data for one or more dinucleotides. - data beta12orEarlier - edam - data - bioinformatics + + + @@ -21682,12 +19921,11 @@ DiProDB ID Identifier of an dinucleotide property from the DiProDB database. - edam beta12orEarlier - data - identifier - identifiers - bioinformatics + + + + @@ -21700,11 +19938,10 @@ Protein structure report (disordered structure) An informative report about disordered structure in a protein. - data - data - bioinformatics beta12orEarlier - edam + + + @@ -21715,13 +19952,12 @@ Protein ID (DisProt) Unique identifier for a protein from the DisProt database. - edam - identifier - identifiers - bioinformatics beta12orEarlier DisProt ID - data + + + + @@ -21729,7 +19965,7 @@ - Embryo annotation + Embryo report @@ -21738,11 +19974,11 @@ beta12orEarlier - data - data - edam - bioinformatics + Embryo annotation Annotation on an embryo or concerning embryological development. + + + @@ -21754,13 +19990,12 @@ Unique identifier for a gene transcript from the Ensembl database. - beta12orEarlier - bioinformatics - edam Transcript ID (Ensembl) - identifiers - data - identifier + beta12orEarlier + + + + @@ -21769,13 +20004,13 @@ Inhibitor annotation - - edam - data + + true An informative report on one or more small molecules that are enzyme inhibitors. - data beta12orEarlier - bioinformatics + 1.4 + + @@ -21787,13 +20022,12 @@ Moby:GeneAccessionList - identifiers - beta12orEarlier - edam - data - bioinformatics An identifier of a promoter of a gene that is catalogued in a database. - identifier + beta12orEarlier + + + + @@ -21803,13 +20037,12 @@ EST accession - data - identifiers beta12orEarlier Identifier of an EST sequence. - identifier - bioinformatics - edam + + + + @@ -21821,11 +20054,10 @@ Identifier of an EST sequence from the COGEME database. beta12orEarlier - bioinformatics - identifiers - identifier - edam - data + + + + @@ -21835,14 +20067,13 @@ COGEME unisequence ID - identifiers beta12orEarlier A unisequence is a single sequence assembled from ESTs. Identifier of a unisequence from the COGEME database. - bioinformatics - edam - identifier - data + + + + @@ -21852,14 +20083,13 @@ Protein family ID (GeneFarm) - bioinformatics Accession number of an entry (family) from the TIGRFam database. - identifier - identifiers beta12orEarlier - data GeneFarm family ID - edam + + + + @@ -21869,13 +20099,12 @@ Family name - edam - identifier - bioinformatics - identifiers The name of a family of organism. - data beta12orEarlier + + + + @@ -21886,15 +20115,11 @@ Genus name (virus) beta12orEarlier - edam - data - bioinformatics beta13 - The name of a genus of viruses. - identifiers - identifier true + The name of a genus of viruses. + @@ -21904,16 +20129,12 @@ Family name (virus) - bioinformatics - data - identifiers + beta12orEarlier true The name of a family of viruses. beta13 - beta12orEarlier - edam - identifier + @@ -21923,16 +20144,12 @@ Database name (SwissRegulon) - data - bioinformatics beta12orEarlier - edam - identifier - true The name of a SwissRegulon database. - identifiers beta13 + true + @@ -21943,13 +20160,12 @@ Sequence feature ID (SwissRegulon) This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". - data A feature identifier as used in the SwissRegulon database. - identifiers - edam beta12orEarlier - identifier - bioinformatics + + + + @@ -21959,14 +20175,13 @@ FIG ID - data - identifiers beta12orEarlier A unique identifier of gene in the NMPDR database. - bioinformatics - identifier A FIG ID consists of four parts: a prefix, genome id, locus type and id number. - edam + + + + @@ -21976,13 +20191,12 @@ Gene ID (Xenbase) - data beta12orEarlier - bioinformatics A unique identifier of gene in the Xenbase database. - identifiers - identifier - edam + + + + @@ -21992,13 +20206,12 @@ Gene ID (Genolist) - bioinformatics - data - edam - identifier A unique identifier of gene in the Genolist database. beta12orEarlier - identifiers + + + + @@ -22008,17 +20221,13 @@ Gene name (Genolist) - identifier - true - beta12orEarlier - bioinformatics - identifiers - edam Name of an entry (gene) from the Genolist genes database. - data 1.3 Genolist gene name + beta12orEarlier + true + @@ -22028,14 +20237,13 @@ ABS ID - bioinformatics - identifiers - edam Identifier of an entry (promoter) from the ABS database. beta12orEarlier ABS identifier - identifier - data + + + + @@ -22045,13 +20253,12 @@ AraC-XylS ID - identifier beta12orEarlier - identifiers Identifier of a transcription factor from the AraC-XylS database. - data - edam - bioinformatics + + + + @@ -22062,15 +20269,11 @@ Gene name (HUGO) Name of an entry (gene) from the HUGO database. - bioinformatics true - edam - beta12orEarlier beta12orEarlier - data - identifiers - identifier + beta12orEarlier + @@ -22081,12 +20284,11 @@ Locus ID (PseudoCAP) Identifier of a locus from the PseudoCAP database. - identifiers - edam - bioinformatics beta12orEarlier - identifier - data + + + + @@ -22096,13 +20298,12 @@ Locus ID (UTR) - data Identifier of a locus from the UTR database. beta12orEarlier - edam - identifiers - bioinformatics - identifier + + + + @@ -22113,12 +20314,11 @@ MonosaccharideDB ID beta12orEarlier - identifier - identifiers - data Unique identifier of a monosaccharide from the MonosaccharideDB database. - bioinformatics - edam + + + + @@ -22128,16 +20328,12 @@ Database name (CMD) - edam - identifier beta13 The name of a subdivision of the Collagen Mutation Database (CMD) database. - identifiers - data - beta12orEarlier true - bioinformatics + beta12orEarlier + @@ -22147,16 +20343,12 @@ Database name (Osteogenesis) - data - true - beta12orEarlier - identifiers - bioinformatics The name of a subdivision of the Osteogenesis database. - edam - identifier beta13 + true + beta12orEarlier + @@ -22166,13 +20358,12 @@ Genome identifier - identifier - edam - data - identifiers beta12orEarlier An identifier of a particular genome. - bioinformatics + + + + @@ -22182,13 +20373,12 @@ GenomeReviews ID - data An identifier of a particular genome. - bioinformatics - identifiers - edam beta12orEarlier - identifier + + + + @@ -22198,14 +20388,13 @@ GlycoMap ID - identifier - bioinformatics - data Identifier of an entry from the GlycosciencesDB database. beta12orEarlier - edam [0-9]+ - identifiers + + + + @@ -22216,11 +20405,10 @@ Carbohydrate conformational map A conformational energy map of the glycosidic linkages in a carbohydrate molecule. - bioinformatics beta12orEarlier - data - data - edam + + + @@ -22232,11 +20420,10 @@ Gene features (intron) beta12orEarlier - edam - bioinformatics An informative report on an intron in a nucleotide sequences. - data - data + + + @@ -22249,11 +20436,10 @@ beta12orEarlier The name of a transcription factor. - identifiers - edam - data - identifier - bioinformatics + + + + @@ -22263,13 +20449,12 @@ TCID - identifier - edam - bioinformatics - data - identifiers beta12orEarlier Identifier of a membrane transport proteins from the transport classification database (TCDB). + + + + @@ -22279,14 +20464,13 @@ Pfam domain name - identifier - data - identifiers - edam PF[0-9]{5} - bioinformatics Name of a domain from the Pfam database. beta12orEarlier + + + + @@ -22297,13 +20481,12 @@ Pfam clan ID Accession number of a Pfam clan. - identifier - data - edam - bioinformatics - identifiers CL[0-9]{4} beta12orEarlier + + + + @@ -22313,14 +20496,13 @@ Gene ID (VectorBase) - edam - identifiers - data Identifier for a gene from the VectorBase database. - bioinformatics - identifier beta12orEarlier VectorBase ID + + + + @@ -22331,12 +20513,11 @@ UTRSite ID beta12orEarlier - data - bioinformatics - identifiers - identifier Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. - edam + + + + @@ -22352,12 +20533,11 @@ - data - bioinformatics beta12orEarlier Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. - data - edam + + + @@ -22367,16 +20547,13 @@ Locus annotation + An informative report on a particular locus. beta12orEarlier beta12orEarlier - Locus report - data - An informative report on a particular locus. true - edam - bioinformatics - data + Locus report + @@ -22386,13 +20563,12 @@ Protein name (UniProt) - identifiers - edam beta12orEarlier - data Official name of a protein as used in the UniProt database. - identifier - bioinformatics + + + + @@ -22402,13 +20578,12 @@ Term ID list - data - edam 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. - data beta12orEarlier - bioinformatics One or more terms from one or more controlled vocabularies which are annotations on an entity. + + + @@ -22418,13 +20593,12 @@ HAMAP ID - data - edam - identifiers - identifier beta12orEarlier Name of a protein family from the HAMAP database. - bioinformatics + + + + @@ -22434,12 +20608,11 @@ Identifier with metadata - data beta12orEarlier - edam - bioinformatics Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. - data + + + @@ -22450,14 +20623,11 @@ Gene symbol annotation beta12orEarlier - data - true - bioinformatics - edam - data Annotation about a gene symbol. beta12orEarlier + true + @@ -22474,13 +20644,12 @@ - identifiers - data - bioinformatics - identifier beta12orEarlier Identifier of a RNA transcript. - edam + + + + @@ -22491,12 +20660,11 @@ HIT ID beta12orEarlier - identifiers - edam - identifier - data Identifier of an RNA transcript from the H-InvDB database. - bioinformatics + + + + @@ -22508,11 +20676,10 @@ beta12orEarlier A unique identifier of gene cluster in the H-InvDB database. - data - identifier - identifiers - edam - bioinformatics + + + + @@ -22522,13 +20689,12 @@ HPA antibody id - bioinformatics Identifier of a antibody from the HPA database. beta12orEarlier - identifier - identifiers - edam - data + + + + @@ -22538,13 +20704,12 @@ IMGT/HLA ID - identifier - edam - identifiers beta12orEarlier Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. - bioinformatics - data + + + + @@ -22554,13 +20719,12 @@ Gene ID (JCVI) - bioinformatics - data beta12orEarlier - edam A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). - identifier - identifiers + + + + @@ -22570,13 +20734,12 @@ Kinase name - identifiers The name of a kinase protein. - data - bioinformatics - identifier beta12orEarlier - edam + + + + @@ -22588,12 +20751,11 @@ beta12orEarlier - bioinformatics - identifiers - edam Identifier of a physical entity from the ConsensusPathDB database. - identifier - data + + + + @@ -22604,13 +20766,12 @@ ConsensusPathDB entity name - bioinformatics - data - edam Name of a physical entity from the ConsensusPathDB database. - identifier beta12orEarlier - identifiers + + + + @@ -22622,11 +20783,10 @@ beta12orEarlier The number of a strain of algae and protozoa from the CCAP database. - identifiers - data - edam - identifier - bioinformatics + + + + @@ -22637,13 +20797,12 @@ Stock number - edam - bioinformatics - data - identifier An identifier of stock from a catalogue of biological resources. - identifiers beta12orEarlier + + + + @@ -22653,13 +20812,12 @@ Stock number (TAIR) - identifier - edam - data - identifiers A stock number from The Arabidopsis information resource (TAIR). - bioinformatics beta12orEarlier + + + + @@ -22669,13 +20827,12 @@ REDIdb ID - data Identifier of an entry from the RNA editing database (REDIdb). - identifier - identifiers - bioinformatics - edam beta12orEarlier + + + + @@ -22686,12 +20843,11 @@ SMART domain name beta12orEarlier - edam - identifier Name of a domain from the SMART database. - bioinformatics - identifiers - data + + + + @@ -22701,14 +20857,13 @@ Protein family ID (PANTHER) - identifiers Panther family ID - data - bioinformatics Accession number of an entry (family) from the PANTHER database. beta12orEarlier - edam - identifier + + + + @@ -22718,14 +20873,13 @@ RNAVirusDB ID - data A unique identifier for a virus from the RNAVirusDB database. - edam Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - identifiers - identifier beta12orEarlier - bioinformatics + + + + @@ -22737,12 +20891,11 @@ An accession of annotation on a (group of) viruses (catalogued in a database). - bioinformatics beta12orEarlier - data - identifier - edam - identifiers + + + + @@ -22753,12 +20906,11 @@ NCBI Genome Project ID beta12orEarlier - edam - identifiers - identifier - bioinformatics - data An identifier of a genome project assigned by NCBI. + + + + @@ -22768,13 +20920,12 @@ NCBI genome accession - identifiers - bioinformatics beta12orEarlier - edam - data - identifier A unique identifier of a whole genome assigned by the NCBI. + + + + @@ -22790,12 +20941,11 @@ - bioinformatics - edam - data beta12orEarlier - data Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on. + + + @@ -22805,14 +20955,13 @@ Protein ID (TopDB) - data - identifiers - identifier Unique identifier for a membrane protein from the TopDB database. TopDB ID - bioinformatics beta12orEarlier - edam + + + + @@ -22822,14 +20971,13 @@ Gel ID - data - identifier - bioinformatics beta12orEarlier Identifier of a two-dimensional (protein) gel. - identifiers - edam Gel identifier + + + + @@ -22841,12 +20989,11 @@ Name of a reference map gel from the SWISS-2DPAGE database. - identifiers - identifier - data - edam beta12orEarlier - bioinformatics + + + + @@ -22858,12 +21005,11 @@ Unique identifier for a peroxidase protein from the PeroxiBase database. beta12orEarlier - bioinformatics - identifier - data PeroxiBase ID - identifiers - edam + + + + @@ -22873,13 +21019,12 @@ SISYPHUS ID - bioinformatics Identifier of an entry from the SISYPHUS database of tertiary structure alignments. beta12orEarlier - identifiers - edam - identifier - data + + + + @@ -22891,12 +21036,11 @@ Accession of an open reading frame (catalogued in a database). - bioinformatics - edam - identifiers - identifier - data beta12orEarlier + + + + @@ -22906,13 +21050,12 @@ ORF identifier - identifier beta12orEarlier An identifier of an open reading frame. - bioinformatics - edam - data - identifiers + + + + @@ -22922,13 +21065,12 @@ Linucs ID - edam beta12orEarlier - identifiers Identifier of an entry from the GlycosciencesDB database. - data - identifier - bioinformatics + + + + @@ -22938,14 +21080,13 @@ Protein ID (LGICdb) - identifiers Unique identifier for a ligand-gated ion channel protein from the LGICdb database. - edam LGICdb ID - data - bioinformatics - identifier beta12orEarlier + + + + @@ -22955,13 +21096,12 @@ MaizeDB ID - bioinformatics - data - identifiers - identifier Identifier of an EST sequence from the MaizeDB database. - edam beta12orEarlier + + + + @@ -22971,13 +21111,12 @@ Gene ID (MfunGD) - identifier A unique identifier of gene in the MfunGD database. - data - bioinformatics - identifiers beta12orEarlier - edam + + + + @@ -22993,13 +21132,12 @@ - identifiers An identifier of a disease from the Orpha database. - data - bioinformatics beta12orEarlier - identifier - edam + + + + @@ -23009,13 +21147,12 @@ Protein ID (EcID) - identifier - bioinformatics Unique identifier for a protein from the EcID database. - data beta12orEarlier - edam - identifiers + + + + @@ -23026,13 +21163,12 @@ Clone ID (RefSeq) - identifier - identifiers - edam - data beta12orEarlier - bioinformatics A unique identifier of a cDNA molecule catalogued in the RefSeq database. + + + + @@ -23042,13 +21178,12 @@ Protein ID (ConoServer) - data - bioinformatics Unique identifier for a cone snail toxin protein from the ConoServer database. - identifiers beta12orEarlier - identifier - edam + + + + @@ -23059,12 +21194,11 @@ GeneSNP ID beta12orEarlier - identifier - identifiers - bioinformatics - data - edam Identifier of a GeneSNP database entry. + + + + @@ -23086,13 +21220,12 @@ - bioinformatics - edam beta12orEarlier - identifier - data - identifiers Identifier of a lipid. + + + + @@ -23103,13 +21236,10 @@ Databank beta12orEarlier - edam A flat-file (textual) data archive. beta12orEarlier - data true - bioinformatics - data + @@ -23120,13 +21250,10 @@ Web portal beta12orEarlier - data - edam true - bioinformatics - data beta12orEarlier A web site providing data (web pages) on a common theme to a HTTP client. + @@ -23136,14 +21263,13 @@ Gene ID (VBASE2) - edam - identifiers VBASE2 ID beta12orEarlier - identifier - bioinformatics Identifier for a gene from the VBASE2 database. - data + + + + @@ -23153,14 +21279,13 @@ DPVweb ID - bioinformatics A unique identifier for a virus from the DPVweb database. - identifier beta12orEarlier - edam - identifiers - data DPVweb virus ID + + + + @@ -23170,14 +21295,13 @@ Pathway ID (BioSystems) - data - edam [0-9]+ - bioinformatics Identifier of a pathway from the BioSystems pathway database. beta12orEarlier - identifier - identifiers + + + + @@ -23187,15 +21311,12 @@ Experimental data (proteomics) - bioinformatics - beta12orEarlier - true - edam - data beta12orEarlier + beta12orEarlier Data concerning a proteomics experiment. - data + true + @@ -23205,12 +21326,11 @@ Abstract - bioinformatics - data An abstract of a scientific article. - edam beta12orEarlier - data + + + @@ -23220,12 +21340,11 @@ Lipid structure - data - bioinformatics 3D coordinate and associated data for a lipid structure. - data beta12orEarlier - edam + + + @@ -23235,12 +21354,11 @@ Drug structure - bioinformatics 3D coordinate and associated data for the (3D) structure of a drug. - data beta12orEarlier - edam - data + + + @@ -23251,11 +21369,10 @@ Toxin structure beta12orEarlier - data 3D coordinate and associated data for the (3D) structure of a toxin. - bioinformatics - data - edam + + + @@ -23266,12 +21383,11 @@ Position-specific scoring matrix - data A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. - edam - bioinformatics - data beta12orEarlier + + + @@ -23281,12 +21397,11 @@ Distance matrix - data - edam - data beta12orEarlier - bioinformatics A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. + + + @@ -23296,12 +21411,11 @@ Structural distance matrix - data - edam - bioinformatics beta12orEarlier Distances (values representing similarity) between a group of molecular structures. - data + + + @@ -23319,11 +21433,10 @@ Bibliographic data concerning scientific article(s). - data - edam beta12orEarlier - data - bioinformatics + + + @@ -23339,13 +21452,12 @@ - bioinformatics - data - data A concept from a biological ontology. This includes any fields from the concept definition such as concept name, definition, comments and so on. beta12orEarlier - edam + + + @@ -23355,12 +21467,11 @@ Codon usage bias - data - data beta12orEarlier A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. - edam - bioinformatics + + + @@ -23370,12 +21481,11 @@ Experiment annotation (Northern blot) - data - bioinformatics - data beta12orEarlier - edam General annotation on a Northern Blot experiment. + + + @@ -23386,14 +21496,13 @@ Nucleic acid features (VNTR) VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - data - beta12orEarlier - edam Variable number of tandem repeat polymorphism - bioinformatics VNTR annotation - data + beta12orEarlier Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + + + @@ -23403,14 +21512,13 @@ Nucleic acid features (microsatellite) - bioinformatics beta12orEarlier 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. Microsatellite annotation - edam - data Annotation on a microsatellite polymorphism in a DNA sequence. - data + + + @@ -23420,14 +21528,13 @@ Nucleic acid features (RFLP) - data Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence. - data - edam An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. RFLP annotation - bioinformatics beta12orEarlier + + + @@ -23437,14 +21544,13 @@ Radiation hybrid map - data beta12orEarlier RH map - edam - data A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. - bioinformatics 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. + + + @@ -23454,12 +21560,11 @@ ID list - edam - bioinformatics - data beta12orEarlier A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. - data + + + @@ -23469,12 +21574,11 @@ Phylogenetic gene frequencies data - data - bioinformatics - data Gene frequencies data that may be read during phylogenetic tree calculation. beta12orEarlier - edam + + + @@ -23484,15 +21588,12 @@ Sequence set (polymorphic) - data - edam - beta13 A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. true - bioinformatics beta12orEarlier - data + beta13 + @@ -23502,12 +21603,11 @@ DRCAT resource - data - edam beta12orEarlier - data An entry (resource) from the DRCAT bioinformatics resource catalogue. - bioinformatics + + + @@ -23517,12 +21617,11 @@ Protein complex - bioinformatics - edam - data 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. beta12orEarlier - data + + + @@ -23532,12 +21631,11 @@ Protein structural motif - data 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. - edam - bioinformatics beta12orEarlier - data + + + @@ -23548,11 +21646,10 @@ Lipid structure report Annotation on or information derived from one or more specific lipid 3D structure(s). - bioinformatics - data - edam - data beta12orEarlier + + + @@ -23561,13 +21658,13 @@ Secondary structure image - + + true Image of one or more molecular secondary structures. - edam - bioinformatics - data - data + 1.4 beta12orEarlier + + @@ -23577,13 +21674,12 @@ Secondary structure report - edam An informative report on general information, properties or features of one or more molecular secondary structures. - bioinformatics - data beta12orEarlier Secondary structure-derived report - data + + + @@ -23593,15 +21689,12 @@ DNA features - data beta12orEarlier - beta12orEarlier - data - edam - bioinformatics true DNA sequence-specific feature annotation (not in a feature table). + beta12orEarlier + @@ -23611,13 +21704,12 @@ Nucleic acid features (RNA features) - bioinformatics RNA features Features concerning RNA or regions of DNA that encode an RNA molecule. beta12orEarlier - data - data - edam + + + @@ -23629,13 +21721,10 @@ beta12orEarlier true - edam - data - data - bioinformatics Biological data that is plotted as a graph of some type. beta12orEarlier + @@ -23647,11 +21736,10 @@ beta12orEarlier Annotation on a polymorphism. - edam Polymorphism annotation - data - data - bioinformatics + + + @@ -23662,13 +21750,12 @@ Sequence record (protein) - data - edam Protein sequence record - bioinformatics - data beta12orEarlier A protein sequence and associated metadata. + + + @@ -23679,14 +21766,13 @@ Sequence record (nucleic acid) - edam - data + beta12orEarlier Nucleic acid sequence record - bioinformatics A nucleic acid sequence and associated metadata. Nucleotide sequence record - data - beta12orEarlier + + + @@ -23697,13 +21783,12 @@ Sequence record full (protein) - data beta12orEarlier - data - bioinformatics A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. SO:2000061 - edam + + + @@ -23714,13 +21799,12 @@ Sequence record full (nucleic acid) - data - edam SO:2000061 beta12orEarlier A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - bioinformatics - data + + + @@ -23731,13 +21815,12 @@ Biological model accession - identifier Accession of a mathematical model, typically an entry from a database. beta12orEarlier - edam - identifiers - data - bioinformatics + + + + @@ -23749,12 +21832,11 @@ beta12orEarlier - data - bioinformatics - identifiers The name of a type or group of cells. - edam - identifier + + + + @@ -23765,13 +21847,12 @@ Cell type accession - identifier - identifiers Accession of a type or group of cells (catalogued in a database). beta12orEarlier - data - bioinformatics - edam + + + + @@ -23783,14 +21864,13 @@ Chemical compound accession - edam beta12orEarlier Accession of an entry from a database of chemicals. - identifier - data - identifiers Small molecule accession - bioinformatics + + + + @@ -23801,13 +21881,12 @@ Drug accession - data beta12orEarlier - identifiers - edam Accession of a drug. - identifier - bioinformatics + + + + @@ -23818,13 +21897,12 @@ Toxin name - bioinformatics - edam - data beta12orEarlier - identifier Name of a toxin. - identifiers + + + + @@ -23835,13 +21913,12 @@ Toxin accession - identifier - identifiers - bioinformatics - data - edam Accession of a toxin (catalogued in a database). beta12orEarlier + + + + @@ -23852,13 +21929,12 @@ Monosaccharide accession - bioinformatics - identifier beta12orEarlier - data - identifiers - edam Accession of a monosaccharide (catalogued in a database). + + + + @@ -23870,12 +21946,11 @@ Common name of a drug. - identifiers - bioinformatics - edam - data beta12orEarlier - identifier + + + + @@ -23886,13 +21961,12 @@ Carbohydrate accession - bioinformatics beta12orEarlier - edam Accession of an entry from a database of carbohydrates. - data - identifier - identifiers + + + + @@ -23903,13 +21977,12 @@ Molecule accession - bioinformatics beta12orEarlier - data - identifiers - identifier - edam Accession of a specific molecule (catalogued in a database). + + + + @@ -23921,12 +21994,11 @@ Accession of a data definition (catalogued in a database). - bioinformatics beta12orEarlier - data - edam - identifier - identifiers + + + + @@ -23939,11 +22011,10 @@ beta12orEarlier An accession of a particular genome (in a database). - data - identifiers - edam - identifier - bioinformatics + + + + @@ -23954,13 +22025,12 @@ Map accession - identifiers beta12orEarlier - edam An accession of a map of a molecular sequence (deposited in a database). - bioinformatics - data - identifier + + + + @@ -23972,12 +22042,11 @@ Accession of an entry from a database of lipids. - identifiers - data - edam - identifier beta12orEarlier - bioinformatics + + + + @@ -23989,12 +22058,11 @@ Accession of a peptide deposited in a database. - identifier - identifiers - data - bioinformatics beta12orEarlier - edam + + + + @@ -24006,12 +22074,11 @@ Accession of a protein deposited in a database. - identifier - bioinformatics - data beta12orEarlier - identifiers - edam + + + + @@ -24022,13 +22089,12 @@ Organism accession - edam beta12orEarlier - identifier - identifiers - data - bioinformatics An accession of annotation on a (group of) organisms (catalogued in a database). + + + + @@ -24039,20 +22105,19 @@ Organism name - identifiers The name of an organism (or group of organisms). - data Moby:OrganismsLongName beta12orEarlier - edam Moby:InfraspecificEpithet Moby:FirstEpithet Moby:BriefOccurrenceRecord Moby:OccurrenceRecord - bioinformatics Moby:OrganismsShortName - identifier Moby:Organism_Name + + + + @@ -24063,13 +22128,12 @@ Protein family accession - edam - bioinformatics - identifiers beta12orEarlier Accession of a protein family (that is deposited in a database). - data - identifier + + + + @@ -24081,13 +22145,12 @@ - beta12orEarlier - edam - identifier - bioinformatics - data Accession of an entry from a database of transcription factors or binding sites. - identifiers + beta12orEarlier + + + + @@ -24104,13 +22167,12 @@ - identifier - edam Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - data - identifiers - bioinformatics beta12orEarlier + + + + @@ -24120,19 +22182,12 @@ Virus identifier - - - - - - - edam - identifiers - identifier beta12orEarlier An accession of annotation on a (group of) viruses (catalogued in a database). - data - bioinformatics + + + + @@ -24142,12 +22197,11 @@ Sequence features metadata - data - edam Metadata on sequence features. - data - bioinformatics beta12orEarlier + + + @@ -24157,13 +22211,12 @@ Gramene identifier - bioinformatics - identifier Identifier of a Gramene database entry. - data - identifiers - edam beta12orEarlier + + + + @@ -24174,15 +22227,14 @@ DDBJ accession An identifier of an entry from the DDBJ sequence database. - identifier - bioinformatics - data DDBJ identifier DDBJ ID - edam - identifiers beta12orEarlier DDBJ accession number + + + + @@ -24193,12 +22245,11 @@ ConsensusPathDB identifier An identifier of an entity from the ConsensusPathDB database. - identifier beta12orEarlier - data - edam - identifiers - bioinformatics + + + + @@ -24210,15 +22261,12 @@ Data concerning molecular sequence(s). true - bioinformatics beta13 - edam - data - data beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. + @@ -24228,17 +22276,14 @@ Codon usage data + This is a broad data type and is used a placeholder for other, more specific types. Data concerning codon usage. + beta13 true beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - bioinformatics - data - beta13 - data - edam + @@ -24248,12 +22293,11 @@ Article report - data Data concerning or derived from the analysis of a scientific article. - edam - bioinformatics - data beta12orEarlier + + + @@ -24263,13 +22307,12 @@ Sequence report - edam An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata). - bioinformatics - data Sequence-derived report - data beta12orEarlier + + + @@ -24279,12 +22322,11 @@ Protein secondary structure report - edam - data - data beta12orEarlier - bioinformatics An informative report about the properties or features of one or more protein secondary structures. + + + @@ -24294,12 +22336,11 @@ Hopp and Woods plot - data - bioinformatics - data - edam beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. + + + @@ -24309,13 +22350,12 @@ Nucleic acid melting curve - bioinformatics beta12orEarlier 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. - edam - data - data + + + @@ -24325,13 +22365,12 @@ Nucleic acid probability profile - data Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature - data - bioinformatics A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). beta12orEarlier - edam + + + @@ -24341,14 +22380,13 @@ Nucleic acid temperature profile - data Melting map beta12orEarlier - edam - data - bioinformatics Plots melting temperature versus base position. A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + + + @@ -24366,10 +22404,9 @@ beta12orEarlier A report typically including a map (diagram) of a gene regulatory network. - data - data - bioinformatics - edam + + + @@ -24380,12 +22417,11 @@ 2D PAGE image (annotated) 2D PAGE image annotation - edam beta12orEarlier - bioinformatics - data - data An informative report on a two-dimensional (2D PAGE) gel. + + + @@ -24395,12 +22431,11 @@ Oligonucleotide probe sets annotation - data - data 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. - bioinformatics beta12orEarlier - edam + + + @@ -24411,13 +22446,12 @@ Microarray image - edam - bioinformatics An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. - data Gene expression image beta12orEarlier - data + + + @@ -24427,13 +22461,12 @@ Image - Image data - edam - bioinformatics - data Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. beta12orEarlier - data + Image data + + + @@ -24446,12 +22479,11 @@ Sequence image - bioinformatics - data - edam beta12orEarlier - data Image of a molecular sequence, possibly with sequence features or properties shown. + + + @@ -24461,13 +22493,12 @@ Protein hydropathy data - data beta12orEarlier - edam A report on protein properties concerning hydropathy. Protein hydropathy report - data - bioinformatics + + + @@ -24477,16 +22508,13 @@ Workflow data - data true - bioinformatics - beta12orEarlier - data Data concerning a computational workflow. - edam beta13 + beta12orEarlier + @@ -24497,11 +22525,10 @@ Workflow A computational workflow. - data - bioinformatics beta12orEarlier - edam - data + + + @@ -24512,15 +22539,12 @@ Secondary structure data Data concerning molecular secondary structure data. - bioinformatics beta12orEarlier - beta13 - data - data true - edam + beta13 + @@ -24531,12 +22555,11 @@ Raw sequence (protein) - edam A raw protein sequence (string of characters). - bioinformatics beta12orEarlier - data - data + + + @@ -24547,12 +22570,11 @@ Raw sequence (nucleic acid) - data A raw nucleic acid sequence. - edam - data beta12orEarlier - bioinformatics + + + @@ -24562,12 +22584,11 @@ Protein sequence - bioinformatics - data - edam beta12orEarlier One or more protein sequences, possibly with associated annotation. - data + + + @@ -24579,14 +22600,13 @@ Nucleic acid sequence Nucleic acid sequences - data One or more nucleic acid sequences, possibly with associated annotation. Nucleotide sequences Nucleotide sequence - bioinformatics - data - edam beta12orEarlier + + + @@ -24597,15 +22617,14 @@ Reaction data - bioinformatics + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. Reaction annotation - edam - data + beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. - data Enzyme kinetics annotation - Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. - beta12orEarlier + + + @@ -24615,13 +22634,12 @@ Peptide property - data Data concerning small peptides. - data Peptide data - edam beta12orEarlier - bioinformatics + + + @@ -24638,14 +22656,13 @@ - bioinformatics - edam beta12orEarlier Data concerning the classification of protein sequences or structures. - data Protein classification data - data This is a broad data type and is used a placeholder for other, more specific types. + + + @@ -24657,14 +22674,11 @@ This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier + Data concerning specific or conserved pattern in molecular sequences. beta13 true - bioinformatics - Data concerning specific or conserved pattern in molecular sequences. - data - data - edam + @@ -24675,15 +22689,12 @@ Sequence profile data Data concerning models representing a (typically multiple) sequence alignment. - data beta13 This is a broad data type and is used a placeholder for other, more specific types. true - bioinformatics beta12orEarlier - data - edam + @@ -24694,15 +22705,12 @@ Pathway or network data beta12orEarlier - data + true beta13 - data Data concerning a specific biological pathway or network. - bioinformatics - edam - true + @@ -24720,10 +22728,9 @@ An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. beta12orEarlier - bioinformatics - data - edam - data + + + @@ -24733,14 +22740,13 @@ Nucleic acid thermodynamic data - data - edam - data beta12orEarlier Nucleic acid thermodynamic property A thermodynamic or kinetic property of a nucleic acid molecule. Nucleic acid property (thermodynamic or kinetic) - bioinformatics + + + @@ -24757,14 +22763,13 @@ - data - data This is a broad data type and is used a placeholder for other, more specific types. - edam - bioinformatics Nucleic acid classification data Data concerning the classification of nucleic acid sequences or structures. beta12orEarlier + + + @@ -24774,14 +22779,13 @@ Classification - bioinformatics Classification data - data - data Data concerning a classification of molecular sequences, structures or other entities. beta12orEarlier This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. - edam + + + @@ -24791,12 +22795,11 @@ Protein features (key folding sites) - data - bioinformatics beta12orEarlier A report on key residues involved in protein folding. - data - edam + + + @@ -24806,13 +22809,12 @@ Protein torsion angle data - edam - data beta12orEarlier - data Torsion angle data for a protein structure. - bioinformatics Torsion angle data + + + @@ -24824,12 +22826,11 @@ Structure image (protein) - edam - data - bioinformatics beta12orEarlier - data An image of protein structure. + + + @@ -24839,12 +22840,11 @@ Phylogenetic character weights - data beta12orEarlier - edam Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. - bioinformatics - data + + + @@ -24859,12 +22859,11 @@ Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. Annotation track Genomic track - data - data - edam - bioinformatics Genome annotation track beta12orEarlier + + + @@ -24881,20 +22880,19 @@ UniProt accession number - identifier - bioinformatics UniProtKB accession Accession number of a UniProt (protein sequence) database entry. - [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] - identifiers TrEMBL entry accession Swiss-Prot entry accession - data - edam + [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} UniProt entry accession P43353|Q7M1G0|Q9C199|A5A6J6 beta12orEarlier UniProtKB accession number + + + + @@ -24905,15 +22903,14 @@ NCBI genetic code ID - identifiers - identifier Identifier of a genetic code in the NCBI list of genetic codes. - bioinformatics - data beta12orEarlier - edam 16 [1-9][0-9]? + + + + @@ -24930,12 +22927,11 @@ beta12orEarlier - identifier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - bioinformatics - identifiers - data - edam + + + + @@ -24947,14 +22943,10 @@ beta12orEarlier beta12orEarlier - bioinformatics The name of a concept for a biological process from the GO ontology. - identifiers - data - edam - identifier true + @@ -24964,16 +22956,12 @@ GO concept name (molecular function) - edam - The name of a concept for a molecular function from the GO ontology. - identifier beta12orEarlier - identifiers - bioinformatics - data + The name of a concept for a molecular function from the GO ontology. true beta12orEarlier + @@ -24990,13 +22978,12 @@ Taxonomic data - data - edam - beta12orEarlier Data concerning the classification, identification and naming of organisms. + beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. - data - bioinformatics + + + @@ -25006,14 +22993,13 @@ Protein ID (EMBL/GenBank/DDBJ) - data - identifiers - edam 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. EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. beta13 - identifier - bioinformatics + + + + @@ -25024,12 +23010,11 @@ Core data beta13 - data - data - edam - bioinformatics 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. + + + @@ -25046,12 +23031,11 @@ Name or other identifier of molecular sequence feature(s). - identifier - data beta13 - edam - bioinformatics - identifiers + + + + @@ -25067,13 +23051,12 @@ - bioinformatics An identifier of a molecular tertiary structure, typically an entry from a structure database. - identifiers - identifier - edam - data beta13 + + + + @@ -25089,13 +23072,12 @@ - edam beta13 - identifier - identifiers An identifier of an array of numerical values, such as a comparison matrix. - bioinformatics - data + + + + @@ -25107,11 +23089,10 @@ Sequence property (protein composition) A report (typically a table) on character or word composition / frequency of protein sequence(s). - bioinformatics - data - data beta13 - edam + + + @@ -25124,11 +23105,10 @@ beta13 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). - bioinformatics - data - edam Sequence property (nucleic acid composition) - data + + + @@ -25138,12 +23118,11 @@ Protein domain classification node - bioinformatics - edam - data A node from a classification of protein structural domain(s). beta13 - data + + + @@ -25153,14 +23132,13 @@ CAS number - edam Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. - bioinformatics - identifier - data CAS registry number beta13 - identifiers + + + + @@ -25172,11 +23150,10 @@ beta13 Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). - edam - bioinformatics - identifier - identifiers - data + + + + @@ -25189,11 +23166,10 @@ 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). beta13 - identifier - bioinformatics - identifiers - data - edam + + + + @@ -25204,11 +23180,10 @@ Geotemporal metadata Basic information concerning geographical location or time. - data - data beta13 - edam - bioinformatics + + + @@ -25218,12 +23193,11 @@ System metadata - data - data beta13 Metadata concerning the software, hardware or other aspects of a computer system. - edam - bioinformatics + + + @@ -25235,12 +23209,11 @@ beta13 - edam - data A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. - identifiers - identifier - bioinformatics + + + + @@ -25250,20 +23223,19 @@ Experimental measurement - Measurement data Raw experimental data + Measurement data Measurement metadata Experimentally measured data Measured data 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. - edam Measurement Experimental measurement data - bioinformatics Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. - data beta13 - data + + + @@ -25275,12 +23247,11 @@ Such data as found in Affymetrix CEL or GPR files. - data Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. - edam - bioinformatics beta13 - data + + + @@ -25297,16 +23268,15 @@ - data - edam Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. Gene expression report Microarray probe set data beta13 Gene annotation (expression) - data - bioinformatics Data generated from processing and analysis of probe set data from a microarray experiment. + + + @@ -25320,11 +23290,10 @@ The final processed (normalised) data for a set of hybridisations in a microarray experiment. This combines data from all hybridisations. beta13 - edam - bioinformatics - data Gene expression matrix - data + + + @@ -25334,13 +23303,12 @@ Sample annotation - data - bioinformatics beta13 This might include compound and dose in a dose response experiment. - data Annotation on a biological sample, for example experimental factors and their values. - edam + + + @@ -25350,13 +23318,12 @@ Microarray annotation - data beta13 Annotation on the array itself used in a microarray experiment. - bioinformatics - edam This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. - data + + + @@ -25368,11 +23335,10 @@ Annotation on laboratory and/or data processing protocols used in an microarray experiment. beta13 - data - data This might describe e.g. the normalisation methods used to process the raw data. - edam - bioinformatics + + + @@ -25383,11 +23349,10 @@ Microarray hybridisation data beta13 - data Data concerning the hybridisations measured during a microarray experiment. - edam - bioinformatics - data + + + @@ -25403,13 +23368,12 @@ - bioinformatics Summary of topological domains such as cytoplasmic regions in a protein. beta13 Protein topological domains - data - data - edam + + + @@ -25420,11 +23384,10 @@ Sequence features (compositionally-biased regions) A report of regions in a molecular sequence that are biased to certain characters. - edam - data beta13 - data - bioinformatics + + + @@ -25434,12 +23397,11 @@ Protein features (sequence variants) - data A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. - edam - bioinformatics beta13 - data + + + @@ -25449,12 +23411,11 @@ Nucleic acid features (difference and change) - data - edam A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. - data - bioinformatics beta13 + + + @@ -25464,12 +23425,11 @@ Nucleic acid features (expression signal) - data - data - edam A report on regions within a nucleic acid sequence containing a signal that alters a biological function. beta13 - bioinformatics + + + @@ -25481,11 +23441,10 @@ A report on regions of a nucleic acid sequence that bind some other molecule. This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - data - edam beta13 - data - bioinformatics + + + @@ -25496,13 +23455,12 @@ Nucleic acid features (repeats) - edam beta13 - bioinformatics A report on repetitive elements within a nucleic acid sequence. - data - data This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. + + + @@ -25512,13 +23470,12 @@ Nucleic acid features (replication and recombination) - data - data This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. - bioinformatics A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination. - edam beta13 + + + @@ -25529,11 +23486,10 @@ Nucleic acid features (structure) beta13 - edam - bioinformatics - data - data A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. + + + @@ -25545,11 +23501,10 @@ beta13 - data - data - edam - bioinformatics Location of short repetitive subsequences (repeat sequences) in a protein sequence. + + + @@ -25561,12 +23516,11 @@ Use this concept if another, more specific concept is not available. - edam - bioinformatics beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. - data - data + + + @@ -25577,13 +23531,12 @@ Nucleic acid features (motifs) - bioinformatics - data - edam beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. Use this concept if another, more specific concept is not available. - data + + + @@ -25593,13 +23546,12 @@ Nucleic acid features (d-loop) - edam - data A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. - data A report on displacement loops in a mitochondrial DNA sequence. - bioinformatics beta13 + + + @@ -25610,12 +23562,11 @@ Nucleic acid features (stem loop) 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. - bioinformatics A report on stem loops in a DNA sequence. - data - data beta13 - edam + + + @@ -25625,14 +23576,13 @@ Nucleic acid features (mRNA features) - edam - bioinformatics - data beta13 Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. - data This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). mRNA features + + + @@ -25642,13 +23592,12 @@ Nucleic acid features (signal or transit peptide) - data - data beta13 - bioinformatics - edam 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. A report on a coding sequence for a signal or transit peptide. + + + @@ -25661,11 +23610,10 @@ Non-coding RNA features beta13 Features concerning non-coding or functional RNA molecules, including tRNA and rRNA. - data - edam - bioinformatics ncRNA features - data + + + @@ -25676,12 +23624,11 @@ Nucleic acid features (transcriptional) beta13 - data Features concerning transcription of DNA into RNA including the regulation of transcription. - data - edam 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. - bioinformatics + + + @@ -25693,11 +23640,10 @@ beta13 A report on sequence tagged sites (STS) in nucleic acid sequences. - edam - bioinformatics - data 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. - data + + + @@ -25708,11 +23654,10 @@ 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. - edam - data beta13 - data - bioinformatics + + + @@ -25723,11 +23668,10 @@ SCOP class Information on a 'class' node from the SCOP database. - data beta13 - data - bioinformatics - edam + + + @@ -25737,12 +23681,11 @@ SCOP fold - edam - data Information on a 'fold' node from the SCOP database. beta13 - data - bioinformatics + + + @@ -25752,12 +23695,11 @@ SCOP superfamily - bioinformatics - data Information on a 'superfamily' node from the SCOP database. - data beta13 - edam + + + @@ -25767,12 +23709,11 @@ SCOP family - bioinformatics beta13 Information on a 'family' node from the SCOP database. - data - data - edam + + + @@ -25782,12 +23723,11 @@ SCOP protein - data - bioinformatics beta13 Information on a 'protein' node from the SCOP database. - edam - data + + + @@ -25797,12 +23737,11 @@ SCOP species - bioinformatics - data Information on a 'species' node from the SCOP database. beta13 - edam - data + + + @@ -25814,10 +23753,9 @@ General annotation on a mass spectrometry experiment. beta13 - bioinformatics - data - edam - data + + + @@ -25828,12 +23766,11 @@ Gene family annotation - data - data - edam 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. - bioinformatics beta13 + + + @@ -25843,12 +23780,11 @@ Protein image - edam An image of a protein. - bioinformatics beta13 - data - data + + + @@ -25859,12 +23795,11 @@ Protein alignment - data - edam beta13 - data - bioinformatics An alignment of protein sequences and/or structures. + + + @@ -25880,12 +23815,11 @@ - data Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. - data - bioinformatics 1.0 - edam + + + @@ -25896,12 +23830,13 @@ Sequence assembly report - data + Assembly report + 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. 1.1 - edam - bioinformatics - data An informative report about a DNA sequence assembly. + + + @@ -25911,13 +23846,12 @@ Genome index - edam 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. 1.1 - data - data - bioinformatics + + + @@ -25928,12 +23862,11 @@ Experiment annotation (GWAS) Experiment annotation (genome-wide association study) - data Metadata on a genome-wide association study (GWAS). 1.1 - data - edam - bioinformatics + + + @@ -25943,13 +23876,12 @@ Cytoband position - bioinformatics - edam - data - data Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. The position of a cytogenetic band in a genome. 1.2 + + + @@ -25960,16 +23892,15 @@ Cell type ontology ID - identifiers - identifier - bioinformatics beta12orEarlier CL_[0-9]{7} - edam - data 1.2 Cell type ontology concept ID. CL ID + + + + @@ -25981,10 +23912,9 @@ Mathematical model of a network, that contains biochemical kinetics. 1.2 - bioinformatics - data - data - edam + + + @@ -25994,17 +23924,16 @@ COSMIC ID - cosmic identifier 1.3 - bioinformatics - edam + cosmic identifier COSMIC identifier cosmic id - identifier - data Identifier of a COSMIC database entry. cosmic ID - identifiers + + + + @@ -26016,15 +23945,14 @@ hgmd identifier Identifier of a HGMD database entry. - edam - data hgmd id HGMD identifier - 1.3 + beta12orEarlier hgmd ID - identifier - bioinformatics - identifiers + + + + @@ -26035,13 +23963,12 @@ Sequence assembly ID 1.3 - data - identifier - bioinformatics Unique identifier of sequence assembly. - edam - identifiers Sequence assembly version + + + + @@ -26051,12 +23978,11 @@ Sequence feature type - bioinformatics 1.3 - data - edam 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. - data + + + @@ -26066,15 +23992,14 @@ Gene annotation (homology) + This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. An informative report on gene homologues between species. Homology information - data + beta12orEarlier Gene annotation (homology information) - This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. - edam - data - bioinformatics - 1.3 + + + @@ -26086,14 +24011,13 @@ 1.3 - data - identifier ENSGT00390000003602 - edam Unique identifier for a gene tree from the Ensembl database. - bioinformatics Ensembl ID (gene tree) - identifiers + + + + @@ -26103,12 +24027,11 @@ Gene tree - edam A phylogenetic tree that is an estimate of the character's phylogeny. - data - data - bioinformatics 1.3 + + + @@ -26118,12 +24041,11 @@ Species tree - data - data - bioinformatics 1.3 - edam A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. + + + @@ -26140,14 +24062,13 @@ - identifiers Name or other identifier of an entry from a biosample database. - data - edam Sample accession - bioinformatics - identifier 1.3 + + + + @@ -26159,12 +24080,11 @@ 1.3 - identifiers - data Identifier of an object from the MGI database. - bioinformatics - edam - identifier + + + + @@ -26176,14 +24096,63 @@ Phenotype - identifier 1.3 - data - identifiers Phenotypes Name of a phenotype. - bioinformatics - edam + + + + + + + + + + + + Transition matrix + + 1.4 + 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. + A HMM transition matrix contains the probabilities of switching from one HMM state to another. + + + + + + + + + Emission matrix + + 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. + 1.4 + 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. + + + + + + + + + Hidden Markov model + + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. + 1.4 + + + + + + + + + Format identifier + + 1.4 + An identifier of a data format. + @@ -26194,14 +24163,13 @@ SMILES - formats - bioinformatics - format Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. - edam beta12orEarlier + + + @@ -26214,12 +24182,11 @@ InChI - format - bioinformatics - edam beta12orEarlier - formats Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. + + + @@ -26230,13 +24197,12 @@ mf - format The general MF query format consists of a series of valid atomic symbols, with an optional number or range. - bioinformatics beta12orEarlier - edam Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. - formats + + + @@ -26247,13 +24213,12 @@ inchikey - bioinformatics An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. beta12orEarlier - format The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. - edam - formats + + + @@ -26263,12 +24228,11 @@ smarts - bioinformatics - formats - edam beta12orEarlier SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. - format + + + @@ -26279,12 +24243,11 @@ unambiguous pure - bioinformatics - formats - format - edam Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. beta12orEarlier + + + @@ -26295,14 +24258,13 @@ nucleotide + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. beta12orEarlier - bioinformatics - edam - format - formats Non-sequence characters may be used for example for gaps. - Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. + + + @@ -26314,13 +24276,12 @@ Non-sequence characters may be used for gaps and translation stop. - formats - edam - format beta12orEarlier Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. - bioinformatics + + + @@ -26331,12 +24292,11 @@ consensus - formats Alphabet for the consensus of two or more molecular sequences. - bioinformatics - edam beta12orEarlier - format + + + @@ -26347,12 +24307,11 @@ pure nucleotide - edam Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. - formats beta12orEarlier - bioinformatics - format + + + @@ -26363,12 +24322,11 @@ unambiguous pure nucleotide - formats Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . - bioinformatics beta12orEarlier - edam - format + + + @@ -26378,13 +24336,12 @@ dna - formats - edam Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. - bioinformatics beta12orEarlier - format + + + @@ -26395,12 +24352,11 @@ rna beta12orEarlier - format - formats - edam Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. - bioinformatics + + + @@ -26411,12 +24367,11 @@ unambiguous pure dna - formats beta12orEarlier - format - edam Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. - bioinformatics + + + @@ -26427,12 +24382,11 @@ pure dna - format beta12orEarlier - formats - edam - bioinformatics Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + @@ -26443,12 +24397,11 @@ unambiguous pure rna sequence - bioinformatics beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. - formats - format - edam + + + @@ -26460,11 +24413,10 @@ beta12orEarlier - edam - bioinformatics Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - format - formats + + + @@ -26475,12 +24427,11 @@ unambiguous pure protein - bioinformatics Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. - format beta12orEarlier - edam - formats + + + @@ -26491,12 +24442,11 @@ pure protein - format - edam - formats Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. beta12orEarlier - bioinformatics + + + @@ -26506,16 +24456,13 @@ UniGene entry format - formats - edam true beta12orEarlier - format - bioinformatics 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. Format of an entry from UniGene. beta12orEarlier + @@ -26525,15 +24472,12 @@ COG sequence cluster format - edam - beta12orEarlier - formats Format of an entry from the COG database of clusters of (related) protein sequences. - bioinformatics - format + beta12orEarlier true beta12orEarlier + @@ -26547,10 +24491,9 @@ Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. Feature location beta12orEarlier - format - bioinformatics - edam - formats + + + @@ -26562,11 +24505,10 @@ beta12orEarlier - format - edam - bioinformatics Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). - formats + + + @@ -26578,11 +24520,10 @@ Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). - formats - edam beta12orEarlier - format - bioinformatics + + + @@ -26593,12 +24534,11 @@ EMBOSS repeat - formats - bioinformatics - format beta12orEarlier Report format for tandem repeats in a sequence (an EMBOSS report format). - edam + + + @@ -26610,11 +24550,10 @@ Format of a report on exon-intron structure generated by EMBOSS est2genome. - edam - formats - bioinformatics beta12orEarlier - format + + + @@ -26625,12 +24564,11 @@ restrict format - bioinformatics beta12orEarlier - edam - format - formats Report format for restriction enzyme recognition sites used by EMBOSS restrict program. + + + @@ -26643,10 +24581,9 @@ Report format for restriction enzyme recognition sites used by EMBOSS restover program. beta12orEarlier - format - formats - edam - bioinformatics + + + @@ -26658,11 +24595,10 @@ Report format for restriction enzyme recognition sites used by REBASE database. - format - edam - bioinformatics - formats beta12orEarlier + + + @@ -26673,13 +24609,12 @@ FASTA search results format - format - bioinformatics - formats This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) beta12orEarlier Format of results of a sequence database search using FASTA. - edam + + + @@ -26690,13 +24625,12 @@ BLAST results - formats This includes score data, alignment data and summary table. - format - edam beta12orEarlier - bioinformatics Format of results of a sequence database search using some variant of BLAST. + + + @@ -26708,11 +24642,10 @@ Format of results of a sequence database search using some variant of MSPCrunch. - bioinformatics - formats beta12orEarlier - format - edam + + + @@ -26723,12 +24656,11 @@ Smith-Waterman format - formats - bioinformatics Format of results of a sequence database search using some variant of Smith Waterman. beta12orEarlier - format - edam + + + @@ -26739,13 +24671,12 @@ dhf - bioinformatics - formats - format 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. beta12orEarlier - edam + + + @@ -26756,13 +24687,12 @@ lhf - format The hits are putative ligand-binding sequences and are found from a search of a sequence database. Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. - edam - bioinformatics - formats beta12orEarlier + + + @@ -26773,12 +24703,11 @@ InterPro hits format - edam - bioinformatics beta12orEarlier Results format for searches of the InterPro database. - formats - format + + + @@ -26789,12 +24718,11 @@ InterPro protein view report format beta12orEarlier - edam - bioinformatics - formats The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. - format + + + @@ -26804,13 +24732,12 @@ InterPro match table format - bioinformatics - edam - format - formats 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. beta12orEarlier Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. + + + @@ -26823,10 +24750,9 @@ Dirichlet distribution HMMER format. beta12orEarlier - formats - bioinformatics - format - edam + + + @@ -26837,12 +24763,11 @@ MEME Dirichlet prior - bioinformatics Dirichlet distribution MEME format. beta12orEarlier - edam - formats - format + + + @@ -26853,12 +24778,11 @@ HMMER emission and transition - formats - bioinformatics - format beta12orEarlier Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. - edam + + + @@ -26869,12 +24793,11 @@ prosite-pattern - formats - edam beta12orEarlier Format of a regular expression pattern from the Prosite database. - bioinformatics - format + + + @@ -26887,10 +24810,9 @@ beta12orEarlier Format of an EMBOSS sequence pattern. - bioinformatics - edam - formats - format + + + @@ -26901,12 +24823,11 @@ meme-motif - formats - bioinformatics - format - edam beta12orEarlier A motif in the format generated by the MEME program. + + + @@ -26917,12 +24838,11 @@ prosite-profile - bioinformatics beta12orEarlier - formats - format - edam Sequence profile (sequence classifier) format used in the PROSITE database. + + + @@ -26934,11 +24854,10 @@ A profile (sequence classifier) in the format used in the JASPAR database. - formats - bioinformatics - edam beta12orEarlier - format + + + @@ -26950,11 +24869,10 @@ beta12orEarlier - edam - format - formats - bioinformatics Format of the model of random sequences used by MEME. + + + @@ -26965,12 +24883,11 @@ HMMER format - formats - format - bioinformatics beta12orEarlier Format of a hidden Markov model representation used by the HMMER package. - edam + + + @@ -26982,12 +24899,11 @@ - formats FASTA-style format for multiple sequences aligned by HMMER package to an HMM. - edam beta12orEarlier - format - bioinformatics + + + @@ -26999,11 +24915,10 @@ beta12orEarlier - edam - formats - bioinformatics Format of multiple sequences aligned by DIALIGN package. - format + + + @@ -27014,13 +24929,12 @@ daf - formats beta12orEarlier - bioinformatics - format - edam 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. + + + @@ -27033,10 +24947,9 @@ Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. beta12orEarlier - bioinformatics - formats - format - edam + + + @@ -27047,12 +24960,11 @@ HMMER profile alignment (sequences versus HMMs) - formats beta12orEarlier - format - bioinformatics Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. - edam + + + @@ -27063,12 +24975,11 @@ HMMER profile alignment (HMM versus sequences) - formats beta12orEarlier Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. - bioinformatics - edam - format + + + @@ -27079,13 +24990,12 @@ Phylip distance matrix - format - edam Format of PHYLIP phylogenetic distance matrix data. - formats beta12orEarlier Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). - bioinformatics + + + @@ -27096,12 +25006,11 @@ ClustalW dendrogram - formats - edam - format Dendrogram (tree file) format generated by ClustalW. beta12orEarlier - bioinformatics + + + @@ -27112,12 +25021,11 @@ Phylip tree raw - formats - edam beta12orEarlier - bioinformatics Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. - format + + + @@ -27129,11 +25037,10 @@ PHYLIP file format for continuous quantitative character data. - bioinformatics - format beta12orEarlier - formats - edam + + + @@ -27143,15 +25050,12 @@ Phylogenetic property values format - format - formats true + beta12orEarlier beta12orEarlier - edam Format of phylogenetic property data. - bioinformatics - beta12orEarlier + @@ -27162,12 +25066,11 @@ Phylip character frequencies format - edam PHYLIP file format for phylogenetics character frequency data. - format beta12orEarlier - bioinformatics - formats + + + @@ -27178,12 +25081,11 @@ Phylip discrete states format - bioinformatics - format - edam - formats beta12orEarlier Format of PHYLIP discrete states data. + + + @@ -27194,12 +25096,11 @@ Phylip cliques format - edam Format of PHYLIP cliques data. - bioinformatics - formats - format beta12orEarlier + + + @@ -27211,11 +25112,10 @@ beta12orEarlier - edam - format - formats - bioinformatics Phylogenetic tree data format used by the PHYLIP program. + + + @@ -27226,12 +25126,11 @@ TreeBASE format - format The format of an entry from the TreeBASE database of phylogenetic data. beta12orEarlier - formats - bioinformatics - edam + + + @@ -27243,11 +25142,10 @@ The format of an entry from the TreeFam database of phylogenetic data. - format - formats - edam beta12orEarlier - bioinformatics + + + @@ -27258,12 +25156,11 @@ Phylip tree distance format - format - formats beta12orEarlier - bioinformatics - edam Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. + + + @@ -27275,12 +25172,11 @@ Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). - bioinformatics - edam - formats - format 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. beta12orEarlier + + + @@ -27292,11 +25188,10 @@ beta12orEarlier - format Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). - bioinformatics - formats - edam + + + @@ -27308,13 +25203,12 @@ 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. beta12orEarlier - Vienna RNA format - edam - formats - format - bioinformatics + + + @@ -27326,11 +25220,10 @@ beta12orEarlier - edam - bioinformatics Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. - formats - format + + + @@ -27346,13 +25239,12 @@ - edam - format Format of an entry (or part of an entry) from the PDB database. beta12orEarlier - bioinformatics PDB entry format - formats + + + @@ -27365,11 +25257,10 @@ Entry format of PDB database in PDB format. beta12orEarlier - bioinformatics - format PDB - edam - formats + + + @@ -27381,12 +25272,12 @@ mmcif - edam - formats beta12orEarlier - bioinformatics Entry format of PDB database in mmCIF format. - format + Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif + + + @@ -27397,12 +25288,11 @@ PDBML - format beta12orEarlier - formats - edam - bioinformatics Entry format of PDB database in PDBML (XML) format. + + + @@ -27412,14 +25302,11 @@ Domainatrix 3D-1D scoring matrix format - formats - bioinformatics Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. - format beta12orEarlier true beta12orEarlier - edam + @@ -27431,11 +25318,10 @@ beta12orEarlier - format - formats - edam - bioinformatics Amino acid index format used by the AAindex database. + + + @@ -27445,16 +25331,13 @@ IntEnz enzyme report format - bioinformatics + true IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. - edam + Format of an entry from IntEnz (The Integrated Relational Enzyme Database). beta12orEarlier beta12orEarlier - formats - true - format - Format of an entry from IntEnz (The Integrated Relational Enzyme Database). + @@ -27465,14 +25348,11 @@ BRENDA enzyme report format beta12orEarlier + beta12orEarlier Format of an entry from the BRENDA enzyme database. - format true - edam - beta12orEarlier - formats - bioinformatics + @@ -27484,13 +25364,10 @@ beta12orEarlier Format of an entry from the KEGG REACTION database of biochemical reactions. - bioinformatics - true - format - edam - formats beta12orEarlier + true + @@ -27500,15 +25377,12 @@ KEGG ENZYME enzyme report format - edam - format beta12orEarlier Format of an entry from the KEGG ENZYME database. true beta12orEarlier - formats - bioinformatics + @@ -27518,15 +25392,12 @@ REBASE proto enzyme report format - format beta12orEarlier - formats - edam - Format of an entry from the proto section of the REBASE enzyme database. - bioinformatics beta12orEarlier true + Format of an entry from the proto section of the REBASE enzyme database. + @@ -27536,15 +25407,12 @@ REBASE withrefm enzyme report format - format - beta12orEarlier - beta12orEarlier - formats Format of an entry from the withrefm section of the REBASE enzyme database. - bioinformatics + beta12orEarlier true - edam + beta12orEarlier + @@ -27555,13 +25423,12 @@ Pcons report format - edam 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. - format beta12orEarlier - formats Format of output of the Pcons Model Quality Assessment Program (MQAP). - bioinformatics + + + @@ -27574,11 +25441,10 @@ 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. - edam - formats - bioinformatics beta12orEarlier - format + + + @@ -27593,11 +25459,8 @@ Format of SMART domain assignment data. true beta12orEarlier - format - edam - bioinformatics - formats + @@ -27607,15 +25470,12 @@ BIND entry format - formats - edam beta12orEarlier true beta12orEarlier - bioinformatics Entry format for the BIND database of protein interaction. - format + @@ -27625,15 +25485,12 @@ IntAct entry format - formats Entry format for the IntAct database of protein interaction. true - format - edam - beta12orEarlier - bioinformatics beta12orEarlier + beta12orEarlier + @@ -27643,16 +25500,13 @@ InterPro entry format - format - 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 beta12orEarlier - edam - formats beta12orEarlier - bioinformatics + 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. Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. + true + @@ -27662,16 +25516,13 @@ InterPro entry abstract format - beta12orEarlier Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. - format + beta12orEarlier References are included and a functional inference is made where possible. - formats beta12orEarlier - edam true - bioinformatics + @@ -27682,14 +25533,11 @@ Gene3D entry format beta12orEarlier - edam - format - Entry format for the Gene3D protein secondary database. - bioinformatics beta12orEarlier true - formats + Entry format for the Gene3D protein secondary database. + @@ -27700,14 +25548,11 @@ PIRSF entry format beta12orEarlier - bioinformatics + true beta12orEarlier Entry format for the PIRSF protein secondary database. - format - formats - true - edam + @@ -27717,15 +25562,12 @@ PRINTS entry format - true - beta12orEarlier - formats - edam Entry format for the PRINTS protein secondary database. - bioinformatics + true beta12orEarlier - format + beta12orEarlier + @@ -27735,15 +25577,12 @@ Panther Families and HMMs entry format - bioinformatics true Entry format for the Panther library of protein families and subfamilies. beta12orEarlier - edam beta12orEarlier - formats - format + @@ -27753,15 +25592,12 @@ Pfam entry format - edam beta12orEarlier - formats - format + beta12orEarlier true Entry format for the Pfam protein secondary database. - beta12orEarlier - bioinformatics + @@ -27771,15 +25607,12 @@ SMART entry format - formats - edam - true - bioinformatics beta12orEarlier Entry format for the SMART protein secondary database. beta12orEarlier - format + true + @@ -27789,15 +25622,12 @@ Superfamily entry format - format beta12orEarlier true - formats Entry format for the Superfamily protein secondary database. beta12orEarlier - bioinformatics - edam + @@ -27807,15 +25637,12 @@ TIGRFam entry format - Entry format for the TIGRFam protein secondary database. - format - beta12orEarlier beta12orEarlier - bioinformatics - edam - formats + Entry format for the TIGRFam protein secondary database. true + beta12orEarlier + @@ -27827,13 +25654,10 @@ true beta12orEarlier - edam beta12orEarlier Entry format for the ProDom protein domain classification database. - bioinformatics - formats - format + @@ -27843,15 +25667,12 @@ FSSP entry format + beta12orEarlier true - bioinformatics Entry format for the FSSP database. beta12orEarlier - format - edam - beta12orEarlier - formats + @@ -27863,11 +25684,10 @@ 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). - formats - bioinformatics - edam beta12orEarlier - format + + + @@ -27878,14 +25698,11 @@ Ensembl gene report format true - formats - Entry format of Ensembl genome database. beta12orEarlier - format - bioinformatics + Entry format of Ensembl genome database. beta12orEarlier - edam + @@ -27895,15 +25712,12 @@ DictyBase gene report format - beta12orEarlier - edam - bioinformatics - formats - format - true Entry format of DictyBase genome database. + beta12orEarlier beta12orEarlier + true + @@ -27913,15 +25727,12 @@ CGD gene report format - beta12orEarlier - format - beta12orEarlier - bioinformatics - edam - formats Entry format of Candida Genome database. + beta12orEarlier true + beta12orEarlier + @@ -27932,14 +25743,11 @@ DragonDB gene report format true - format beta12orEarlier Entry format of DragonDB genome database. - bioinformatics - edam - formats beta12orEarlier + @@ -27953,11 +25761,8 @@ beta12orEarlier beta12orEarlier Entry format of EcoCyc genome database. - bioinformatics - edam - format - formats + @@ -27968,14 +25773,11 @@ FlyBase gene report format Entry format of FlyBase genome database. - bioinformatics beta12orEarlier - format - true beta12orEarlier - edam - formats + true + @@ -27985,15 +25787,12 @@ Gramene gene report format - edam - beta12orEarlier - bioinformatics true Entry format of Gramene genome database. + beta12orEarlier beta12orEarlier - format - formats + @@ -28004,14 +25803,11 @@ KEGG GENES gene report format beta12orEarlier - formats Entry format of KEGG GENES genome database. beta12orEarlier - edam - format - bioinformatics true + @@ -28022,14 +25818,11 @@ MaizeGDB gene report format Entry format of the Maize genetics and genomics database (MaizeGDB). - edam - bioinformatics - beta12orEarlier - format true + beta12orEarlier beta12orEarlier - formats + @@ -28039,15 +25832,12 @@ MGD gene report format - edam - format - beta12orEarlier - Entry format of the Mouse Genome Database (MGD). true - formats beta12orEarlier - bioinformatics + beta12orEarlier + Entry format of the Mouse Genome Database (MGD). + @@ -28057,15 +25847,12 @@ RGD gene report format - Entry format of the Rat Genome Database (RGD). - edam - bioinformatics - formats - true beta12orEarlier - format + Entry format of the Rat Genome Database (RGD). beta12orEarlier + true + @@ -28077,13 +25864,10 @@ beta12orEarlier Entry format of the Saccharomyces Genome Database (SGD). - bioinformatics - formats - true - format - edam beta12orEarlier + true + @@ -28096,12 +25880,9 @@ beta12orEarlier beta12orEarlier true - bioinformatics - edam - format - formats Entry format of the Sanger GeneDB genome database. + @@ -28112,14 +25893,11 @@ TAIR gene report format true - format Entry format of The Arabidopsis Information Resource (TAIR) genome database. beta12orEarlier - bioinformatics - edam - formats beta12orEarlier + @@ -28129,15 +25907,12 @@ WormBase gene report format - formats - format - Entry format of the WormBase genomes database. true - edam beta12orEarlier beta12orEarlier - bioinformatics + Entry format of the WormBase genomes database. + @@ -28148,14 +25923,11 @@ ZFIN gene report format true + Entry format of the Zebrafish Information Network (ZFIN) genome database. beta12orEarlier - formats - edam beta12orEarlier - format - Entry format of the Zebrafish Information Network (ZFIN) genome database. - bioinformatics + @@ -28165,15 +25937,12 @@ TIGR gene report format - bioinformatics beta12orEarlier beta12orEarlier - formats Entry format of the TIGR genome database. - format - edam true + @@ -28183,15 +25952,12 @@ dbSNP polymorphism report format - bioinformatics - true - formats - beta12orEarlier - format beta12orEarlier + true Entry format for the dbSNP database. - edam + beta12orEarlier + @@ -28202,14 +25968,11 @@ OMIM entry format Format of an entry from the OMIM database of genotypes and phenotypes. - edam beta12orEarlier - bioinformatics true beta12orEarlier - formats - format + @@ -28219,15 +25982,12 @@ HGVbase entry format + beta12orEarlier beta12orEarlier - format Format of a record from the HGVbase database of genotypes and phenotypes. - formats - beta12orEarlier - bioinformatics true - edam + @@ -28237,15 +25997,12 @@ HIVDB entry format - formats + Format of a record from the HIVDB database of genotypes and phenotypes. true - format beta12orEarlier beta12orEarlier - edam - Format of a record from the HIVDB database of genotypes and phenotypes. - bioinformatics + @@ -28257,13 +26014,10 @@ beta12orEarlier true - format - edam - formats - bioinformatics Format of an entry from the KEGG DISEASE database. beta12orEarlier + @@ -28274,12 +26028,11 @@ Primer3 primer - edam beta12orEarlier Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. - bioinformatics - formats - format + + + @@ -28290,12 +26043,11 @@ ABI - formats beta12orEarlier - edam - format A format of raw sequence read data from an Applied Biosystems sequencing machine. - bioinformatics + + + @@ -28306,12 +26058,11 @@ mira - formats beta12orEarlier - bioinformatics - format Format of MIRA sequence trace information file. - edam + + + @@ -28322,14 +26073,13 @@ CAF - formats beta12orEarlier - format - edam - bioinformatics Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. - + + + + @@ -28340,12 +26090,11 @@ exp - edam beta12orEarlier - formats - bioinformatics - format Sequence assembly project file EXP format. + + + @@ -28356,12 +26105,11 @@ SCF - bioinformatics - edam - formats - Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. beta12orEarlier - format + Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. + + + @@ -28374,14 +26122,13 @@ PHD - bioinformatics - beta12orEarlier - formats - format PHD sequence trace format to store serialised chromatogram data (reads). - edam - + beta12orEarlier + + + + @@ -28398,13 +26145,12 @@ - beta12orEarlier - edam Affymetrix image data file format Format of Affymetrix data file of raw image data. - bioinformatics - formats - format + beta12orEarlier + + + @@ -28424,10 +26170,9 @@ Format of Affymetrix data file of information about (raw) expression levels of the individual probes. Affymetrix probe raw data format beta12orEarlier - bioinformatics - format - edam - formats + + + @@ -28438,12 +26183,11 @@ affymetrix - bioinformatics - format beta12orEarlier Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. - edam - formats + + + @@ -28453,15 +26197,12 @@ ArrayExpress entry format - format + beta12orEarlier Entry format for the ArrayExpress microarrays database. - edam - bioinformatics true - formats beta12orEarlier - beta12orEarlier + @@ -28473,12 +26214,11 @@ beta12orEarlier - edam - format - formats Affymetrix experimental conditions data file format Affymetrix data file format for information about experimental conditions and protocols. - bioinformatics + + + @@ -28496,12 +26236,11 @@ Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. - format - edam - formats - bioinformatics beta12orEarlier Affymetrix probe normalised data format + + + @@ -28511,15 +26250,12 @@ EMDB entry format - edam beta12orEarlier - bioinformatics - formats - beta12orEarlier true Format of an entry from the Electron Microscopy DataBase (EMDB). - format + beta12orEarlier + @@ -28529,15 +26265,12 @@ KEGG PATHWAY entry format - format true The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. - formats - edam - beta12orEarlier beta12orEarlier - bioinformatics + beta12orEarlier + @@ -28547,15 +26280,12 @@ MetaCyc entry format + beta12orEarlier The format of an entry from the MetaCyc metabolic pathways database. beta12orEarlier - formats - bioinformatics - format - edam true - beta12orEarlier + @@ -28565,15 +26295,12 @@ HumanCyc entry format - format + beta12orEarlier beta12orEarlier - edam true - bioinformatics - beta12orEarlier - formats The format of a report from the HumanCyc metabolic pathways database. + @@ -28583,15 +26310,12 @@ INOH entry format - bioinformatics - formats - true - edam beta12orEarlier The format of an entry from the INOH signal transduction pathways database. - format + true beta12orEarlier + @@ -28602,14 +26326,11 @@ PATIKA entry format true - format + beta12orEarlier The format of an entry from the PATIKA biological pathways database. beta12orEarlier - bioinformatics - edam - beta12orEarlier - formats + @@ -28622,12 +26343,9 @@ beta12orEarlier true The format of an entry from the reactome biological pathways database. - format beta12orEarlier - formats - edam - bioinformatics + @@ -28638,14 +26356,11 @@ aMAZE entry format beta12orEarlier - true - bioinformatics - edam The format of an entry from the aMAZE biological pathways and molecular interactions database. - format - formats + true beta12orEarlier + @@ -28655,15 +26370,12 @@ CPDB entry format - edam - format - formats beta12orEarlier beta12orEarlier true The format of an entry from the CPDB database. - bioinformatics + @@ -28673,15 +26385,12 @@ Panther Pathways entry format - bioinformatics The format of an entry from the Panther Pathways database. - edam - formats + beta12orEarlier true beta12orEarlier - format - beta12orEarlier + @@ -28692,12 +26401,11 @@ Taverna workflow format - formats - bioinformatics beta12orEarlier - format Format of Taverna workflows. - edam + + + @@ -28707,16 +26415,13 @@ BioModel mathematical model format - Format of mathematical models from the BioModel database. - format - beta12orEarlier Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. true - bioinformatics - formats - edam + Format of mathematical models from the BioModel database. + beta12orEarlier beta12orEarlier + @@ -28726,15 +26431,12 @@ KEGG LIGAND entry format - bioinformatics true beta12orEarlier beta12orEarlier The format of an entry from the KEGG LIGAND chemical database. - format - formats - edam + @@ -28744,15 +26446,12 @@ KEGG COMPOUND entry format - bioinformatics - The format of an entry from the KEGG COMPOUND database. - edam beta12orEarlier - format true - formats + The format of an entry from the KEGG COMPOUND database. beta12orEarlier + @@ -28762,15 +26461,12 @@ KEGG PLANT entry format - edam - format - formats true The format of an entry from the KEGG PLANT database. - bioinformatics beta12orEarlier beta12orEarlier + @@ -28781,14 +26477,11 @@ KEGG GLYCAN entry format beta12orEarlier - edam - bioinformatics The format of an entry from the KEGG GLYCAN database. - formats beta12orEarlier - format true + @@ -28798,15 +26491,12 @@ PubChem entry format - bioinformatics beta12orEarlier - format - The format of an entry from PubChem. - edam - formats true beta12orEarlier + The format of an entry from PubChem. + @@ -28816,15 +26506,12 @@ ChemSpider entry format - edam - bioinformatics - format true beta12orEarlier The format of an entry from a database of chemical structures and property predictions. - formats beta12orEarlier + @@ -28836,14 +26523,11 @@ ChEBI includes an ontological classification defining relations between entities or classes of entities. true - formats The format of an entry from Chemical Entities of Biological Interest (ChEBI). beta12orEarlier - edam - bioinformatics beta12orEarlier - format + @@ -28854,14 +26538,11 @@ MSDchem ligand dictionary entry format beta12orEarlier - formats + true beta12orEarlier The format of an entry from the MSDchem ligand dictionary. - edam - true - bioinformatics - format + @@ -28872,12 +26553,11 @@ HET group dictionary entry format - bioinformatics beta12orEarlier - format - formats - edam The format of an entry from the HET group dictionary (HET groups from PDB files). + + + @@ -28887,15 +26567,12 @@ KEGG DRUG entry format - format - true - bioinformatics - formats beta12orEarlier beta12orEarlier - edam + true The format of an entry from the KEGG DRUG database. + @@ -28906,12 +26583,11 @@ PubMed citation - formats Format of bibliographic reference as used by the PubMed database. - bioinformatics beta12orEarlier - edam - format + + + @@ -28922,13 +26598,12 @@ Medline Display Format - format - edam - bioinformatics Bibliographic reference information including citation information is included - formats Format for abstracts of scientific articles from the Medline database. beta12orEarlier + + + @@ -28939,12 +26614,11 @@ CiteXplore-core - edam - formats CiteXplore 'core' citation format including title, journal, authors and abstract. - format beta12orEarlier - bioinformatics + + + @@ -28955,12 +26629,11 @@ CiteXplore-all - edam beta12orEarlier - formats - bioinformatics - format CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. + + + @@ -28971,12 +26644,11 @@ pmc - formats - format Article format of the PubMed Central database. - edam beta12orEarlier - bioinformatics + + + @@ -28987,12 +26659,11 @@ iHOP text mining abstract format - format iHOP abstract format. - bioinformatics - edam - formats beta12orEarlier + + + @@ -29003,13 +26674,12 @@ Oscar3 - edam - bioinformatics - formats beta12orEarlier Text mining abstract format from the Oscar 3 application. - format Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. + + + @@ -29020,14 +26690,11 @@ PDB atom record format Format of an ATOM record (describing data for an individual atom) from a PDB file. - format beta12orEarlier - bioinformatics - formats - edam true beta13 + @@ -29039,14 +26706,11 @@ true beta12orEarlier - beta12orEarlier Format of CATH domain classification information for a polypeptide chain. - edam + beta12orEarlier 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. - format - formats - bioinformatics + @@ -29057,15 +26721,12 @@ CATH PDB report format 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. - Format of CATH domain classification information for a protein PDB file. true + Format of CATH domain classification information for a protein PDB file. beta12orEarlier - formats - bioinformatics - format - edam beta12orEarlier + @@ -29075,15 +26736,12 @@ NCBI gene report format - formats beta12orEarlier beta12orEarlier Entry (gene) format of the NCBI database. - format true - bioinformatics - edam + @@ -29093,17 +26751,14 @@ GeneIlluminator gene report format + true Moby:GI_Gene beta12orEarlier - bioinformatics - format - edam - true - formats beta12orEarlier This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. + @@ -29113,16 +26768,13 @@ BacMap gene card format - format - edam - Moby:BacMapGeneCard beta12orEarlier + Moby:BacMapGeneCard beta12orEarlier - formats - bioinformatics true Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. + @@ -29132,16 +26784,13 @@ ColiCard report format + Moby:ColiCard beta12orEarlier beta12orEarlier - formats true - bioinformatics Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). - Moby:ColiCard - format - edam + @@ -29153,11 +26802,10 @@ Map of a plasmid (circular DNA) in PlasMapper TextMap format. - bioinformatics beta12orEarlier - format - edam - formats + + + @@ -29169,12 +26817,11 @@ Phylogenetic tree Newick (text) format. - format - formats beta12orEarlier nh - bioinformatics - edam + + + @@ -29186,11 +26833,10 @@ Phylogenetic tree TreeCon (text) format. - bioinformatics beta12orEarlier - edam - format - formats + + + @@ -29201,12 +26847,11 @@ Nexus format - formats beta12orEarlier - format Phylogenetic tree Nexus (text) format. - edam - bioinformatics + + + @@ -29219,19 +26864,18 @@ 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. - format Data format - formats A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. - bioinformatics beta12orEarlier Exchange format Data model File format - edam + + + @@ -29245,20 +26889,14 @@ - GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. - - - - - BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format. - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. @@ -29269,22 +26907,28 @@ - Data model - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. - + + - Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + Format can be a quality of a data record. - + - Format can be a quality of a data record. + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + Data model + + + + + Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + - @@ -29294,15 +26938,12 @@ Atomic data format - edam + true Data format for an individual atom. - formats beta13 - format - bioinformatics - true beta12orEarlier + @@ -29318,12 +26959,11 @@ - formats beta12orEarlier - edam Data format for a molecular sequence record. - bioinformatics - format + + + @@ -29339,12 +26979,11 @@ - bioinformatics Data format for molecular sequence feature information. - edam - formats beta12orEarlier - format + + + @@ -29362,10 +27001,9 @@ beta12orEarlier Data format for molecular sequence alignment information. - edam - formats - format - bioinformatics + + + @@ -29375,12 +27013,11 @@ acedb - format - formats ACEDB sequence format. beta12orEarlier - bioinformatics - edam + + + @@ -29390,15 +27027,12 @@ clustal sequence format - formats - edam + beta12orEarlier Clustalw output format. beta12orEarlier - bioinformatics - beta12orEarlier true - format + @@ -29410,11 +27044,10 @@ beta12orEarlier - format Codata entry format. - bioinformatics - formats - edam + + + @@ -29424,12 +27057,11 @@ dbid - bioinformatics - formats - format - edam beta12orEarlier Fasta format variant with database name before ID. + + + @@ -29440,14 +27072,13 @@ EMBL format - bioinformatics + beta12orEarlier EMBL EMBL sequence format EMBL entry format. - beta12orEarlier - edam - formats - format + + + @@ -29458,12 +27089,11 @@ Staden experiment format - formats - edam beta12orEarlier - format Staden experiment file format. - bioinformatics + + + @@ -29474,14 +27104,13 @@ FASTA - FASTA sequence format - beta12orEarlier - format FASTA format including NCBI-style IDs. - edam + FASTA sequence format FASTA format - formats - bioinformatics + beta12orEarlier + + + @@ -29491,12 +27120,11 @@ FASTQ - formats beta12orEarlier - edam - bioinformatics - format FASTQ short read format ignoring quality scores. + + + @@ -29506,12 +27134,11 @@ FASTQ-illumina - format - formats beta12orEarlier - bioinformatics FASTQ Illumina 1.3 short read format. - edam + + + @@ -29522,11 +27149,10 @@ FASTQ-sanger beta12orEarlier - formats - edam - bioinformatics - format FASTQ short read format with phred quality. + + + @@ -29537,11 +27163,10 @@ FASTQ-solexa beta12orEarlier - formats - edam - bioinformatics - format FASTQ Solexa/Illumina 1.0 short read format. + + + @@ -29552,12 +27177,11 @@ fitch program - edam beta12orEarlier - formats Fitch program format. - bioinformatics - format + + + @@ -29568,12 +27192,11 @@ gcg - formats - edam - format - bioinformatics beta12orEarlier GCG sequence format. + + + @@ -29584,12 +27207,11 @@ GenBank format - format - bioinformatics - formats Genbank entry format. beta12orEarlier - edam + + + @@ -29600,12 +27222,11 @@ genpept Genpept protein entry format. - format Currently identical to refseqp format - edam - bioinformatics beta12orEarlier - formats + + + @@ -29616,12 +27237,11 @@ GFF2-seq - bioinformatics - format beta12orEarlier - formats GFF feature file format with sequence in the header. - edam + + + @@ -29632,12 +27252,11 @@ GFF3-seq - formats - edam beta12orEarlier GFF3 feature file format with sequence. - bioinformatics - format + + + @@ -29648,11 +27267,10 @@ giFASTA format beta12orEarlier - bioinformatics - format - formats FASTA sequence format including NCBI-style GIs. - edam + + + @@ -29663,12 +27281,11 @@ hennig86 - edam Hennig86 output sequence format. - bioinformatics beta12orEarlier - format - formats + + + @@ -29680,11 +27297,10 @@ beta12orEarlier - format - formats - bioinformatics Intelligenetics sequence format. - edam + + + @@ -29695,12 +27311,11 @@ igstrict - format - Intelligenetics sequence format (strict version). beta12orEarlier - formats - edam - bioinformatics + Intelligenetics sequence format (strict version). + + + @@ -29711,12 +27326,11 @@ jackknifer - formats - format beta12orEarlier - bioinformatics - edam Jackknifer interleaved and non-interleaved sequence format. + + + @@ -29728,11 +27342,10 @@ Mase program sequence format. - edam beta12orEarlier - bioinformatics - format - formats + + + @@ -29743,12 +27356,11 @@ mega-seq - format Mega interleaved and non-interleaved sequence format. - edam beta12orEarlier - formats - bioinformatics + + + @@ -29760,12 +27372,11 @@ - edam - format - formats GCG MSF (multiple sequence file) file format. beta12orEarlier - bioinformatics + + + @@ -29776,12 +27387,11 @@ nbrf - bioinformatics - edam - formats beta12orEarlier - format NBRF/PIR entry sequence format. + + + @@ -29793,12 +27403,11 @@ - edam - bioinformatics - formats Nexus/paup interleaved sequence format. - format beta12orEarlier + + + @@ -29811,12 +27420,11 @@ PDB sequence format (ATOM lines). - bioinformatics beta12orEarlier - formats - format pdb format in EMBOSS. - edam + + + @@ -29828,13 +27436,12 @@ - formats - format + PDB nucleotide sequence format (ATOM lines). pdbnuc format in EMBOSS. beta12orEarlier - PDB nucleotide sequence format (ATOM lines). - bioinformatics - edam + + + @@ -29846,13 +27453,12 @@ - edam beta12orEarlier PDB nucleotide sequence format (SEQRES lines). - format - formats - bioinformatics pdbnucseq format in EMBOSS. + + + @@ -29864,13 +27470,12 @@ - bioinformatics - edam pdbseq format in EMBOSS. beta12orEarlier PDB sequence format (SEQRES lines). - format - formats + + + @@ -29881,11 +27486,10 @@ Pearson format Plain old FASTA sequence format (unspecified format for IDs). - edam - bioinformatics - format beta12orEarlier - formats + + + @@ -29895,15 +27499,12 @@ phylip sequence format - bioinformatics beta12orEarlier - Phylip interleaved sequence format. - format true - formats beta12orEarlier - edam + Phylip interleaved sequence format. + @@ -29913,15 +27514,12 @@ phylipnon sequence format - edam beta12orEarlier beta12orEarlier - format - bioinformatics - formats Phylip non-interleaved sequence format. true + @@ -29932,12 +27530,11 @@ raw - format Raw sequence format with no non-sequence characters. beta12orEarlier - bioinformatics - formats - edam + + + @@ -29949,12 +27546,11 @@ Currently identical to genpept format - bioinformatics - format - formats - edam Refseq protein entry sequence format. beta12orEarlier + + + @@ -29965,14 +27561,11 @@ selex sequence format Selex sequence format. - beta12orEarlier - formats - bioinformatics - edam beta12orEarlier true - format + beta12orEarlier + @@ -29983,12 +27576,11 @@ Staden format - edam beta12orEarlier Staden suite sequence format. - formats - bioinformatics - format + + + @@ -30003,14 +27595,13 @@ Stockholm format - formats - Stockholm multiple sequence alignment format (used by Pfam and Rfam). - edam - format - bioinformatics beta12orEarlier - + Stockholm multiple sequence alignment format (used by Pfam and Rfam). + + + + @@ -30021,12 +27612,11 @@ strider format - formats beta12orEarlier DNA strider output sequence format. - edam - format - bioinformatics + + + @@ -30038,10 +27628,9 @@ beta12orEarlier UniProtKB entry sequence format. - formats - format - bioinformatics - edam + + + @@ -30052,12 +27641,11 @@ plain text format (unformatted) - formats Plain text sequence format (essentially unformatted). beta12orEarlier - edam - format - bioinformatics + + + @@ -30068,14 +27656,11 @@ treecon sequence format Treecon output sequence format. - bioinformatics - format - formats - true - edam beta12orEarlier beta12orEarlier + true + @@ -30086,12 +27671,11 @@ ASN.1 sequence format - format - bioinformatics beta12orEarlier NCBI ASN.1-based sequence format. - formats - edam + + + @@ -30102,13 +27686,12 @@ DAS format - formats - edam - bioinformatics beta12orEarlier - format DAS sequence (XML) format (any type). das sequence format + + + @@ -30119,13 +27702,12 @@ dasdna - format - formats - bioinformatics The use of this format is deprecated. - edam DAS sequence (XML) format (nucleotide-only). beta12orEarlier + + + @@ -30136,12 +27718,11 @@ debug-seq - format - edam - bioinformatics beta12orEarlier EMBOSS debugging trace sequence format of full internal data content. - formats + + + @@ -30152,12 +27733,11 @@ jackknifernon - bioinformatics - format Jackknifer output sequence non-interleaved format. beta12orEarlier - edam - formats + + + @@ -30167,15 +27747,12 @@ meganon sequence format - bioinformatics - beta12orEarlier - formats - edam true Mega non-interleaved output sequence format. - format + beta12orEarlier beta12orEarlier + @@ -30187,11 +27764,10 @@ beta12orEarlier There are several variants of this. - bioinformatics NCBI FASTA sequence format with NCBI-style IDs. - edam - formats - format + + + @@ -30203,12 +27779,11 @@ - bioinformatics beta12orEarlier - edam Nexus/paup non-interleaved sequence format. - formats - format + + + @@ -30218,12 +27793,11 @@ GFF2 - format - formats - edam General Feature Format (GFF) of sequence features. - bioinformatics beta12orEarlier + + + @@ -30236,11 +27810,10 @@ GFF3 Generic Feature Format version 3 (GFF3) of sequence features. - format - formats beta12orEarlier - bioinformatics - edam + + + @@ -30253,12 +27826,11 @@ pir - format beta12orEarlier - formats PIR feature format. - bioinformatics - edam + + + @@ -30268,15 +27840,12 @@ swiss feature - edam - format - true - bioinformatics beta12orEarlier beta12orEarlier Swiss-Prot feature format. - formats + true + @@ -30287,14 +27856,13 @@ DASGFF - edam - format beta12orEarlier DASGFF feature - bioinformatics - formats DAS GFF (XML) feature format. das feature + + + @@ -30305,12 +27873,11 @@ debug-feat - bioinformatics - format - edam - formats beta12orEarlier EMBOSS debugging trace feature format of full internal data content. + + + @@ -30320,15 +27887,12 @@ EMBL feature - formats - true - bioinformatics - EMBL feature format. beta12orEarlier - edam - format + true beta12orEarlier + EMBL feature format. + @@ -30339,14 +27903,11 @@ GenBank feature true - edam beta12orEarlier Genbank feature format. beta12orEarlier - formats - bioinformatics - format + @@ -30357,12 +27918,11 @@ ClustalW format - bioinformatics ClustalW format for (aligned) sequences. - formats - format beta12orEarlier - edam + + + @@ -30374,11 +27934,10 @@ beta12orEarlier - formats - edam - format - bioinformatics EMBOSS alignment format for debugging trace of full internal data content. + + + @@ -30389,12 +27948,11 @@ FASTA-aln - edam Fasta format for (aligned) sequences. - bioinformatics - format beta12orEarlier - formats + + + @@ -30406,10 +27964,9 @@ Pearson MARKX0 alignment format. beta12orEarlier - format - formats - edam - bioinformatics + + + @@ -30419,12 +27976,11 @@ markx1 - edam beta12orEarlier - bioinformatics - format Pearson MARKX1 alignment format. - formats + + + @@ -30434,12 +27990,11 @@ markx10 - bioinformatics - format - formats Pearson MARKX10 alignment format. beta12orEarlier - edam + + + @@ -30449,12 +28004,11 @@ markx2 - format - bioinformatics Pearson MARKX2 alignment format. beta12orEarlier - formats - edam + + + @@ -30465,11 +28019,10 @@ markx3 Pearson MARKX3 alignment format. - format - formats beta12orEarlier - edam - bioinformatics + + + @@ -30480,12 +28033,11 @@ match - edam beta12orEarlier - bioinformatics - format - formats Alignment format for start and end of matches between sequence pairs. + + + @@ -30495,12 +28047,11 @@ mega - format beta12orEarlier - formats Mega format for (typically aligned) sequences. - bioinformatics - edam + + + @@ -30512,10 +28063,9 @@ beta12orEarlier Mega non-interleaved format for (typically aligned) sequences. - format - formats - bioinformatics - edam + + + @@ -30525,15 +28075,12 @@ msf alignment format - formats - bioinformatics - beta12orEarlier - edam - format - beta12orEarlier MSF format for (aligned) sequences. + beta12orEarlier true + beta12orEarlier + @@ -30544,14 +28091,11 @@ nexus alignment format true - edam - format - formats beta12orEarlier - bioinformatics beta12orEarlier Nexus/paup format for (aligned) sequences. + @@ -30561,15 +28105,12 @@ nexusnon alignment format - format - edam beta12orEarlier + Nexus/paup non-interleaved format for (aligned) sequences. true - bioinformatics beta12orEarlier - Nexus/paup non-interleaved format for (aligned) sequences. - formats + @@ -30579,12 +28120,11 @@ pair - format - bioinformatics beta12orEarlier - formats EMBOSS simple sequence pair alignment format. - edam + + + @@ -30594,12 +28134,11 @@ Phylip format - formats - bioinformatics - edam Phylip format for (aligned) sequences. beta12orEarlier - format + + + @@ -30609,12 +28148,11 @@ Phylipnon - formats - bioinformatics Phylip non-interleaved format for (aligned) sequences. beta12orEarlier - edam - format + + + @@ -30625,12 +28163,11 @@ scores format - edam Alignment format for score values for pairs of sequences. - formats beta12orEarlier - bioinformatics - format + + + @@ -30643,11 +28180,10 @@ SELEX format for (aligned) sequences. - formats beta12orEarlier - edam - format - bioinformatics + + + @@ -30658,12 +28194,11 @@ EMBOSS simple format - formats - edam beta12orEarlier - format - bioinformatics EMBOSS simple multiple alignment format. + + + @@ -30675,11 +28210,10 @@ Simple multiple sequence (alignment) format for SRS. - formats - bioinformatics - format beta12orEarlier - edam + + + @@ -30690,12 +28224,11 @@ srspair - bioinformatics - edam - formats - format Simple sequence pair (alignment) format for SRS. beta12orEarlier + + + @@ -30706,12 +28239,11 @@ T-Coffee format - bioinformatics beta12orEarlier - formats T-Coffee program alignment format. - edam - format + + + @@ -30724,11 +28256,10 @@ beta12orEarlier - formats Treecon format for (aligned) sequences. - edam - format - bioinformatics + + + @@ -30744,12 +28275,11 @@ - bioinformatics beta12orEarlier Data format for a phylogenetic tree. - format - formats - edam + + + @@ -30766,11 +28296,10 @@ Data format for a biological pathway or network. - bioinformatics - format - formats - edam beta12orEarlier + + + @@ -30786,12 +28315,11 @@ - format - bioinformatics Data format for a sequence-profile alignment. - edam beta12orEarlier - formats + + + @@ -30801,15 +28329,12 @@ Sequence-profile alignment (HMM) format - beta12orEarlier - edam - format - beta12orEarlier Data format for a sequence-HMM profile alignment. - formats true - bioinformatics + beta12orEarlier + beta12orEarlier + @@ -30825,12 +28350,11 @@ - bioinformatics beta12orEarlier - edam - formats - format Data format for an amino acid index. + + + @@ -30846,13 +28370,12 @@ - formats - format Data format for a full-text scientific article. - bioinformatics - edam Literature format beta12orEarlier + + + @@ -30868,12 +28391,11 @@ - formats Data format for an abstract (report) from text mining. - format beta12orEarlier - edam - bioinformatics + + + @@ -30889,12 +28411,11 @@ - bioinformatics - edam - format - formats beta12orEarlier Data format for reports on enzyme kinetics. + + + @@ -30910,13 +28431,12 @@ - format Format of a report on a chemical compound. - bioinformatics Chemical compound annotation format - edam - formats beta12orEarlier + + + @@ -30932,12 +28452,11 @@ - bioinformatics - format - formats beta12orEarlier Format of a report on a particular locus, gene, gene system or groups of genes. - edam + + + @@ -30953,12 +28472,11 @@ - formats Format of a workflow. beta12orEarlier - edam - format - bioinformatics + + + @@ -30968,12 +28486,11 @@ Tertiary structure format - edam Data format for a molecular tertiary structure. beta12orEarlier - formats - bioinformatics - format + + + @@ -30983,15 +28500,12 @@ Biological model format - edam - 1.2 - bioinformatics - Data format for a biological model. true - formats + 1.2 beta12orEarlier - format + Data format for a biological model. + @@ -31007,12 +28521,11 @@ - bioinformatics - edam - format - formats Text format of a chemical formula. beta12orEarlier + + + @@ -31028,12 +28541,11 @@ - bioinformatics Format of raw (unplotted) phylogenetic data. - format - formats - edam beta12orEarlier + + + @@ -31050,11 +28562,10 @@ beta12orEarlier - edam Format of phylogenetic continuous quantitative character data. - bioinformatics - formats - format + + + @@ -31070,12 +28581,11 @@ - edam - format beta12orEarlier - bioinformatics Format of phylogenetic discrete states data. - formats + + + @@ -31091,12 +28601,11 @@ - format beta12orEarlier - bioinformatics Format of phylogenetic cliques data. - formats - edam + + + @@ -31112,12 +28621,11 @@ - formats - format Format of phylogenetic invariants data. - edam - bioinformatics beta12orEarlier + + + @@ -31128,14 +28636,11 @@ Electron microscopy model format Annotation format for electron microscopy models. - format - bioinformatics beta12orEarlier true beta12orEarlier - formats - edam + @@ -31151,12 +28656,11 @@ - edam - bioinformatics - formats beta12orEarlier - format Format for phylogenetic tree distance data. + + + @@ -31166,14 +28670,11 @@ Polymorphism report format - formats - format 1.0 Format for sequence polymorphism data. - bioinformatics true beta12orEarlier - edam + @@ -31189,12 +28690,11 @@ - formats - edam - format - bioinformatics beta12orEarlier Format for reports on a protein family. + + + @@ -31211,11 +28711,10 @@ Format for molecular interaction data. - bioinformatics beta12orEarlier - edam - format - formats + + + @@ -31232,11 +28731,10 @@ Format for sequence assembly data. - bioinformatics - formats beta12orEarlier - format - edam + + + @@ -31254,10 +28752,9 @@ Format for microarray experimental data. beta12orEarlier - formats - edam - format - bioinformatics + + + @@ -31273,12 +28770,11 @@ - format beta12orEarlier - edam - formats - bioinformatics Format for sequence trace data (i.e. including base call information). + + + @@ -31295,11 +28791,10 @@ beta12orEarlier - bioinformatics - edam Format for a report on gene expression. - format - formats + + + @@ -31309,15 +28804,12 @@ Genotype and phenotype annotation format - bioinformatics - edam + beta12orEarlier Format of a report on genotype / phenotype information. true beta12orEarlier - beta12orEarlier - format - formats + @@ -31333,12 +28825,11 @@ - bioinformatics - format beta12orEarlier - formats - edam Format of a map of (typically one) molecular sequence annotated with features. + + + @@ -31354,12 +28845,11 @@ - formats Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. - format - edam beta12orEarlier - bioinformatics + + + @@ -31376,11 +28866,10 @@ beta12orEarlier - format - formats - bioinformatics - edam Format of a report of general information about a specific protein. + + + @@ -31390,15 +28879,12 @@ Protein report (enzyme) format - bioinformatics - edam - Format of a report of general information about a specific enzyme. - formats - format beta12orEarlier true beta12orEarlier + Format of a report of general information about a specific enzyme. + @@ -31414,12 +28900,11 @@ - formats Format of a matrix of 3D-1D scores (amino acid environment probabilities). beta12orEarlier - format - edam - bioinformatics + + + @@ -31435,12 +28920,11 @@ - edam - formats beta12orEarlier Format of a report on the quality of a protein three-dimensional model. - bioinformatics - format + + + @@ -31457,11 +28941,10 @@ beta12orEarlier - formats - format Format of a report on sequence hits and associated data from searching a sequence database. - bioinformatics - edam + + + @@ -31479,10 +28962,9 @@ Format of a matrix of genetic distances between molecular sequences. beta12orEarlier - bioinformatics - format - edam - formats + + + @@ -31499,11 +28981,10 @@ beta12orEarlier - format Format of a sequence motif. - edam - bioinformatics - formats + + + @@ -31519,12 +29000,11 @@ - edam - formats - bioinformatics beta12orEarlier Format of a sequence profile. - format + + + @@ -31540,12 +29020,11 @@ - bioinformatics Format of a hidden Markov model. - edam - formats - format beta12orEarlier + + + @@ -31561,12 +29040,11 @@ - format - formats - bioinformatics beta12orEarlier - edam Data format of a dirichlet distribution. + + + @@ -31583,11 +29061,10 @@ beta12orEarlier - format - edam - formats - bioinformatics Data format for the emission and transition counts of a hidden Markov model. + + + @@ -31604,11 +29081,10 @@ Format for secondary structure (predicted or real) of an RNA molecule. - edam - format - bioinformatics beta12orEarlier - formats + + + @@ -31625,11 +29101,10 @@ beta12orEarlier - format Format for secondary structure (predicted or real) of a protein molecule. - edam - formats - bioinformatics + + + @@ -31645,12 +29120,11 @@ - format - formats - edam - bioinformatics Format used to specify range(s) of sequence positions. beta12orEarlier + + + @@ -31661,12 +29135,11 @@ pure - bioinformatics beta12orEarlier - formats - edam Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. - format + + + @@ -31677,12 +29150,11 @@ unpure - formats - edam - bioinformatics beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. - format + + + @@ -31693,12 +29165,11 @@ unambiguous sequence - formats - format - bioinformatics beta12orEarlier - edam Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. + + + @@ -31709,12 +29180,11 @@ ambiguous - edam - formats - format Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. beta12orEarlier - bioinformatics + + + @@ -31731,11 +29201,10 @@ Format used for map of repeats in molecular (typically nucleotide) sequences. - format - bioinformatics - edam beta12orEarlier - formats + + + @@ -31752,11 +29221,10 @@ Format used for report on restriction enzyme recognition sites in nucleotide sequences. - bioinformatics - formats - format beta12orEarlier - edam + + + @@ -31772,12 +29240,11 @@ - formats Format used for report on coding regions in nucleotide sequences. beta12orEarlier - format - bioinformatics - edam + + + @@ -31793,12 +29260,11 @@ - format - edam Format used for clusters of molecular sequences. - bioinformatics - formats beta12orEarlier + + + @@ -31810,10 +29276,9 @@ beta12orEarlier Format used for clusters of protein sequences. - bioinformatics - edam - format - formats + + + @@ -31824,11 +29289,10 @@ Sequence cluster format (nucleic acid) beta12orEarlier - edam - format - bioinformatics - formats Format used for clusters of nucleotide sequences. + + + @@ -31838,15 +29302,12 @@ Gene cluster format - formats - format + Format used for clusters of genes. beta12orEarlier beta13 - Format used for clusters of genes. - edam true - bioinformatics + @@ -31858,12 +29319,11 @@ A text format resembling EMBL entry format. - bioinformatics - edam - formats beta12orEarlier - format This concept may be used for the many non-standard EMBL-like text formats. + + + @@ -31875,12 +29335,11 @@ beta12orEarlier - formats This concept may be used for non-standard FASTQ short read-like formats. - format - bioinformatics A text format resembling FASTQ short read format. - edam + + + @@ -31890,12 +29349,11 @@ EMBLXML - edam - formats beta12orEarlier - bioinformatics - format XML format for EMBL entries. + + + @@ -31905,12 +29363,11 @@ cdsxml - bioinformatics - format beta12orEarlier - edam XML format for EMBL entries. - formats + + + @@ -31920,12 +29377,11 @@ insdxml - formats - format XML format for EMBL entries. - edam - bioinformatics beta12orEarlier + + + @@ -31935,12 +29391,11 @@ geneseq - format - edam beta12orEarlier Geneseq sequence format. - formats - bioinformatics + + + @@ -31951,12 +29406,11 @@ UniProt-like (text) - bioinformatics - format - formats - edam beta12orEarlier A text sequence format resembling uniprotkb entry format. + + + @@ -31966,12 +29420,11 @@ UniProt format - formats UniProt entry sequence format. - format beta12orEarlier - bioinformatics - edam + + + @@ -31981,12 +29434,11 @@ ipi - formats - bioinformatics - format ipi sequence format. - edam beta12orEarlier + + + @@ -31997,12 +29449,11 @@ medline - format beta12orEarlier - bioinformatics - formats Abstract format used by MedLine database. - edam + + + @@ -32018,12 +29469,11 @@ - edam - bioinformatics beta12orEarlier - format Format used for ontologies. - formats + + + @@ -32034,11 +29484,10 @@ OBO format A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. - bioinformatics - format beta12orEarlier - edam - formats + + + @@ -32049,12 +29498,11 @@ OWL format - formats beta12orEarlier A serialisation format conforming to the Web Ontology Language (OWL) model. - edam - bioinformatics - format + + + @@ -32065,14 +29513,13 @@ FASTA-like (text) - edam + A text format resembling FASTA format. beta12orEarlier This concept may also be used for the many non-standard FASTA-like formats. - formats - bioinformatics - format - A text format resembling FASTA format. + + + @@ -32088,12 +29535,11 @@ - bioinformatics - format - edam - formats Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. beta12orEarlier + + + @@ -32110,11 +29556,10 @@ 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. - bioinformatics - format - edam - formats beta12orEarlier + + + @@ -32124,13 +29569,12 @@ EMBL format (XML) - formats - edam - format This is a placeholder for other more specific concepts. It should not normally be used for annotation. - bioinformatics An XML format for EMBL entries. beta12orEarlier + + + @@ -32142,12 +29586,11 @@ beta12orEarlier - edam This concept may be used for the non-standard GenBank-like text formats. - bioinformatics - formats A text format resembling GenBank entry (plain text) format. - format + + + @@ -32157,12 +29600,11 @@ Sequence feature table format (text) - bioinformatics - format beta12orEarlier Text format for a sequence feature table. - edam - formats + + + @@ -32172,14 +29614,11 @@ Strain data format - format true 1.0 beta12orEarlier - formats - edam - bioinformatics Format of a report on organism strain data / cell line. + @@ -32191,13 +29630,10 @@ beta12orEarlier beta12orEarlier - format - formats - edam - bioinformatics true Format for a report of strain data as used for CIP database entries. + @@ -32207,15 +29643,12 @@ phylip property values - formats - PHYLIP file format for phylogenetic property data. - format beta12orEarlier beta12orEarlier - edam - bioinformatics + PHYLIP file format for phylogenetic property data. true + @@ -32227,13 +29660,10 @@ Entry format (HTML) for the STRING database of protein interaction. beta12orEarlier - format - edam - beta12orEarlier - bioinformatics - formats true + beta12orEarlier + @@ -32244,12 +29674,11 @@ STRING entry format (XML) - format beta12orEarlier - formats - edam Entry format (XML) for the STRING database of protein interaction. - bioinformatics + + + @@ -32260,12 +29689,11 @@ GFF - bioinformatics beta12orEarlier GFF feature format (of indeterminate version). - formats - format - edam + + + @@ -32275,15 +29703,14 @@ GTF - edam beta12orEarlier - bioinformatics Gene Transfer Format (GTF), a restricted version of GFF. - format - formats + + + @@ -32294,12 +29721,11 @@ FASTA-HTML - format - bioinformatics - formats beta12orEarlier FASTA format wrapped in HTML elements. - edam + + + @@ -32311,11 +29737,10 @@ beta12orEarlier - formats - format - edam - bioinformatics EMBL entry format wrapped in HTML elements. + + + @@ -32327,13 +29752,10 @@ Format of an entry from the BioCyc enzyme database. beta12orEarlier - true - bioinformatics - formats - format - edam beta12orEarlier + true + @@ -32343,15 +29765,12 @@ ENZYME enzyme report format - format - Format of an entry from the Enzyme nomenclature database (ENZYME). - formats true beta12orEarlier beta12orEarlier - bioinformatics - edam + Format of an entry from the Enzyme nomenclature database (ENZYME). + @@ -32362,14 +29781,11 @@ PseudoCAP gene report format Format of a report on a gene from the PseudoCAP database. - edam - format - formats beta12orEarlier beta12orEarlier true - bioinformatics + @@ -32379,15 +29795,12 @@ GeneCards gene report format - bioinformatics - beta12orEarlier - Format of a report on a gene from the GeneCards database. - edam true beta12orEarlier - format - formats + beta12orEarlier + Format of a report on a gene from the GeneCards database. + @@ -32399,33 +29812,35 @@ beta12orEarlier Plain text - format - formats 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). - bioinformatics Textual format. - edam Tabular format + + + + + + - Tabular format - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + Tabular format + Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - + @@ -32442,14 +29857,13 @@ - bioinformatics - beta12orEarlier - format - edam - formats Hypertext Markup Language + beta12orEarlier HTML format. + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. @@ -32465,15 +29879,14 @@ XML - format - formats - bioinformatics Extensible Markup Language - edam eXtensible Markup Language (XML) format. beta12orEarlier Data in XML format can be serialised into text, or binary format. + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. @@ -32489,13 +29902,12 @@ Binary format - edam - formats - bioinformatics Binary format. beta12orEarlier 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. - format + + + @@ -32505,15 +29917,12 @@ URI format - true - beta13 - bioinformatics - format beta12orEarlier Typical textual representation of a URI. - formats - edam + true + beta13 + @@ -32523,15 +29932,12 @@ NCI-Nature pathway entry format - format - true - formats beta12orEarlier The format of an entry from the NCI-Nature pathways database. - bioinformatics + true beta12orEarlier - edam + @@ -32541,13 +29947,12 @@ Format (typed) - edam A broad class of format distinguished by the scientific nature of the data that is identified. - format beta12orEarlier 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. - bioinformatics - formats + + + @@ -32564,13 +29969,13 @@ - + - + @@ -32580,14 +29985,13 @@ BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). - formats - bioinformatics beta12orEarlier - format BioXSD XML format - edam + + + @@ -32600,10 +30004,9 @@ A serialisation format conforming to the Resource Description Framework (RDF) model. beta12orEarlier - bioinformatics - format - edam - formats + + + @@ -32615,11 +30018,10 @@ Genbank entry format wrapped in HTML elements. - bioinformatics beta12orEarlier - edam - formats - format + + + @@ -32629,15 +30031,12 @@ Protein features (domains) format - formats Format of a report on protein features (domain composition). - bioinformatics - true - format - edam beta12orEarlier + true beta12orEarlier + @@ -32647,13 +30046,12 @@ EMBL-like format - edam - formats This concept may be used for the many non-standard EMBL-like formats. A format resembling EMBL entry (plain text) format. - bioinformatics - format beta12orEarlier + + + @@ -32663,13 +30061,12 @@ FASTQ-like format - bioinformatics beta12orEarlier This concept may be used for non-standard FASTQ short read-like formats. - formats - format A format resembling FASTQ short read format. - edam + + + @@ -32679,13 +30076,12 @@ FASTA-like - format A format resembling FASTA format. - edam - formats beta12orEarlier - bioinformatics This concept may be used for the many non-standard FASTA-like formats. + + + @@ -32698,10 +30094,9 @@ A sequence format resembling uniprotkb entry format. beta12orEarlier - format - edam - formats - bioinformatics + + + @@ -32717,12 +30112,11 @@ - edam beta12orEarlier - format Format for a sequence feature table. - bioinformatics - formats + + + @@ -32734,11 +30128,10 @@ OBO ontology text format. - format - formats - bioinformatics - edam beta12orEarlier + + + @@ -32749,12 +30142,11 @@ OBO-XML - edam OBO ontology XML format. - bioinformatics - formats beta12orEarlier - format + + + @@ -32764,12 +30156,11 @@ Sequence record format (text) - formats - bioinformatics - format beta12orEarlier - edam Data format for a molecular sequence record. + + + @@ -32779,12 +30170,11 @@ Sequence record format (XML) - format - bioinformatics Data format for a molecular sequence record. - edam - formats beta12orEarlier + + + @@ -32794,12 +30184,11 @@ Sequence feature table format (XML) - formats - bioinformatics beta12orEarlier - format XML format for a sequence feature table. - edam + + + @@ -32810,11 +30199,10 @@ Alignment format (text) beta12orEarlier - bioinformatics - edam - format - formats Text format for molecular sequence alignment information. + + + @@ -32825,11 +30213,10 @@ Alignment format (XML) beta12orEarlier - bioinformatics - edam - formats XML format for molecular sequence alignment information. - format + + + @@ -32839,12 +30226,11 @@ Phylogenetic tree format (text) - formats - bioinformatics Text format for a phylogenetic tree. beta12orEarlier - edam - format + + + @@ -32854,12 +30240,11 @@ Phylogenetic tree format (XML) - formats - format XML format for a phylogenetic tree. - edam beta12orEarlier - bioinformatics + + + @@ -32870,13 +30255,12 @@ EMBL-like (XML) - edam - formats beta12orEarlier - format This concept may be used for the any non-standard EMBL-like XML formats. - bioinformatics An XML format resembling EMBL entry format. + + + @@ -32886,13 +30270,12 @@ GenBank-like format - bioinformatics This concept may be used for the non-standard GenBank-like formats. - edam - formats - format beta12orEarlier A format resembling GenBank entry (plain text) format. + + + @@ -32902,15 +30285,12 @@ STRING entry format - bioinformatics + true beta12orEarlier Entry format for the STRING database of protein interaction. - format - edam beta12orEarlier - true - formats + @@ -32921,11 +30301,10 @@ Sequence assembly format (text) Text format for sequence assembly data. - bioinformatics - edam - format beta12orEarlier - formats + + + @@ -32935,15 +30314,12 @@ Amino acid identifier format + beta12orEarlier true - bioinformatics Text format (representation) of amino acid residues. - format beta13 - edam - beta12orEarlier - formats + @@ -32954,12 +30330,11 @@ completely unambiguous - formats Alphabet for a molecular sequence without any unknown positions or ambiguity characters. - format - edam beta12orEarlier - bioinformatics + + + @@ -32971,11 +30346,10 @@ Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. - edam - bioinformatics - format beta12orEarlier - formats + + + @@ -32986,12 +30360,11 @@ completely unambiguous pure nucleotide - edam - format beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . - bioinformatics - formats + + + @@ -33003,11 +30376,10 @@ Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. - formats - bioinformatics - edam - format beta12orEarlier + + + @@ -33018,12 +30390,11 @@ completely unambiguous pure rna sequence - formats - format beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. - edam - bioinformatics + + + @@ -33041,10 +30412,9 @@ Format of a raw molecular sequence (i.e. the alphabet used). beta12orEarlier - formats - edam - format - bioinformatics + + + @@ -33059,10 +30429,9 @@ 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. beta12orEarlier - format - formats - edam - bioinformatics + + + @@ -33076,13 +30445,12 @@ - edam 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. beta12orEarlier 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. - format - formats - bioinformatics + + + @@ -33095,14 +30463,13 @@ SBML - formats beta12orEarlier - edam - format Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. - bioinformatics + + + @@ -33113,12 +30480,11 @@ completely unambiguous pure protein - edam - formats - format Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. beta12orEarlier - bioinformatics + + + @@ -33140,12 +30506,11 @@ - bioinformatics - formats beta12orEarlier - edam Format of a bibliographic reference. - format + + + @@ -33161,12 +30526,11 @@ - bioinformatics - formats - edam beta12orEarlier Format of a sequence annotation track. - format + + + @@ -33182,12 +30546,11 @@ - format Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. - formats - bioinformatics - edam beta12orEarlier + + + @@ -33203,12 +30566,11 @@ - bioinformatics - edam beta12orEarlier Format of sequence variation annotation. - formats - format + + + @@ -33219,12 +30581,11 @@ markx0 variant - format - formats - edam beta12orEarlier Some variant of Pearson MARKX alignment format. - bioinformatics + + + @@ -33237,11 +30598,10 @@ beta12orEarlier - edam Some variant of Mega format for (typically aligned) sequences. - bioinformatics - format - formats + + + @@ -33253,12 +30613,11 @@ - bioinformatics Some variant of Phylip format for (aligned) sequences. - format - edam - formats beta12orEarlier + + + @@ -33269,13 +30628,12 @@ AB1 - format AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. - bioinformatics - formats - edam beta12orEarlier + + + @@ -33286,14 +30644,13 @@ ACE - format - edam - bioinformatics beta12orEarlier ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). - formats - + + + + @@ -33304,15 +30661,14 @@ BED - 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). Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. - edam - bioinformatics + 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). beta12orEarlier - format - formats + + + @@ -33324,13 +30680,12 @@ bigBed format for large sequence annotation tracks, similar to textual BED format. - format beta12orEarlier - bioinformatics - formats - edam - + + + + @@ -33341,14 +30696,13 @@ WIG - edam - bioinformatics - 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. - format beta12orEarlier - formats + 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. + + + @@ -33359,14 +30713,13 @@ bigWig - formats - format beta12orEarlier bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. - edam - bioinformatics + + + @@ -33379,13 +30732,12 @@ beta12orEarlier - formats - edam - bioinformatics - format PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. + + + @@ -33398,14 +30750,13 @@ beta12orEarlier - format 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. - formats - edam Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. - bioinformatics + + + @@ -33416,15 +30767,14 @@ 2bit - format - edam 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. - formats - bioinformatics beta12orEarlier - + + + + @@ -33435,14 +30785,13 @@ .nib - formats - format - beta12orEarlier .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. - bioinformatics - edam + beta12orEarlier + + + @@ -33453,15 +30802,14 @@ genePred - bioinformatics beta12orEarlier - edam - formats - format 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. genePred table format for gene prediction tracks. + + + @@ -33472,14 +30820,13 @@ pgSnp - edam beta12orEarlier - bioinformatics - formats - format Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. + + + @@ -33490,14 +30837,13 @@ axt - axt format of alignments, typically produced from BLASTZ. - format beta12orEarlier - edam - formats - bioinformatics + axt format of alignments, typically produced from BLASTZ. + + + @@ -33508,12 +30854,11 @@ LAV - beta12orEarlier - format LAV format of alignments generated by BLASTZ and LASTZ. - bioinformatics - formats - edam + beta12orEarlier + + + @@ -33526,12 +30871,11 @@ Pileup - bioinformatics - beta12orEarlier - format - formats Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). - edam + beta12orEarlier + + + @@ -33545,11 +30889,10 @@ Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - bioinformatics beta12orEarlier - edam - formats - format + + + @@ -33562,12 +30905,11 @@ SRF - edam beta12orEarlier - formats - bioinformatics Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. - format + + + @@ -33580,14 +30922,13 @@ ZTR - edam - format - formats - ZTR format for storing chromatogram data from DNA sequencing instruments. beta12orEarlier - bioinformatics - + ZTR format for storing chromatogram data from DNA sequencing instruments. + + + + @@ -33598,12 +30939,11 @@ GVF - edam beta12orEarlier - formats - format - bioinformatics Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. + + + @@ -33616,12 +30956,11 @@ BCF - edam - format BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - bioinformatics beta12orEarlier - formats + + + @@ -33639,11 +30978,10 @@ beta13 - formats - format Format of a matrix (array) of numerical values. - bioinformatics - edam + + + @@ -33659,12 +30997,11 @@ - bioinformatics beta13 - formats - edam Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). - format + + + @@ -33674,13 +31011,12 @@ Raw SCOP domain classification format - edam These are the parsable data files provided by SCOP. beta13 - format - formats Format of raw SCOP domain classification data files. - bioinformatics + + + @@ -33690,13 +31026,12 @@ Raw CATH domain classification format - bioinformatics - edam - format Format of raw CATH domain classification data files. beta13 These are the parsable data files provided by CATH. - formats + + + @@ -33706,13 +31041,12 @@ CATH domain report format - bioinformatics 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. - format beta13 Format of summary of domain classification information for a CATH domain. - edam - formats + + + @@ -33723,12 +31057,11 @@ SBRML - format - 1.0 - bioinformatics - formats - edam Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. + 1.0 + + + @@ -33740,14 +31073,13 @@ BioPAX - edam - format - formats - bioinformatics 1.0 BioPAX is an exchange format for pathway data, with its data model defined in OWL. + + + @@ -33759,12 +31091,11 @@ - bioinformatics - edam - format 1.0 EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. - formats + + + @@ -33778,12 +31109,11 @@ MIF - edam XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. - formats - bioinformatics 1.0 - format + + + @@ -33796,14 +31126,13 @@ phyloXML - formats 1.0 - bioinformatics - edam - format phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. + + + @@ -33814,14 +31143,13 @@ NeXML - formats - bioinformatics NeXML is a standardised XML format for rich phyloinformatic data. - edam 1.0 - format + + + @@ -33833,12 +31161,11 @@ - formats 1.0 MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). - format - bioinformatics - edam + + + @@ -33853,11 +31180,10 @@ MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). - formats 1.0 - bioinformatics - edam - format + + + @@ -33876,14 +31202,13 @@ - bioinformatics GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). - format - edam 1.0 - formats + + + @@ -33895,13 +31220,12 @@ GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). - bioinformatics - format - edam - formats 1.0 + + + @@ -33917,12 +31241,11 @@ - edam - formats - bioinformatics - format beta12orEarlier Data format for a report of information derived from a biological pathway or network. + + + @@ -33932,12 +31255,11 @@ Experiment annotation format - format - edam - bioinformatics - formats Data format for annotation on a laboratory experiment. beta12orEarlier + + + @@ -33954,13 +31276,12 @@ - format - formats - edam 1.2 Reflects a UCSC Browser DB table. Cytoband format for chromosome cytobands. - bioinformatics + + + @@ -33974,12 +31295,11 @@ - formats CopasiML, the native format of COPASI. - bioinformatics - edam - format 1.2 + + + @@ -33993,13 +31313,12 @@ 1.2 - formats - bioinformatics - edam CellML, the format for mathematical models of biological and other networks. - format - + + + + @@ -34010,14 +31329,13 @@ PSI MI TAB (MITAB) - format - bioinformatics Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. 1.2 - edam - formats + + + @@ -34028,11 +31346,10 @@ PSI-PAR 1.2 - format - edam - bioinformatics - formats Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. + + + @@ -34046,14 +31363,13 @@ 1.2 - format - edam mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. - bioinformatics - formats mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - + + + + @@ -34070,11 +31386,10 @@ Format for mass spectrometry data. - edam - formats 1.2 - bioinformatics - format + + + @@ -34085,14 +31400,13 @@ TraML - TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - format 1.2 - formats - edam - bioinformatics + TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. + + + @@ -34103,14 +31417,13 @@ mzIdentML - bioinformatics - 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. - edam - format - formats 1.2 + 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. + + + @@ -34121,14 +31434,13 @@ mzQuantML - formats - 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. - format - edam 1.2 - bioinformatics + 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. + + + @@ -34145,14 +31457,13 @@ - formats 1.2 - format - edam GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. - bioinformatics + + + @@ -34169,14 +31480,13 @@ - format - edam 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. 1.2 - formats - bioinformatics + + + @@ -34188,11 +31498,10 @@ 1.2 - bioinformatics - edam - formats A human-readable encoding for the Web Ontology Language (OWL). - format + + + @@ -34203,13 +31512,12 @@ Manchester OWL Syntax - edam - bioinformatics This format was influenced by the OWL Abstract Syntax and the DL style syntax. 1.2 - format - formats A syntax for writing OWL class expressions. + + + @@ -34221,12 +31529,11 @@ 1.2 - edam - format - formats A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". - bioinformatics This format is used in Protege 4. + + + @@ -34238,12 +31545,11 @@ The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. - format 1.2 - formats - bioinformatics - edam The SPARQL Query Language incorporates a very similar syntax. + + + @@ -34256,11 +31562,10 @@ 1.2 A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. - format - formats N-Triples should not be confused with Notation 3 which is a superset of Turtle. - edam - bioinformatics + + + @@ -34271,12 +31576,11 @@ Notation3 - format - bioinformatics A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. N3 - edam - formats + + + @@ -34290,12 +31594,11 @@ RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. 1.2 - edam RDF - formats - bioinformatics Resource Description Framework (RDF) XML format. - format + + + @@ -34307,13 +31610,12 @@ OWL/XML - edam OWL - formats 1.2 OWL ontology XML serialisation format. - bioinformatics - format + + + @@ -34324,14 +31626,13 @@ A2M - bioinformatics 1.3 - formats - edam - format 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. + + + @@ -34343,12 +31644,11 @@ 1.3 - format - bioinformatics 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 - edam - formats + + + @@ -34360,14 +31660,13 @@ MAP - bioinformatics - edam Plink MAP - format - formats 1.3 The MAP file describes SNPs and is used by the Plink package. + + + @@ -34377,14 +31676,13 @@ PED - edam The PED file describes individuals and genetic data and is used by the Plink package. 1.3 - format - formats Plink PED - bioinformatics + + + @@ -34394,12 +31692,11 @@ Individual genetic data format - format - Data format for a metadata on an individual and their genetic data. - formats - bioinformatics 1.3 - edam + Data format for a metadata on an individual and their genetic data. + + + @@ -34410,14 +31707,13 @@ PED/MAP - format - The PED/MAP file describes data used by the Plink package. - formats 1.3 Plink PED/MAP - edam - bioinformatics + The PED/MAP file describes data used by the Plink package. + + + @@ -34428,14 +31724,13 @@ CT - Connect format Connectivity Table file format - bioinformatics + Connect format File format of a CT (Connectivity Table) file from the RNAstructure package. - edam - formats - 1.3 - format + beta12orEarlier + + + @@ -34449,11 +31744,10 @@ XRNA old input style format. - edam - format - bioinformatics - 1.3 - formats + beta12orEarlier + + + @@ -34466,12 +31760,11 @@ - edam + beta12orEarlier RNA Markup Language. - 1.3 - formats - format - bioinformatics + + + @@ -34483,13 +31776,12 @@ GDE - 1.3 - formats + beta12orEarlier Format for the Genetic Data Environment (GDE). - format - bioinformatics - edam + + + @@ -34499,13 +31791,12 @@ BLC - formats - bioinformatics - format - edam Block file format A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. 1.3 + + + @@ -34523,10 +31814,9 @@ 1.3 - edam - format - bioinformatics - formats + + + @@ -34543,11 +31833,10 @@ BAM indexing format - formats 1.3 - format - bioinformatics - edam + + + @@ -34559,12 +31848,11 @@ HMMER2 1.3 - format - formats - edam HMMER profile HMM file for HMMER versions 2.x - bioinformatics + + + @@ -34575,12 +31863,11 @@ HMMER3 HMMER profile HMM file for HMMER versions 3.x - formats - bioinformatics 1.3 - format - edam + + + @@ -34592,10 +31879,9 @@ 1.3 EMBOSS simple sequence pair alignment format. - formats - edam - bioinformatics - format + + + @@ -34607,12 +31893,11 @@ BLAST XML results format - format - bioinformatics - formats 1.3 XML format as produced by the NCBI Blast package - edam + + + @@ -34624,7 +31909,6 @@ Function (programming) - bioinformatics Lambda abstraction Mathematical function Computational procedure @@ -34635,16 +31919,16 @@ sumo:Function Mathematical operation Computational method - edam Function - operations 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. Computational tool - operation + + + @@ -34661,28 +31945,16 @@ - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function - - + - However, one may think that an operation is not a process. + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. - - - + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. @@ -34697,6 +31969,12 @@ + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. + + + + + Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. @@ -34709,22 +31987,22 @@ - GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process - - Function, including an operation, can be a quality/property of e.g. a computational tool. + BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). - + - BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). + Computational tool + Computational tool provides one or more operations. - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. @@ -34733,22 +32011,28 @@ - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + However, one may think that an operation is not a process. - + + - Process - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Function, including an operation, can be a quality/property of e.g. a computational tool. + - Computational tool provides one or more operations. - Computational tool + GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + + + + + + Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. + @@ -34760,23 +32044,22 @@ - - + + - - + + - bioinformatics - operations - operation Database retrieval Search or query a data resource and retrieve entries and / or annotation. beta12orEarlier - edam + + + @@ -34786,15 +32069,12 @@ Data retrieval (database cross-reference) - operations + beta13 true Search database to retrieve all relevant references to a particular entity or entry. - beta13 - operation beta12orEarlier - edam - bioinformatics + @@ -34806,23 +32086,22 @@ - - + + - - + + - bioinformatics - 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. - edam beta12orEarlier - operation - operations + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. + + + @@ -34839,12 +32118,11 @@ Database indexing - bioinformatics - operations - edam Generate an index of (typically a file of) biological data. beta12orEarlier - operation + + + @@ -34856,23 +32134,22 @@ - - + + - - + + - edam beta12orEarlier Analyse an index of biological data. - bioinformatics - operation - operations Database index analysis + + + @@ -34885,12 +32162,9 @@ beta12orEarlier Retrieve basic information about a molecular sequence. beta12orEarlier - operation true - operations - bioinformatics - edam + @@ -34900,12 +32174,11 @@ Sequence generation - edam Generate a molecular sequence by some means. beta12orEarlier - operation - operations - bioinformatics + + + @@ -34916,12 +32189,11 @@ Sequence editing - operation - operations beta12orEarlier - bioinformatics - edam Edit or change a molecular sequence, either randomly or specifically. + + + @@ -34931,13 +32203,12 @@ Sequence merging - operations Sequence splicing - operation Merge two or more (typically overlapping) molecular sequences. beta12orEarlier - edam - bioinformatics + + + @@ -34947,12 +32218,11 @@ Sequence conversion - operation beta12orEarlier - operations - bioinformatics - edam Convert a molecular sequence from one type to another. + + + @@ -34964,22 +32234,21 @@ - - + + - - + + - operations - edam Calculate sequence complexity, for example to find low-complexity regions in sequences. - operation beta12orEarlier - bioinformatics + + + @@ -35002,11 +32271,10 @@ beta12orEarlier - operations Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. - bioinformatics - operation - edam + + + @@ -35018,22 +32286,21 @@ - - + + - - + + - edam Calculate character or word composition or frequency of a molecular sequence. - operations - bioinformatics beta12orEarlier - operation + + + @@ -35050,12 +32317,11 @@ 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. - edam beta12orEarlier Find and/or analyse repeat sequences in (typically nucleotide) sequences. - operation - operations - bioinformatics + + + @@ -35073,13 +32339,12 @@ beta12orEarlier - edam - operations Motif discovery Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). - operation - bioinformatics Motifs and patterns might be conserved or over-represented (occur with improbable frequency). + + + @@ -35102,15 +32367,14 @@ - bioinformatics Sequence motif detection - operation Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). - edam beta12orEarlier - operations Motif detection Motif recognition + + + @@ -35129,10 +32393,9 @@ Find motifs shared by molecular sequences. beta12orEarlier - operations - edam - operation - bioinformatics + + + @@ -35143,15 +32406,12 @@ Transcription regulatory sequence analysis true - beta12orEarlier - operation - edam + Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. beta13 For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. - Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. - bioinformatics - operations + beta12orEarlier + @@ -35168,13 +32428,12 @@ - operation Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). beta12orEarlier - bioinformatics - operations - edam 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. + + + @@ -35187,24 +32446,23 @@ - - + + - - + + - operations This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. - bioinformatics Protein structural property calculation - operation - edam beta12orEarlier Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. + + + @@ -35215,19 +32473,12 @@ Protein flexibility and motion analysis - - - - - - - bioinformatics 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. Analyse flexibility and motion in protein structure. - operations beta12orEarlier - operation - edam + + + @@ -35251,12 +32502,11 @@ Protein structural feature identification beta12orEarlier - operations - operation 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. Identify or screen for 3D structural motifs in protein structure(s). - bioinformatics - edam + + + @@ -35279,11 +32529,10 @@ Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). - bioinformatics - edam - operations beta12orEarlier - operation + + + @@ -35293,18 +32542,11 @@ Protein architecture analysis - - - - - - Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). - operations - operation beta12orEarlier - bioinformatics - edam + + + @@ -35326,20 +32568,19 @@ - operation WHATIF: SymShellOneXML WHATIF: SymShellFiveXML Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). - bioinformatics WHATIF:ListContactsNormal beta12orEarlier - operations WHATIF:ListSideChainContactsNormal - edam WHATIF:ListSideChainContactsRelaxed WHATIF: SymShellTwoXML WHATIF:ListContactsRelaxed WHATIF: SymShellTenXML + + + @@ -35355,12 +32596,11 @@ - operation - bioinformatics Calculate, visualise or analyse phi/psi angles of a protein structure. beta12orEarlier - operations - edam + + + @@ -35390,13 +32630,12 @@ Protein property rendering - operation beta12orEarlier This includes methods to render and visualise the properties of a protein sequence. - operations - bioinformatics - edam Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + + + @@ -35409,23 +32648,22 @@ - - + + - - + + - edam - bioinformatics - operations - operation Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. 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. beta12orEarlier + + + @@ -35438,24 +32676,23 @@ - - + + - - + + SO:0000110 - bioinformatics beta12orEarlier Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. - operation - edam - operations Sequence feature detection + + + @@ -35465,15 +32702,12 @@ Data retrieval (feature table) - operation - bioinformatics - Extract a sequence feature table from a sequence database entry. - beta13 - operations true beta12orEarlier - edam + Extract a sequence feature table from a sequence database entry. + beta13 + @@ -35491,22 +32725,21 @@ - - + + - - + + - beta12orEarlier - edam - operations Query the features (in a feature table) of molecular sequence(s). - bioinformatics - operation + beta12orEarlier + + + @@ -35520,23 +32753,22 @@ - + - + - edam Feature table comparison - operations - operation Compare the feature tables of two or more molecular sequences. Sequence feature comparison beta12orEarlier - bioinformatics + + + @@ -35546,15 +32778,12 @@ Data retrieval (sequence alignment) - operations - beta12orEarlier - edam - operation Display basic information about a sequence alignment. beta13 true - bioinformatics + beta12orEarlier + @@ -35567,22 +32796,21 @@ - - + + - - + + beta12orEarlier - operation - bioinformatics Analyse a molecular sequence alignment. - operations - edam + + + @@ -35593,13 +32821,12 @@ Sequence alignment comparison - bioinformatics - edam - operation See also 'Sequence profile alignment'. beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. - operations + + + @@ -35609,12 +32836,11 @@ Sequence alignment conversion - operation Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). - edam beta12orEarlier - operations - bioinformatics + + + @@ -35627,12 +32853,9 @@ beta13 Process (read and / or write) physicochemical property data of nucleic acids. true - operations - operation - edam - bioinformatics beta12orEarlier + @@ -35648,12 +32871,11 @@ - edam Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. - operation beta12orEarlier - operations - bioinformatics + + + @@ -35669,12 +32891,11 @@ - operations Predict splicing alternatives or transcript isoforms from analysis of sequence data. - operation beta12orEarlier - bioinformatics - edam + + + @@ -35691,13 +32912,12 @@ - operation Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. - edam - operations - bioinformatics - Detect frameshift errors in DNA sequences (from sequencing projects). beta12orEarlier + Detect frameshift errors in DNA sequences (from sequencing projects). + + + @@ -35708,12 +32928,11 @@ Vector sequence detection - operation - edam Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. - operations - bioinformatics beta12orEarlier + + + @@ -35728,13 +32947,13 @@ - + - + @@ -35744,13 +32963,12 @@ beta12orEarlier - edam Predict secondary structure of protein sequences. - operations Secondary structure prediction (protein) - operation - bioinformatics 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. + + + @@ -35766,13 +32984,12 @@ - bioinformatics Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. Predict super-secondary structure of protein sequence(s). - operations - edam - operation beta12orEarlier + + + @@ -35789,12 +33006,11 @@ - edam beta12orEarlier - bioinformatics - operation Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. - operations + + + @@ -35816,13 +33032,12 @@ - bioinformatics - operation - operations 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). 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. beta12orEarlier - edam + + + @@ -35835,22 +33050,21 @@ - - + + - - + + - edam beta12orEarlier - bioinformatics - operation Predict tertiary structure of a molecular (biopolymer) sequence. - operations + + + @@ -35867,13 +33081,12 @@ - Methods usually involve multiple sequence alignment analysis. beta12orEarlier Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. - operation - operations - edam - bioinformatics + Methods usually involve multiple sequence alignment analysis. + + + @@ -35885,22 +33098,21 @@ - - + + - - + + beta12orEarlier - bioinformatics - operation - edam - operations Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + + + @@ -35912,11 +33124,10 @@ Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. - operations - operation - bioinformatics - edam beta12orEarlier + + + @@ -35927,12 +33138,11 @@ Protein-protein interaction prediction (from protein structure) - bioinformatics Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. beta12orEarlier - operations - edam - operation + + + @@ -35946,22 +33156,21 @@ - - + + - - + + - edam - operation beta12orEarlier Analyse a network of protein interactions. - operations - bioinformatics + + + @@ -35978,12 +33187,11 @@ - operation Compare two or more networks of protein interactions. - edam - operations beta12orEarlier - bioinformatics + + + @@ -36008,11 +33216,10 @@ beta12orEarlier Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). - bioinformatics - operations Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). - operation - edam + + + @@ -36035,14 +33242,13 @@ - operation Nucleic acid folding - bioinformatics - operations Nucleic acid folding modelling Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. - edam beta12orEarlier + + + @@ -36052,16 +33258,13 @@ Data retrieval (restriction enzyme annotation) - Retrieve information on restriction enzymes or restriction enzyme sites. - bioinformatics - edam beta12orEarlier - operations + Retrieve information on restriction enzymes or restriction enzyme sites. true Restriction enzyme information retrieval beta13 - operation + @@ -36071,16 +33274,13 @@ Genetic marker identification - edam - operations - beta13 - true - bioinformatics 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. Identify genetic markers in DNA sequences. - operation + beta13 beta12orEarlier + true + @@ -36096,15 +33296,16 @@ - operation + Functional 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. - bioinformatics 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. Genetic map generation - edam Linkage mapping + This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). beta12orEarlier - operations + + + @@ -36116,23 +33317,22 @@ - - + + - - + + - edam + 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. beta12orEarlier - bioinformatics - Analyse genetic linkage. - operation - operations + + + @@ -36148,12 +33348,11 @@ - operations - edam - operation beta12orEarlier - bioinformatics Calculate codon usage statistics and create a codon usage table. + + + @@ -36165,11 +33364,10 @@ Compare two or more codon usage tables. - bioinformatics - edam - operation beta12orEarlier - operations + + + @@ -36181,8 +33379,8 @@ - - + + @@ -36194,29 +33392,28 @@ - + - - + + - - + + - edam synon: Codon usage table analysis - operation Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. - bioinformatics - operations synon: Codon usage data analysis beta12orEarlier + + + @@ -36228,22 +33425,21 @@ - - + + - - + + - bioinformatics beta12orEarlier Identify and plot third base position variability in a nucleotide sequence. - operation - operations - edam + + + @@ -36260,11 +33456,10 @@ beta12orEarlier - bioinformatics - edam - operations Find exact character or word matches between molecular sequences without full sequence alignment. - operation + + + @@ -36286,13 +33481,12 @@ - bioinformatics Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. - operations - edam beta12orEarlier - operation Phylogenetic distance matrix generation + + + @@ -36314,12 +33508,11 @@ - operation Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. - edam - operations - bioinformatics beta12orEarlier + + + @@ -36340,11 +33533,10 @@ Sequence cluster generation Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. beta12orEarlier - bioinformatics - operations - edam - operation The clusters may be output or used internally for some other purpose. + + + @@ -36358,25 +33550,24 @@ - - + + - - + + Sequence alignment computation - operation - operations Sequence alignment - bioinformatics Sequence alignment generation - edam Align (identify equivalent sites within) molecular sequences. beta12orEarlier + + + @@ -36387,15 +33578,12 @@ Hybrid sequence alignment construction Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - edam + beta13 + beta12orEarlier true - operation Hybrid sequence alignment - operations - beta12orEarlier - beta13 - bioinformatics + @@ -36412,12 +33600,11 @@ Align molecular sequences using sequence and structural information. - bioinformatics beta12orEarlier - operation - operations - edam Structure-based sequence alignment + + + @@ -36435,13 +33622,12 @@ - operations - bioinformatics Structure alignment - edam beta12orEarlier Align (superimpose) molecular tertiary structures. - operation + + + @@ -36454,22 +33640,21 @@ - - + + - - + + - operation - beta12orEarlier Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. - operations - bioinformatics - edam + beta12orEarlier + + + @@ -36499,13 +33684,12 @@ - operation - edam beta12orEarlier Generate some type of structural (3D) profile or template from a structure or structure alignment. - operations Structural profile generation - bioinformatics + + + @@ -36529,13 +33713,12 @@ Align sequence profiles (representing sequence alignments). - beta12orEarlier See also 'Sequence alignment comparison'. - bioinformatics - operation + beta12orEarlier Sequence profile alignment - edam - operations + + + @@ -36548,8 +33731,8 @@ - - + + @@ -36560,18 +33743,17 @@ - - + + - bioinformatics Structural (3D) profile alignment Align structural (3D) profiles or templates (representing structures or structure alignments). Structural profile alignment - operation - edam beta12orEarlier - operations + + + @@ -36585,24 +33767,23 @@ - - + + - - + + - operation A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - operations Sequence-profile alignment Align molecular sequence(s) to sequence profile(s). beta12orEarlier - bioinformatics - edam + + + @@ -36629,11 +33810,10 @@ Sequence-3D profile alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). - operations - edam - bioinformatics beta12orEarlier - operation + + + @@ -36646,30 +33826,29 @@ - - + + - - + + - - + + Sequence-structure alignment Align molecular sequence to structure in 3D space (threading). beta12orEarlier - edam 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. - operation - operations - bioinformatics + + + @@ -36693,15 +33872,14 @@ - bioinformatics - edam Protein fold prediction - operation 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. Protein domain prediction - operations beta12orEarlier + + + @@ -36717,15 +33895,14 @@ - operation - operations This includes documentation, general information and other metadata on entities such as databases, database entries and tools. beta12orEarlier Data retrieval (metadata) Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. - bioinformatics Data retrieval (documentation) - edam + + + @@ -36737,22 +33914,21 @@ - - + + - - + + - bioinformatics - edam - operation - operations Query the biomedical and informatics literature. beta12orEarlier + + + @@ -36764,14 +33940,14 @@ - - + + - - + + @@ -36781,12 +33957,11 @@ Process and analyse text (typically the biomedical and informatics literature) to extract information from it. - edam Text data mining - operations beta12orEarlier - operation - bioinformatics + + + @@ -36803,11 +33978,10 @@ Perform in-silico (virtual) PCR. - operation - operations - edam - bioinformatics beta12orEarlier + + + @@ -36819,30 +33993,29 @@ - - + + - - + + - - + + - operations - bioinformatics Design or predict oligonucleotide primers for PCR and DNA amplification etc. - edam 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. PCR primer prediction beta12orEarlier - operation + + + @@ -36861,14 +34034,14 @@ - - + + - - + + @@ -36877,13 +34050,12 @@ - operation Microarray probe prediction - edam - bioinformatics beta12orEarlier - operations Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. + + + @@ -36908,12 +34080,11 @@ Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. - bioinformatics - edam - operation - operations 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. beta12orEarlier + + + @@ -36936,13 +34107,12 @@ - edam This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - operations Standardize or normalize microarray data. - operation - bioinformatics beta12orEarlier + + + @@ -36952,15 +34122,12 @@ Sequencing-based expression profile data processing - bioinformatics - edam - operations beta12orEarlier beta12orEarlier true - operation Process (read and / or write) SAGE, MPSS or SBS experimental data. + @@ -36976,12 +34143,11 @@ - edam Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. beta12orEarlier - operation - operations - bioinformatics + + + @@ -36999,12 +34165,11 @@ Gene expression profiling beta12orEarlier - Generate a gene expression profile or pattern, for example from microarray data. - edam - operations Expression profiling - bioinformatics - operation + Generate a gene expression profile or pattern, for example from microarray data. + + + @@ -37022,11 +34187,10 @@ Compare gene expression profiles or patterns. - operation beta12orEarlier - edam - operations - bioinformatics + + + @@ -37036,15 +34200,12 @@ Functional profiling - operation beta12orEarlier + Interpret (in functional terms) and annotate gene expression data. beta12orEarlier true - bioinformatics - operations - Interpret (in functional terms) and annotate gene expression data. - edam + @@ -37054,16 +34215,13 @@ EST and cDNA sequence analysis - bioinformatics - true - operation - For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. beta12orEarlier + true beta12orEarlier - edam - operations + For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. Analyse EST or cDNA sequences. + @@ -37074,15 +34232,12 @@ Structural genomics target selection true - operations - beta12orEarlier - bioinformatics - operation Methods will typically navigate a graph of protein families of known structure. Identify and select targets for protein structural determination. - edam + beta12orEarlier beta12orEarlier + @@ -37095,22 +34250,21 @@ - - + + - - + + - bioinformatics - edam Assign secondary structure from protein coordinate or experimental data. - operation beta12orEarlier - operations + + + @@ -37132,12 +34286,11 @@ - edam - operation - operations Assign a protein tertiary structure (3D coordinates) from raw experimental data. beta12orEarlier - bioinformatics + + + @@ -37150,26 +34303,26 @@ - - + + - + - - + + - + @@ -37179,13 +34332,12 @@ beta12orEarlier - operations WHATIF: UseFileDB - operation 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. - edam - bioinformatics Evaluate the quality or correctness a protein three-dimensional model. + + + @@ -37196,14 +34348,13 @@ Protein model refinement - WHATIF: CorrectedPDBasXML - operation - bioinformatics - edam 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. - operations beta12orEarlier Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc. + WHATIF: CorrectedPDBasXML + + + @@ -37227,14 +34378,13 @@ Phylogenetic tree generation - edam beta12orEarlier Construct a phylogenetic tree. Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. - bioinformatics - operations Phylogenetic tree construction - operation + + + @@ -37256,12 +34406,11 @@ - bioinformatics - edam - operation - operations Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. beta12orEarlier + + + @@ -37272,13 +34421,12 @@ Phylogenetic tree comparison - operations - operation 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. Compare two or more phylogenetic trees. beta12orEarlier - bioinformatics - edam + + + @@ -37301,12 +34449,11 @@ - edam - operation - Edit a phylogenetic tree. beta12orEarlier - bioinformatics - operations + Edit a phylogenetic tree. + + + @@ -37322,13 +34469,12 @@ - operation Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). beta12orEarlier - bioinformatics - operations - edam 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. + + + @@ -37338,12 +34484,11 @@ Protein folding simulation - edam Simulate the folding of a protein. beta12orEarlier - bioinformatics - operations - operation + + + @@ -37354,12 +34499,11 @@ Protein folding pathway prediction - edam - operations beta12orEarlier - bioinformatics - operation Predict the folding pathway(s) or non-native structural intermediates of a protein. + + + @@ -37381,12 +34525,11 @@ - bioinformatics - edam Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). - operations - operation beta12orEarlier + + + @@ -37409,14 +34552,13 @@ - operations beta12orEarlier - operation Methods might predict silent or pathological mutations. - edam Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. Protein mutation modelling - bioinformatics + + + @@ -37426,15 +34568,12 @@ Immunogen design - operation - beta12orEarlier beta12orEarlier - operations - edam + beta12orEarlier Design molecules that elicit an immune response (immunogens). - bioinformatics true + @@ -37457,12 +34596,11 @@ - edam - operations beta12orEarlier Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). - bioinformatics - operation + + + @@ -37474,22 +34612,21 @@ - - + + - - + + - operation Calculate Km, Vmax and derived data for an enzyme reaction. - edam beta12orEarlier - operations - bioinformatics + + + @@ -37497,14 +34634,14 @@ - File reformatting + File format conversion - edam - operation - operations + File reformatting Reformat a file of data (or equivalent entity in memory). beta12orEarlier - bioinformatics + + + @@ -37515,12 +34652,11 @@ File validation - bioinformatics - operation - operations beta12orEarlier - edam Test and validate the format and content of a data file. + + + @@ -37532,29 +34668,28 @@ - - + + - - + + - - + + - operation - edam Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. Visualisation - bioinformatics - operations beta12orEarlier + + + @@ -37567,23 +34702,22 @@ - - + + - - + + - operations beta12orEarlier - operation - bioinformatics This excludes direct retrieval methods (e.g. the dbfetch program). - edam Search a sequence database by sequence comparison and retrieve similar sequences. + + + @@ -37596,22 +34730,21 @@ - - + + - - + + - operation - bioinformatics - beta12orEarlier - operations Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. - edam + beta12orEarlier + + + @@ -37634,14 +34767,14 @@ - edam - operations + Sequence profile database search Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. beta12orEarlier Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). - operation - bioinformatics Protein sequence classification + + + @@ -37659,12 +34792,11 @@ - operations - bioinformatics Screen a sequence against a motif or pattern database. beta12orEarlier - edam - operation + + + @@ -37673,21 +34805,13 @@ Sequence profile database search - - - - - - - - - - operations + + 1.4 Search a database of sequence profiles with a query sequence. - operation - bioinformatics - edam beta12orEarlier + true + + @@ -37697,15 +34821,12 @@ Transmembrane protein database search - edam - operation - bioinformatics beta12orEarlier Search a database of transmembrane proteins, for example for sequence or structural similarities. - beta12orEarlier - operations true + beta12orEarlier + @@ -37716,11 +34837,10 @@ Sequence retrieval (by code) beta12orEarlier - edam - operations - operation - bioinformatics Query a database and retrieve sequences with a given entry code or accession number. + + + @@ -37730,12 +34850,11 @@ Sequence retrieval (by keyword) - edam beta12orEarlier - bioinformatics - operations - operation Query a database and retrieve sequences containing a given keyword. + + + @@ -37749,11 +34868,10 @@ beta12orEarlier Search a sequence database and retrieve sequences that are similar to a query sequence. - operations - bioinformatics Sequence similarity search - edam - operation + + + @@ -37770,12 +34888,11 @@ - bioinformatics - edam - operation beta12orEarlier - operations Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + + + @@ -37787,22 +34904,21 @@ - - + + - - + + beta12orEarlier - operation - operations Search a sequence database and retrieve sequences of a given amino acid composition. - edam - bioinformatics + + + @@ -37812,12 +34928,11 @@ Sequence database search (by physicochemical property) - operation beta12orEarlier Search a sequence database and retrieve sequences with a specified physicochemical property. - operations - edam - bioinformatics + + + @@ -37828,14 +34943,13 @@ Sequence database search (by sequence using word-based methods) - operation - bioinformatics Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. - operations Sequence similarity search (word-based methods) 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. - edam beta12orEarlier + + + @@ -37846,14 +34960,13 @@ Sequence database search (by sequence using profile-based methods) - operations This includes tools based on PSI-BLAST. beta12orEarlier - bioinformatics 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. Sequence similarity search (profile-based methods) - edam - operation + + + @@ -37872,12 +34985,11 @@ This includes tools based on the Smith-Waterman algorithm or FASTA. Sequence similarity search (local alignment-based methods) - operation beta12orEarlier - bioinformatics - operations Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. - edam + + + @@ -37894,14 +35006,13 @@ - edam - bioinformatics Sequence similarity search (global alignment-based methods) beta12orEarlier - operations 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. - operation + + + @@ -37917,14 +35028,13 @@ - edam Sequence similarity search (primer sequences) - operation - operations STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. - bioinformatics Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. beta12orEarlier + + + @@ -37936,30 +35046,29 @@ - - + + - + - - + + beta12orEarlier - edam Peptide mass fingerprinting - bioinformatics - operations Protein fingerprinting - operation 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. + + + @@ -37975,12 +35084,11 @@ - bioinformatics - edam - operation Search sequence(s) or a sequence database for sequences of a given isoelectric point. - operations beta12orEarlier + + + @@ -37991,11 +35099,10 @@ Structure retrieval (by code) beta12orEarlier - operation - bioinformatics Query a tertiary structure database and retrieve entries with a given entry code or accession number. - operations - edam + + + @@ -38006,11 +35113,10 @@ Structure retrieval (by keyword) beta12orEarlier - operation - operations Query a tertiary structure database and retrieve entries containing a given keyword. - edam - bioinformatics + + + @@ -38022,13 +35128,12 @@ - operation Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. - operations - bioinformatics Structure retrieval by sequence - edam beta12orEarlier + + + @@ -38044,14 +35149,13 @@ - operation - Structural similarity search - operations Structure retrieval by structure - bioinformatics - edam Search a tertiary structure database and retrieve structures that are similar to a query structure. + Structural similarity search beta12orEarlier + + + @@ -38074,11 +35178,10 @@ Annotate a molecular sequence record with terms from a controlled vocabulary. - edam beta12orEarlier - operations - bioinformatics - operation + + + @@ -38089,11 +35192,10 @@ Genome annotation Annotate a genome sequence with terms from a controlled vocabulary. - operations - bioinformatics beta12orEarlier - edam - operation + + + @@ -38104,11 +35206,10 @@ Nucleic acid sequence reverse and complement Generate the reverse and / or complement of a nucleotide sequence. - operation beta12orEarlier - operations - edam - bioinformatics + + + @@ -38119,11 +35220,10 @@ Random sequence generation beta12orEarlier - operations - operation - bioinformatics Generate a random sequence, for example, with a specific character composition. - edam + + + @@ -38146,12 +35246,11 @@ - operations - edam Generate digest fragments for a nucleotide sequence containing restriction sites. - bioinformatics - operation beta12orEarlier + + + @@ -38174,12 +35273,11 @@ - edam Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. - bioinformatics beta12orEarlier - operations - operation + + + @@ -38189,12 +35287,11 @@ Sequence mutation and randomization - operations - edam - operation - bioinformatics Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. beta12orEarlier + + + @@ -38210,13 +35307,12 @@ - bioinformatics - operations beta12orEarlier - edam - operation For example, SNPs or repeats in a DNA sequence might be masked. Mask characters in a molecular sequence (replacing those characters with a mask character). + + + @@ -38226,12 +35322,11 @@ Sequence cutting - operation beta12orEarlier - operations - edam - bioinformatics Cut (remove) characters or a region from a molecular sequence. + + + @@ -38248,11 +35343,10 @@ beta12orEarlier - operation - bioinformatics - edam Create (or remove) restriction sites in sequences, for example using silent mutations. - operations + + + @@ -38268,12 +35362,11 @@ - operation Translate a DNA sequence into protein. - operations beta12orEarlier - edam - bioinformatics + + + @@ -38290,11 +35383,10 @@ Transcribe a nucleotide sequence into mRNA sequence(s). - operation - edam beta12orEarlier - bioinformatics - operations + + + @@ -38306,11 +35398,10 @@ beta12orEarlier - operations - edam - bioinformatics Calculate base frequency or word composition of a nucleotide sequence. - operation + + + @@ -38321,12 +35412,11 @@ Sequence composition calculation (protein) - bioinformatics beta12orEarlier Calculate amino acid frequency or word composition of a protein sequence. - edam - operation - operations + + + @@ -38343,12 +35433,11 @@ - operations Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - bioinformatics - operation - edam beta12orEarlier + + + @@ -38361,10 +35450,9 @@ Analyse repeat sequence organization such as periodicity. beta12orEarlier - edam - operations - bioinformatics - operation + + + @@ -38375,12 +35463,11 @@ Protein hydropathy calculation (from structure) - edam beta12orEarlier - operations Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. - bioinformatics - operation + + + @@ -38403,11 +35490,10 @@ Calculate solvent accessible or buried surface areas in protein structures. - bioinformatics - edam - operation beta12orEarlier - operations + + + @@ -38418,12 +35504,11 @@ Protein hydropathy cluster calculation - operation Identify clusters of hydrophobic or charged residues in a protein structure. - bioinformatics beta12orEarlier - operations - edam + + + @@ -38439,12 +35524,11 @@ - edam Calculate whether a protein structure has an unusually large net charge (dipole moment). - bioinformatics - operation beta12orEarlier - operations + + + @@ -38460,18 +35544,11 @@ - - - - - - Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. - bioinformatics beta12orEarlier - edam - operations - operation + + + @@ -38482,13 +35559,12 @@ Binding site prediction (from structure) - edam - operation Ligand-binding and active site prediction (from structure) - bioinformatics beta12orEarlier Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. - operations + + + @@ -38511,11 +35587,10 @@ beta12orEarlier - edam - operation - operations - bioinformatics Analyse RNA or DNA-binding sites in protein structure. + + + @@ -38531,12 +35606,11 @@ - edam - operation - bioinformatics Decompose a structure into compact or globular fragments (protein peeling). - operations beta12orEarlier + + + @@ -38552,12 +35626,11 @@ - operations - edam Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. - operation - bioinformatics beta12orEarlier + + + @@ -38573,12 +35646,11 @@ - operations Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. - operation - bioinformatics - edam beta12orEarlier + + + @@ -38595,12 +35667,11 @@ beta12orEarlier - edam Calculate clusters of contacting residues in protein structures. - operations Cluster of contacting residues might be key structural residues. - operation - bioinformatics + + + @@ -38617,15 +35688,14 @@ Identify potential hydrogen bonds between amino acids and other groups. - operations - edam WHATIF:ShowHydrogenBonds - operation WHATIF:ShowHydrogenBondsM - bioinformatics beta12orEarlier The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. WHATIF:HasHydrogenBonds + + + @@ -38636,18 +35706,11 @@ Residue non-canonical interaction detection - - - - - - Calculate non-canonical atomic interactions in protein structures. - bioinformatics - operations beta12orEarlier - edam - operation + + + @@ -38663,12 +35726,11 @@ - bioinformatics - operations - operation beta12orEarlier Calculate a Ramachandran plot of a protein structure. - edam + + + @@ -38690,12 +35752,11 @@ - operation Analyse (typically to validate) a Ramachandran plot of a protein structure. - edam - operations beta12orEarlier - bioinformatics + + + @@ -38717,12 +35778,11 @@ - operations beta12orEarlier - edam Calculate the molecular weight of a protein sequence or fragments. - operation - bioinformatics + + + @@ -38739,11 +35799,10 @@ Predict extinction coefficients or optical density of a protein sequence. - operations - operation - edam - bioinformatics beta12orEarlier + + + @@ -38767,10 +35826,9 @@ beta12orEarlier Calculate pH-dependent properties from pKa calculations of a protein sequence. - operation - bioinformatics - edam - operations + + + @@ -38780,12 +35838,11 @@ Protein hydropathy calculation (from sequence) - edam beta12orEarlier - operations Hydropathy calculation on a protein sequence. - operation - bioinformatics + + + @@ -38801,12 +35858,11 @@ - bioinformatics Plot a protein titration curve. - edam - operation - operations beta12orEarlier + + + @@ -38822,12 +35878,11 @@ - operations Calculate isoelectric point of a protein sequence. - bioinformatics beta12orEarlier - operation - edam + + + @@ -38843,12 +35898,11 @@ - operation beta12orEarlier - bioinformatics - operations - edam Estimate hydrogen exchange rate of a protein sequence. + + + @@ -38860,10 +35914,9 @@ beta12orEarlier Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. - edam - bioinformatics - operations - operation + + + @@ -38879,12 +35932,11 @@ - edam - bioinformatics - operations Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. beta12orEarlier - operation + + + @@ -38900,13 +35952,12 @@ - operations - edam Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. - operation - bioinformatics Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. beta12orEarlier + + + @@ -38922,12 +35973,11 @@ - edam - operation - operations - bioinformatics beta12orEarlier Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. + + + @@ -38943,12 +35993,11 @@ - edam - operation - operations - bioinformatics beta12orEarlier Predict the solubility or atomic solvation energy of a protein sequence. + + + @@ -38964,12 +36013,11 @@ - operations Predict crystallizability of a protein sequence. - operation - edam beta12orEarlier - bioinformatics + + + @@ -38980,11 +36028,10 @@ Protein signal peptide detection (eukaryotes) Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. - operation - operations - bioinformatics - edam beta12orEarlier + + + @@ -38996,10 +36043,9 @@ beta12orEarlier Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. - operations - bioinformatics - operation - edam + + + @@ -39010,11 +36056,10 @@ MHC peptide immunogenicity prediction beta12orEarlier - bioinformatics - operation - operations - edam Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. + + + @@ -39025,14 +36070,13 @@ Protein feature prediction (from sequence) - edam - bioinformatics Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. - operation Sequence feature detection (protein) beta12orEarlier Methods typically involve scanning for known motifs, patterns and regular expressions. - operations + + + @@ -39057,14 +36101,13 @@ - operation - edam - operations beta12orEarlier - bioinformatics Methods typically involve scanning for known motifs, patterns and regular expressions. 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) + + + @@ -39077,23 +36120,22 @@ - - + + - - + + - operation beta12orEarlier Epitope mapping is commonly done during vaccine design. - operations Predict antigenic determinant sites (epitopes) in protein sequences. - edam - bioinformatics + + + @@ -39105,23 +36147,22 @@ - - + + - - + + 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. - operations - operation - Predict post-translation modification sites in protein sequences. beta12orEarlier - edam - bioinformatics + Predict post-translation modification sites in protein sequences. + + + @@ -39134,23 +36175,22 @@ - - + + - - + + - operations beta12orEarlier - bioinformatics - operation 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. - edam + + + @@ -39161,13 +36201,12 @@ Binding site prediction (from sequence) - operations beta12orEarlier - edam Ligand-binding and active site prediction (from sequence) Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. - bioinformatics - operation + + + @@ -39183,12 +36222,11 @@ - operation - bioinformatics Predict RNA and DNA-binding binding sites in protein sequences. - operations beta12orEarlier - edam + + + @@ -39207,10 +36245,9 @@ beta12orEarlier Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. - operations - bioinformatics - operation - edam + + + @@ -39232,12 +36269,11 @@ - operation Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. beta12orEarlier - operations - bioinformatics - edam + + + @@ -39247,12 +36283,11 @@ Epitope mapping (MHC Class I) - operation beta12orEarlier Predict epitopes that bind to MHC class I molecules. - edam - operations - bioinformatics + + + @@ -39262,12 +36297,11 @@ Epitope mapping (MHC Class II) - bioinformatics - operations beta12orEarlier - operation - edam Predict epitopes that bind to MHC class II molecules. + + + @@ -39277,12 +36311,11 @@ Whole gene prediction - operation - edam Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. - operations - bioinformatics beta12orEarlier + + + @@ -39292,13 +36325,12 @@ Gene component prediction - operations Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. - bioinformatics beta12orEarlier - edam Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - operation + + + @@ -39314,12 +36346,11 @@ - edam - bioinformatics Detect or predict transposons, retrotransposons / retrotransposition signatures etc. - operations - operation beta12orEarlier + + + @@ -39336,11 +36367,10 @@ beta12orEarlier - bioinformatics - operation - edam - operations Detect polyA signals in nucleotide sequences. + + + @@ -39352,24 +36382,23 @@ - - + + - - + + Quadruplex structure prediction beta12orEarlier - edam - operation Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. - operations Detect quadruplex-forming motifs in nucleotide sequences. - bioinformatics + + + @@ -39381,25 +36410,24 @@ - - + + - - + + CpG island and isochores rendering - operations beta12orEarlier - operation CpG island and isochores detection 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. - bioinformatics - edam + + + @@ -39429,10 +36457,9 @@ Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. beta12orEarlier - operation - edam - operations - bioinformatics + + + @@ -39450,10 +36477,9 @@ Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. beta12orEarlier - edam - operation - bioinformatics - operations + + + @@ -39475,13 +36501,12 @@ - operation Methods might require a pre-mRNA or genomic DNA sequence. Identify, predict or analyse splice sites in nucleotide sequences. - edam - bioinformatics - operations beta12orEarlier + + + @@ -39491,12 +36516,11 @@ Integrated gene prediction - operation - bioinformatics beta12orEarlier Predict whole gene structure using a combination of multiple methods to achieve better predictions. - edam - operations + + + @@ -39506,12 +36530,11 @@ Operon prediction - operations - bioinformatics - operation beta12orEarlier Find operons (operators, promoters and genes) in bacteria genes. - edam + + + @@ -39528,11 +36551,10 @@ beta12orEarlier - bioinformatics - operations - operation Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. - edam + + + @@ -39548,13 +36570,12 @@ - edam beta12orEarlier SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. - operation - operations - bioinformatics + + + @@ -39571,12 +36592,11 @@ beta12orEarlier - operations - edam 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. - operation - bioinformatics Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. + + + @@ -39592,12 +36612,11 @@ - bioinformatics - edam - operation - operations Predict translation initiation sites, possibly by searching a database of sites. beta12orEarlier + + + @@ -39613,13 +36632,12 @@ - edam beta12orEarlier - operations Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. - bioinformatics 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. - operation + + + @@ -39630,12 +36648,11 @@ 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. - edam 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. - operation beta12orEarlier - operations - bioinformatics + + + @@ -39646,12 +36663,11 @@ Transcription regulatory element prediction (RNA-cis) beta12orEarlier - operation - operations - bioinformatics - edam 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. + + + @@ -39667,14 +36683,13 @@ - operation Functional RNA identification - bioinformatics - operations 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. - edam beta12orEarlier + + + @@ -39691,12 +36706,11 @@ beta12orEarlier - operation Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. - operations - bioinformatics - edam MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. + + + @@ -39712,12 +36726,11 @@ - bioinformatics Identify or predict transcription factor binding sites in DNA sequences. - operation - operations beta12orEarlier - edam + + + @@ -39729,23 +36742,22 @@ - - + + - - + + - edam beta12orEarlier - bioinformatics - operations - operation 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. + + + @@ -39757,12 +36769,11 @@ beta12orEarlier - operations - edam Evaluate molecular sequence alignment accuracy. - operation - bioinformatics Evaluation might be purely sequence-based or use structural information. + + + @@ -39772,19 +36783,13 @@ Sequence alignment analysis (conservation) - - - - - - - operations - operation 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. - edam - bioinformatics + Residue conservation analysis beta12orEarlier Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. + + + @@ -39794,19 +36799,12 @@ Sequence alignment analysis (site correlation) - - - - - - - bioinformatics beta12orEarlier - operations - edam - operation This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. Analyse correlations between sites in a molecular sequence alignment. + + + @@ -39816,13 +36814,12 @@ Sequence alignment analysis (chimeric sequence detection) - operation Detects chimeric sequences (chimeras) from a sequence alignment. - edam - operations - bioinformatics 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. beta12orEarlier + + + @@ -39832,13 +36829,12 @@ Sequence alignment analysis (recombination detection) - operations - bioinformatics Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. - operation beta12orEarlier - edam + + + @@ -39850,11 +36846,10 @@ 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. - bioinformatics - operations beta12orEarlier - operation - edam + + + @@ -39864,15 +36859,12 @@ Nucleosome formation potential prediction - operations beta12orEarlier - edam - operation Predict nucleosome formation potential of DNA sequences. beta12orEarlier true - bioinformatics + @@ -39889,11 +36881,10 @@ beta12orEarlier - operations - edam Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. - operation - bioinformatics + + + @@ -39909,13 +36900,12 @@ - operation - operations - bioinformatics A melting profile is used to visualise and analyse partly melted DNA conformations. beta12orEarlier Calculate and plot a DNA or DNA/RNA melting profile. - edam + + + @@ -39931,13 +36921,12 @@ - edam Calculate and plot a DNA or DNA/RNA stitch profile. - operations - bioinformatics beta12orEarlier - operation A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. + + + @@ -39953,12 +36942,11 @@ - bioinformatics - edam Calculate and plot a DNA or DNA/RNA melting curve. beta12orEarlier - operations - operation + + + @@ -39975,11 +36963,10 @@ Calculate and plot a DNA or DNA/RNA probability profile. - edam - bioinformatics - operation - operations beta12orEarlier + + + @@ -39995,12 +36982,11 @@ - operations - bioinformatics - edam beta12orEarlier - operation Calculate and plot a DNA or DNA/RNA temperature profile. + + + @@ -40022,13 +37008,12 @@ - bioinformatics - operation This includes properties such as. beta12orEarlier - edam Calculate curvature and flexibility / stiffness of a nucleotide sequence. - operations + + + @@ -40046,10 +37031,9 @@ beta12orEarlier Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence. - edam - bioinformatics - operation - operations + + + @@ -40065,12 +37049,11 @@ - edam beta12orEarlier - operations - operation Identify or predict tRNA genes in genomic sequences (tRNA). - bioinformatics + + + @@ -40086,12 +37069,11 @@ - edam - operations - operation beta12orEarlier Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. - bioinformatics + + + @@ -40102,11 +37084,10 @@ Protein secondary structure prediction (integrated) beta12orEarlier - bioinformatics - operations - operation - edam Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. + + + @@ -40118,10 +37099,9 @@ Predict helical secondary structure of protein sequences. beta12orEarlier - bioinformatics - operations - operation - edam + + + @@ -40132,11 +37112,10 @@ Protein secondary structure prediction (turns) beta12orEarlier - operations - edam Predict turn structure (for example beta hairpin turns) of protein sequences. - bioinformatics - operation + + + @@ -40146,12 +37125,11 @@ Protein secondary structure prediction (coils) - edam - bioinformatics Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. - operations - operation beta12orEarlier + + + @@ -40162,11 +37140,10 @@ Protein secondary structure prediction (disulfide bonds) Predict cysteine bonding state and disulfide bond partners in protein sequences. - edam - operation - operations beta12orEarlier - bioinformatics + + + @@ -40178,12 +37155,11 @@ Predict G protein-coupled receptors (GPCR). - edam G protein-coupled receptor (GPCR) prediction beta12orEarlier - bioinformatics - operations - operation + + + @@ -40205,13 +37181,12 @@ - operation G protein-coupled receptor (GPCR) analysis - bioinformatics beta12orEarlier - operations Analyse G-protein coupled receptor proteins (GPCRs). - edam + + + @@ -40227,27 +37202,26 @@ - + - - + + - - + + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. - operation - operations - edam - bioinformatics beta12orEarlier + + + @@ -40262,23 +37236,22 @@ - - + + - - + + - operations Methods might identify thermodynamically stable or evolutionarily conserved structures. - operation - bioinformatics Predict tertiary structure of DNA or RNA. beta12orEarlier - edam + + + @@ -40294,12 +37267,11 @@ - bioinformatics beta12orEarlier - edam - operation Predict tertiary structure of protein sequence(s) without homologs of known structure. - operations + + + @@ -40321,13 +37293,12 @@ Homology structure modelling The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. Homology modelling - bioinformatics Build a three-dimensional protein model based on known (for example homologs) structures. beta12orEarlier - operation Comparative modelling - edam - operations + + + @@ -40340,29 +37311,28 @@ - - + + - - + + - + - edam - bioinformatics 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. - operation beta12orEarlier Model the structure of a protein in complex with a small molecule or another macromolecule. - operations + + + @@ -40372,13 +37342,12 @@ Protein modelling (backbone) - operations - edam beta12orEarlier Methods might require a preliminary C(alpha) trace. - operation Model protein backbone conformation. - bioinformatics + + + @@ -40389,12 +37358,11 @@ Protein modelling (side chains) Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. - bioinformatics - edam - operation Methods might use a residue rotamer library. - operations beta12orEarlier + + + @@ -40405,11 +37373,10 @@ Protein modelling (loops) Model loop conformation in protein structures. - edam - operations - bioinformatics - operation beta12orEarlier + + + @@ -40421,24 +37388,23 @@ - - + + - - + + - edam - bioinformatics Virtual ligand screening Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. - operations beta12orEarlier Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. - operation + + + @@ -40451,24 +37417,23 @@ - - + + - - + + - operations - bioinformatics Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. - edam beta12orEarlier RNA inverse folding - operation Nucleic acid folding family identification + + + @@ -40486,14 +37451,13 @@ - edam - operations - operation - bioinformatics This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. beta12orEarlier Single nucleotide polymorphism detection Find single nucleotide polymorphisms (SNPs) between sequences. + + + @@ -40509,12 +37473,11 @@ - operations - operation beta12orEarlier Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. - bioinformatics - edam + + + @@ -40525,15 +37488,12 @@ Functional mapping beta12orEarlier - operations - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + Map the genetic architecture of dynamic complex traits. true + This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). beta12orEarlier - operation - edam - Map the genetic architecture of dynamic complex traits. - bioinformatics + @@ -40541,7 +37501,8 @@ - Haplotype inference + Haplotype mapping + @@ -40549,15 +37510,14 @@ - Haplotype mapping - bioinformatics Haplotype reconstruction - edam Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). beta12orEarlier 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. - operation - operations + Haplotype inference + + + @@ -40574,12 +37534,11 @@ Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - operations - operation 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. - edam - bioinformatics beta12orEarlier + + + @@ -40596,12 +37555,11 @@ - operations - bioinformatics Predict genetic code from analysis of codon usage data. - edam beta12orEarlier - operation + + + @@ -40618,12 +37576,11 @@ - bioinformatics - operations - edam Draw a dotplot of sequence similarities identified from word-matching or character comparison. beta12orEarlier - operation + + + @@ -40639,14 +37596,13 @@ - bioinformatics beta12orEarlier - edam + Align exactly two molecular sequences. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Pairwise sequence alignment - Align exactly two molecular sequences. - operations - operation + + + @@ -40658,12 +37614,11 @@ beta12orEarlier Multiple sequence alignment - operations 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. Align two or more molecular sequences. - edam - bioinformatics - operation + + + @@ -40674,14 +37629,13 @@ Pairwise sequence alignment construction (local) Local alignment methods identify regions of local similarity. - bioinformatics - operations - operation - Pairwise sequence alignment (local) - Locally align exactly two molecular sequences. Local pairwise sequence alignment construction beta12orEarlier - edam + Pairwise sequence alignment (local) + Locally align exactly two molecular sequences. + + + @@ -40691,15 +37645,14 @@ Pairwise sequence alignment construction (global) - operations - Pairwise sequence alignment (global) - bioinformatics beta12orEarlier Global alignment methods identify similarity across the entire length of the sequences. Globally align exactly two molecular sequences. - operation + Pairwise sequence alignment (global) Global pairwise sequence alignment construction - edam + + + @@ -40710,14 +37663,13 @@ Multiple sequence alignment construction (local) Locally align two or more molecular sequences. - operation - edam Local alignment methods identify regions of local similarity. beta12orEarlier - bioinformatics Local multiple sequence alignment construction - operations Multiple sequence alignment (local) + + + @@ -40727,15 +37679,14 @@ Multiple sequence alignment construction (global) - edam - Global alignment methods identify similarity across the entire length of the sequences. - Globally align two or more molecular sequences. - operations beta12orEarlier + Global alignment methods identify similarity across the entire length of the sequences. Multiple sequence alignment (global) Global multiple sequence alignment construction - operation - bioinformatics + Globally align two or more molecular sequences. + + + @@ -40745,14 +37696,13 @@ Multiple sequence alignment construction (constrained) - operation Constrained multiple sequence alignment construction Multiple sequence alignment (constrained) - edam - bioinformatics - operations Align two or more molecular sequences with user-defined constraints. beta12orEarlier + + + @@ -40762,14 +37712,13 @@ Multiple sequence alignment construction (consensus) - operation Multiple sequence alignment (consensus) Align two or more molecular sequences using multiple methods to achieve higher quality. beta12orEarlier Consensus multiple sequence alignment construction - bioinformatics - operations - edam + + + @@ -40786,14 +37735,13 @@ Multiple sequence alignment (phylogenetic tree-based) - operations - bioinformatics Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. - beta12orEarlier Phylogenetic tree-based multiple sequence alignment construction + beta12orEarlier This is supposed to give a more biologically meaningful alignment than standard alignments. - operation - edam + + + @@ -40807,23 +37755,22 @@ - - + + - - + + Align molecular secondary structure (represented as a 1D string). - edam beta12orEarlier - operations Secondary structure alignment - operation - bioinformatics + + + @@ -40841,13 +37788,12 @@ Secondary structure alignment (protein) - bioinformatics Align protein secondary structures. - operation Protein secondary structure alignment beta12orEarlier - edam - operations + + + @@ -40870,14 +37816,13 @@ - operation beta12orEarlier Secondary structure alignment (RNA) - bioinformatics - edam Align RNA secondary structures. RNA secondary structure alignment - operations + + + @@ -40888,12 +37833,11 @@ Pairwise structure alignment construction Align (superimpose) exactly two molecular tertiary structures. - bioinformatics Pairwise structure alignment - operation - operations - edam beta12orEarlier + + + @@ -40905,12 +37849,11 @@ Multiple structure alignment beta12orEarlier - operations - edam This includes methods that use an existing alignment. - bioinformatics - operation Align (superimpose) two or more molecular tertiary structures. + + + @@ -40920,15 +37863,12 @@ Structure alignment (protein) - edam - operations - beta12orEarlier - operation Align protein tertiary structures. - bioinformatics + beta12orEarlier true beta13 + @@ -40939,14 +37879,11 @@ Structure alignment (RNA) beta12orEarlier - operation - bioinformatics - true Align RNA tertiary structures. - edam - operations + true beta13 + @@ -40956,15 +37893,14 @@ Pairwise structure alignment construction (local) - edam - bioinformatics - operations - operation beta12orEarlier - Local pairwise structure alignment construction Local alignment methods identify regions of local similarity, common substructures etc. Pairwise structure alignment (local) Locally align (superimpose) exactly two molecular tertiary structures. + Local pairwise structure alignment construction + + + @@ -40974,15 +37910,14 @@ Pairwise structure alignment construction (global) + beta12orEarlier Pairwise structure alignment (global) Globally align (superimpose) exactly two molecular tertiary structures. - operations - edam - beta12orEarlier - bioinformatics - operation Global alignment methods identify similarity across the entire structures. Global pairwise structure alignment construction + + + @@ -40992,15 +37927,14 @@ Multiple structure alignment construction (local) - Multiple structure alignment (local) - edam - Locally align (superimpose) two or more molecular tertiary structures. beta12orEarlier - operations + Multiple structure alignment (local) Local alignment methods identify regions of local similarity, common substructures etc. - bioinformatics + Locally align (superimpose) two or more molecular tertiary structures. Local multiple structure alignment construction - operation + + + @@ -41010,15 +37944,14 @@ Multiple structure alignment construction (global) + beta12orEarlier Globally align (superimpose) two or more molecular tertiary structures. Global multiple structure alignment construction - Global alignment methods identify similarity across the entire structures. - operation - edam - beta12orEarlier - bioinformatics Multiple structure alignment (global) - operations + Global alignment methods identify similarity across the entire structures. + + + @@ -41028,15 +37961,14 @@ Sequence profile alignment construction (pairwise) + Pairwise sequence profile alignment construction Align exactly two molecular profiles. beta12orEarlier - operations Sequence profile alignment (pairwise) - bioinformatics - operation - Pairwise sequence profile alignment construction - edam Methods might perform one-to-one, one-to-many or many-to-many comparisons. + + + @@ -41048,12 +37980,11 @@ Sequence profile alignment (multiple) Multiple sequence profile alignment construction - bioinformatics beta12orEarlier - operation - edam Align two or more molecular profiles. - operations + + + @@ -41064,14 +37995,13 @@ Structural (3D) profile alignment construction (pairwise) beta12orEarlier - bioinformatics + Align exactly two molecular Structural (3D) profiles. Structural (3D) profile alignment (pairwise) Methods might perform one-to-one, one-to-many or many-to-many comparisons. - operations - operation - Align exactly two molecular Structural (3D) profiles. - edam Pairwise structural (3D) profile alignment construction + + + @@ -41081,14 +38011,13 @@ Structural (3D) profile alignment construction (multiple) - bioinformatics Structural (3D) profile alignment (multiple) - edam beta12orEarlier Multiple structural (3D) profile alignment construction - operations Align two or more molecular 3D profiles. - operation + + + @@ -41104,14 +38033,13 @@ - Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. - Data retrieval (tool annotation) Tool information retrieval beta12orEarlier - operations - edam - bioinformatics - operation + Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. + Data retrieval (tool annotation) + + + @@ -41127,14 +38055,13 @@ - edam - operations - beta12orEarlier Database information retrieval Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. Data retrieval (database annotation) - operation - bioinformatics + beta12orEarlier + + + @@ -41150,12 +38077,11 @@ - bioinformatics - operation - operations beta12orEarlier - edam Predict primers for large scale sequencing. + + + @@ -41165,12 +38091,11 @@ PCR primer design (for genotyping polymorphisms) - operations - edam - operation Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). beta12orEarlier - bioinformatics + + + @@ -41186,12 +38111,11 @@ - operation - edam - bioinformatics beta12orEarlier - operations Predict primers for gene transcription profiling. + + + @@ -41201,12 +38125,11 @@ PCR primer design (for conserved primers) - bioinformatics - operations Predict primers that are conserved across multiple genomes or species. beta12orEarlier - operation - edam + + + @@ -41222,12 +38145,11 @@ - operation beta12orEarlier - bioinformatics - operations Predict primers based on gene structure, promoters, exon-exon junctions etc. - edam + + + @@ -41237,12 +38159,11 @@ PCR primer design (for methylation PCRs) - operations Predict primers for methylation PCRs. - bioinformatics - edam beta12orEarlier - operation + + + @@ -41252,13 +38173,12 @@ Sequence assembly (mapping assembly) - edam The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - bioinformatics beta12orEarlier Sequence assembly by combining fragments using an existing backbone sequence. - operation - operations + + + @@ -41270,11 +38190,10 @@ beta12orEarlier De-novo assemblers are much slower and more memory intensive than mapping assemblers. - operations - bioinformatics Sequence assembly by combining fragments into a new, previously unknown sequence. - edam - operation + + + @@ -41284,12 +38203,11 @@ Sequence assembly (genome assembly) - edam - bioinformatics - operation beta12orEarlier Sequence assembly capable on a very large scale such as assembly of whole genomes. - operations + + + @@ -41300,12 +38218,11 @@ Sequence assembly (EST assembly) Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. - operations Sequence assembly for EST sequences (transcribed mRNA). - bioinformatics beta12orEarlier - edam - operation + + + @@ -41315,20 +38232,20 @@ Tag mapping + - bioinformatics beta12orEarlier Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. - edam Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. - operation - operations Tag to gene assignment + + + @@ -41339,15 +38256,12 @@ SAGE data processing true - bioinformatics - operation - edam - Serial analysis of gene expression data processing Process (read and / or write) serial analysis of gene expression (SAGE) data. - operations beta12orEarlier + Serial analysis of gene expression data processing beta12orEarlier + @@ -41357,16 +38271,13 @@ MPSS data processing - operations beta12orEarlier - edam - bioinformatics Massively parallel signature sequencing data processing - beta12orEarlier - operation true Process (read and / or write) massively parallel signature sequencing (MPSS) data. + beta12orEarlier + @@ -41376,16 +38287,13 @@ SBS data processing - bioinformatics - operations - edam true - operation Process (read and / or write) sequencing by synthesis (SBS) data. beta12orEarlier - Sequencing by synthesis data processing beta12orEarlier + Sequencing by synthesis data processing + @@ -41404,10 +38312,9 @@ Generate a heat map of gene expression from 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. beta12orEarlier - operations - bioinformatics - operation - edam + + + @@ -41423,13 +38330,12 @@ - edam - operation Analyse one or more gene expression profiles, typically to interpret them in functional terms. - bioinformatics beta12orEarlier - operations Functional profiling + + + @@ -41446,12 +38352,11 @@ - operations Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. beta12orEarlier - edam - operation - bioinformatics + + + @@ -41462,12 +38367,11 @@ Protein secondary structure assignment (from coordinate data) - bioinformatics Assign secondary structure from protein coordinate data. beta12orEarlier - operation - operations - edam + + + @@ -41483,12 +38387,11 @@ - operation - operations - edam - bioinformatics beta12orEarlier Assign secondary structure from circular dichroism (CD) spectroscopic data. + + + @@ -41504,12 +38407,11 @@ - operations beta12orEarlier - bioinformatics - operation - edam Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. + + + @@ -41525,12 +38427,11 @@ - operation - operations - edam Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. - bioinformatics beta12orEarlier + + + @@ -41541,11 +38442,10 @@ Phylogenetic tree construction (data centric) Construct a phylogenetic tree from a specific type of data. - operations beta12orEarlier - operation - bioinformatics - edam + + + @@ -41555,12 +38455,11 @@ Phylogenetic tree construction (method centric) - operation - operations beta12orEarlier Construct a phylogenetic tree using a specific method. - edam - bioinformatics + + + @@ -41572,12 +38471,11 @@ Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. - operations - bioinformatics - operation beta12orEarlier Phylogenetic tree construction from molecular sequences. - edam + + + @@ -41593,12 +38491,11 @@ - operation Phylogenetic tree construction from continuous quantitative character data. - bioinformatics beta12orEarlier - operations - edam + + + @@ -41622,10 +38519,9 @@ beta12orEarlier Phylogenetic tree construction from gene frequency data. - bioinformatics - operation - edam - operations + + + @@ -41641,12 +38537,11 @@ - bioinformatics - operation beta12orEarlier - operations Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. - edam + + + @@ -41658,10 +38553,9 @@ beta12orEarlier Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. - bioinformatics - edam - operations - operation + + + @@ -41672,12 +38566,11 @@ Phylogenetic tree construction (parsimony methods) beta12orEarlier - operation This includes evolutionary parsimony (invariants) 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. - operations - bioinformatics - edam + + + @@ -41688,12 +38581,11 @@ 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. - edam beta12orEarlier - bioinformatics - operations This includes neighbor joining (NJ) clustering method. - operation + + + @@ -41703,13 +38595,12 @@ Phylogenetic tree construction (maximum likelihood and Bayesian methods) - edam beta12orEarlier - operations - operation - bioinformatics 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. Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. + + + @@ -41720,11 +38611,10 @@ 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. - operation - edam - operations beta12orEarlier - bioinformatics + + + @@ -41735,11 +38625,10 @@ Phylogenetic tree construction (AI methods) beta12orEarlier - operation - edam - operations Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. - bioinformatics + + + @@ -41752,22 +38641,21 @@ - - + + - - + + - bioinformatics - beta12orEarlier - operations - edam Identify a plausible model of DNA substitution that explains a DNA sequence alignment. - operation + beta12orEarlier + + + @@ -41777,19 +38665,12 @@ Phylogenetic tree analysis (shape) - - - - - - beta12orEarlier Analyse the shape (topology) of a phylogenetic tree. - bioinformatics - edam - operation Phylogenetic tree topology analysis - operations + + + @@ -41800,18 +38681,11 @@ Phylogenetic tree bootstrapping - - - - - - - operations - bioinformatics - operation beta12orEarlier Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. - edam + + + @@ -41823,22 +38697,21 @@ - - + + - - + + beta12orEarlier - edam - bioinformatics - operation - operations Predict families of genes and gene function based on their position in a phylogenetic tree. + + + @@ -41848,13 +38721,12 @@ Phylogenetic tree analysis (natural selection) - bioinformatics 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. - edam - operations - operation beta12orEarlier + + + @@ -41865,13 +38737,12 @@ Phylogenetic tree construction (consensus) - edam - operations - bioinformatics beta12orEarlier Methods typically test for topological similarity between trees using for example a congruence index. - operation Compare two or more phylogenetic trees to produce a consensus tree. + + + @@ -41883,10 +38754,9 @@ Compare two or more phylogenetic trees to detect subtrees or supertrees. beta12orEarlier - bioinformatics - edam - operation - operations + + + @@ -41902,12 +38772,11 @@ - operations - bioinformatics - edam - operation Compare two or more phylogenetic trees to calculate distances between trees. beta12orEarlier + + + @@ -41918,12 +38787,11 @@ Phylogenetic tree annotation - operation Annotate a phylogenetic tree with terms from a controlled vocabulary. - operations - bioinformatics - edam beta12orEarlier + + + @@ -41937,28 +38805,27 @@ - - + + - + - - + + Predict and optimise peptide ligands that elicit an immunological response. beta12orEarlier - operations - edam - bioinformatics - operation + + + @@ -41972,21 +38839,20 @@ - + - + - edam - operation - bioinformatics - beta12orEarlier - operations Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. + beta12orEarlier + + + @@ -41999,22 +38865,22 @@ - + - + - bioinformatics - operation - operations - edam + Sequence file format conversion Reformat (a file or other report of) molecular sequence(s). beta12orEarlier + + + @@ -42037,12 +38903,11 @@ - operation - edam beta12orEarlier Reformat (a file or other report of) molecular sequence alignment(s). - operations - bioinformatics + + + @@ -42055,22 +38920,21 @@ - + - + - edam beta12orEarlier - operations - bioinformatics Reformat a codon usage table. - operation + + + @@ -42093,12 +38957,11 @@ - edam - operations - beta12orEarlier - bioinformatics - operation Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. + beta12orEarlier + + + @@ -42121,12 +38984,11 @@ - Visualise, format or print a molecular sequence alignment. - bioinformatics - operations - operation beta12orEarlier - edam + Visualise, format or print a molecular sequence alignment. + + + @@ -42144,11 +39006,10 @@ Visualise, format or render sequence clusters. - operation - bioinformatics - edam - operations beta12orEarlier + + + @@ -42165,12 +39026,11 @@ - operation - operations - bioinformatics - edam beta12orEarlier Visualise or plot a phylogenetic tree. + + + @@ -42189,10 +39049,9 @@ beta12orEarlier Visualise RNA secondary structure, knots, pseudoknots etc. - operation - edam - bioinformatics - operations + + + @@ -42209,12 +39068,11 @@ - bioinformatics - operations - edam beta12orEarlier Render and visualise protein secondary structure. - operation + + + @@ -42227,22 +39085,21 @@ - - + + - - + + - Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. beta12orEarlier - bioinformatics - operation - edam - operations + Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. + + + @@ -42255,22 +39112,21 @@ - - + + - - + + - operations beta12orEarlier - bioinformatics - edam Visualise microarray data. - operation + + + @@ -42287,12 +39143,11 @@ - edam - bioinformatics Identify and analyse networks of protein interactions. - operation beta12orEarlier - operations + + + @@ -42309,13 +39164,12 @@ - edam - operation - operations Render and visualise a DNA map. DNA map rendering - bioinformatics beta12orEarlier + + + @@ -42325,15 +39179,12 @@ Sequence motif rendering - edam - Render a sequence with motifs. - operations - operation beta12orEarlier beta12orEarlier - bioinformatics true + Render a sequence with motifs. + @@ -42351,11 +39202,10 @@ beta12orEarlier - operation - bioinformatics - operations - edam Visualise restriction maps in DNA sequences. + + + @@ -42365,15 +39215,12 @@ DNA linear map rendering - bioinformatics Draw a linear maps of DNA. - beta12orEarlier - operation - edam - operations true beta12orEarlier + beta12orEarlier + @@ -42384,11 +39231,10 @@ DNA circular map rendering Draw a circular maps of DNA, for example a plasmid map. - bioinformatics - edam - operations beta12orEarlier - operation + + + @@ -42405,11 +39251,10 @@ beta12orEarlier - bioinformatics - edam - operation - operations Visualise operon structure etc. + + + @@ -42419,15 +39264,12 @@ Nucleic acid folding family identification - operation - bioinformatics - edam - beta12orEarlier - true beta12orEarlier Identify folding families of related RNAs. - operations + beta12orEarlier + true + @@ -42437,12 +39279,11 @@ Nucleic acid folding energy calculation - edam - operations Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. - bioinformatics beta12orEarlier - operation + + + @@ -42454,14 +39295,11 @@ true beta12orEarlier - operations - edam - Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. - operation 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. beta12orEarlier - bioinformatics + @@ -42478,13 +39316,12 @@ - operation For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. - beta12orEarlier - edam - operations Predict general functional properties of a protein. - bioinformatics + beta12orEarlier + + + @@ -42501,12 +39338,11 @@ - bioinformatics beta12orEarlier - edam - operation Compare the functional properties of two or more proteins. - operations + + + @@ -42528,12 +39364,11 @@ - operation beta12orEarlier - edam - bioinformatics Submit a molecular sequence to a database. - operations + + + @@ -42551,11 +39386,10 @@ Analyse a known network of gene regulation. - operations - bioinformatics - edam - operation beta12orEarlier + + + @@ -42571,15 +39405,14 @@ - operation Data submission - edam beta12orEarlier Prepare or load a user-specified data file so that it is available for use. Database submission - operations - bioinformatics WHATIF:UploadPDB + + + @@ -42597,13 +39430,12 @@ beta12orEarlier - operation - operations This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. - edam - bioinformatics Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. Data retrieval (sequences) + + + @@ -42620,15 +39452,14 @@ - operation Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. - edam WHATIF:EchoPDB - operations - bioinformatics This includes direct retrieval methods but not those that perform calculations on the sequence or structure. WHATIF:DownloadPDB beta12orEarlier + + + @@ -42639,14 +39470,13 @@ Surface rendering - edam A dot has three coordinates (x,y,z) and (typically) a color. - bioinformatics - beta12orEarlier - operation Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. WHATIF:GetSurfaceDots - operations + beta12orEarlier + + + @@ -42656,15 +39486,14 @@ Protein atom surface calculation (accessible) + Waters are not considered. Calculate the solvent accessibility ('accessible surface') for each atom in a structure. WHATIF:AtomAccessibilitySolvent - operation WHATIF:AtomAccessibilitySolventPlus beta12orEarlier - Waters are not considered. - edam - bioinformatics - operations + + + @@ -42674,15 +39503,14 @@ Protein atom surface calculation (accessible molecular) - operation - Waters are not considered. - operations WHATIF:AtomAccessibilityMolecularPlus WHATIF:AtomAccessibilityMolecular - edam + Waters are not considered. Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. - bioinformatics beta12orEarlier + + + @@ -42695,11 +39523,10 @@ Calculate the solvent accessibility ('accessible surface') for each residue in a structure. beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - operations - bioinformatics WHATIF:ResidueAccessibilitySolvent - edam - operation + + + @@ -42710,13 +39537,12 @@ Protein residue surface calculation (vacuum accessible) beta12orEarlier - edam - operations WHATIF:ResidueAccessibilityVacuum - operation - bioinformatics 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). + + + @@ -42727,13 +39553,12 @@ Protein residue surface calculation (accessible molecular) beta12orEarlier - edam - bioinformatics Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - operations Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. WHATIF:ResidueAccessibilityMolecular - operation + + + @@ -42744,13 +39569,12 @@ Protein residue surface calculation (vacuum molecular) WHATIF:ResidueAccessibilityVacuumMolecular - operations 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. beta12orEarlier - edam - operation - bioinformatics Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + + + @@ -42763,10 +39587,9 @@ Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. WHATIF:TotAccessibilityMolecular beta12orEarlier - operations - edam - operation - bioinformatics + + + @@ -42776,13 +39599,12 @@ Protein surface calculation (accessible) - operations - bioinformatics - operation Calculate the solvent accessibility ('accessible surface') for a structure as a whole. beta12orEarlier WHATIF:TotAccessibilitySolvent - edam + + + @@ -42795,10 +39617,9 @@ Calculate for each residue in a protein structure all its backbone torsion angles. WHATIF:ResidueTorsionsBB beta12orEarlier - operations - edam - bioinformatics - operation + + + @@ -42811,10 +39632,9 @@ WHATIF:ResidueTorsions Calculate for each residue in a protein structure all its torsion angles. beta12orEarlier - operation - bioinformatics - operations - edam + + + @@ -42824,13 +39644,12 @@ Cysteine torsion angle calculation - edam - operation - operations Calculate for each cysteine (bridge) all its torsion angles. WHATIF:CysteineTorsions - bioinformatics beta12orEarlier + + + @@ -42840,14 +39659,13 @@ Tau angle calculation - operation For each amino acid in a protein structure calculate the backbone angle tau. - bioinformatics Tau is the backbone angle N-Calpha-C (angle over the C-alpha). beta12orEarlier - edam WHATIF:ShowTauAngle - operations + + + @@ -42857,13 +39675,12 @@ Cysteine bridge detection - operation beta12orEarlier - bioinformatics Detect cysteine bridges (from coordinate data) in a protein structure. WHATIF:ShowCysteineBridge - edam - operations + + + @@ -42874,13 +39691,12 @@ Free cysteine detection WHATIF:ShowCysteineFree - bioinformatics - operations Detect free cysteines in a protein structure. beta12orEarlier A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. - operation - edam + + + @@ -42891,12 +39707,11 @@ Metal-bound cysteine detection Detect cysteines that are bound to metal in a protein structure. - operation - operations WHATIF:ShowCysteineMetal - edam - bioinformatics beta12orEarlier + + + @@ -42908,14 +39723,13 @@ - operations - bioinformatics - edam Calculate protein residue contacts with nucleic acids in a structure. WHATIF:ShowProteiNucleicContacts WHATIF:HasNucleicContacts - operation beta12orEarlier + + + @@ -42926,14 +39740,13 @@ Residue contact calculation (residue-metal) - edam WHATIF:HasMetalContactsPlus - operation - WHATIF:HasMetalContacts - bioinformatics - operations Calculate protein residue contacts with metal in a structure. beta12orEarlier + WHATIF:HasMetalContacts + + + @@ -42945,12 +39758,11 @@ WHATIF:HasNegativeIonContacts beta12orEarlier - bioinformatics WHATIF:HasNegativeIonContactsPlus - edam - operations Calculate ion contacts in a structure (all ions for all side chain atoms). - operation + + + @@ -42961,12 +39773,11 @@ 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. - operation - operations - edam - bioinformatics beta12orEarlier WHATIF:ShowBumps + + + @@ -42976,14 +39787,13 @@ Residue symmetry contact calculation - bioinformatics - operations - operation beta12orEarlier A symmetry contact is a contact between two atoms in different asymmetric unit. WHATIF:SymmetryContact - edam Calculate the number of symmetry contacts made by residues in a protein structure. + + + @@ -42996,13 +39806,12 @@ WHATIF:ShowDrugContacts WHATIF:ShowDrugContactsShort - bioinformatics beta12orEarlier WHATIF:ShowLigandContacts - operation Calculate contacts between residues and ligands in a protein structure. - operations - edam + + + @@ -43013,16 +39822,15 @@ Salt bridge calculation WHATIF:HasSaltBridgePlus - operation - edam - operations Calculate (and possibly score) salt bridges in a protein structure. - bioinformatics WHATIF:ShowSaltBridgesH WHATIF:HasSaltBridge beta12orEarlier WHATIF:ShowSaltBridges Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. + + + @@ -43032,23 +39840,22 @@ Rotamer likelihood prediction - bioinformatics beta12orEarlier WHATIF:ShowLikelyRotamers100 WHATIF:ShowLikelyRotamers200 WHATIF:ShowLikelyRotamers300 WHATIF:ShowLikelyRotamers400 WHATIF:ShowLikelyRotamers700 - operation Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. WHATIF:ShowLikelyRotamers900 - operations WHATIF:ShowLikelyRotamers800 WHATIF:ShowLikelyRotamers600 Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. WHATIF:ShowLikelyRotamers500 WHATIF:ShowLikelyRotamers - edam + + + @@ -43059,12 +39866,11 @@ Proline mutation value calculation beta12orEarlier - operation WHATIF:ProlineMutationValue - edam 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. - operations - bioinformatics + + + @@ -43074,13 +39880,12 @@ Residue packing validation - bioinformatics - operations - edam Identify poorly packed residues in protein structures. WHATIF: PackingQuality - operation beta12orEarlier + + + @@ -43091,13 +39896,12 @@ Dihedral angle validation WHATIF: ImproperQualityMax - edam - operation beta12orEarlier - bioinformatics Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. WHATIF: ImproperQualitySum - operations + + + @@ -43108,15 +39912,12 @@ PDB file sequence retrieval beta12orEarlier - edam - bioinformatics true - operations WHATIF: PDB_sequence beta12orEarlier - operation Extract a molecular sequence from a PDB file. + @@ -43130,10 +39931,9 @@ beta12orEarlier Identify HET groups in PDB files. WHATIF: HETGroupNames - bioinformatics - operation - edam - operations + + + @@ -43143,16 +39943,13 @@ DSSP secondary structure assignment - operations - beta12orEarlier - edam - Determine for residue the DSSP determined secondary structure in three-state (HSC). - operation - bioinformatics - true WHATIF: ResidueDSSP + true + beta12orEarlier beta12orEarlier + Determine for residue the DSSP determined secondary structure in three-state (HSC). + @@ -43163,13 +39960,12 @@ Structure reformatting - bioinformatics WHATIF: PDBasXML - operation beta12orEarlier Reformat (a file or other report of) tertiary structure data. - edam - operations + + + @@ -43186,11 +39982,10 @@ beta12orEarlier - operations - bioinformatics Assign cysteine bonding state and disulfide bond partners in protein structures. - edam - operation + + + @@ -43202,12 +39997,11 @@ 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). WHATIF: UseResidueDB - operation beta12orEarlier Identify poor quality amino acid positions in protein structures. - operations - edam - bioinformatics + + + @@ -43217,13 +40011,12 @@ Structure retrieval (water) - operation Query a tertiary structure database and retrieve water molecules. - bioinformatics WHATIF:MovedWaterPDB - operations - edam beta12orEarlier + + + @@ -43245,12 +40038,11 @@ - operations - edam Identify or predict siRNA duplexes in RNA. beta12orEarlier - operation - bioinformatics + + + @@ -43262,11 +40054,10 @@ beta12orEarlier - edam Refine an existing sequence alignment. - operations - bioinformatics - operation + + + @@ -43278,10 +40069,9 @@ beta12orEarlier Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). - bioinformatics - operation - operations - edam + + + @@ -43293,11 +40083,10 @@ beta12orEarlier - edam - operations - operation - bioinformatics Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences. + + + @@ -43308,12 +40097,11 @@ Sequence alignment file processing - operations - bioinformatics Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. - operation beta12orEarlier - edam + + + @@ -43323,15 +40111,12 @@ Small molecule data processing - operation Process (read and / or write) physicochemical property data for small molecules. - operations beta12orEarlier - beta13 - edam - bioinformatics true + beta13 + @@ -43342,15 +40127,12 @@ Data retrieval (ontology annotation) beta12orEarlier - operation - bioinformatics + Search and retrieve documentation on a bioinformatics ontology. true Ontology information retrieval - operations - edam - Search and retrieve documentation on a bioinformatics ontology. beta13 + @@ -43360,16 +40142,13 @@ Data retrieval (ontology concept) - bioinformatics - beta12orEarlier + Ontology retrieval beta13 - operation + beta12orEarlier Query an ontology and retrieve concepts or relations. - operations - Ontology retrieval - edam true + @@ -43385,12 +40164,11 @@ - bioinformatics beta12orEarlier - operation - operations - edam Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + + + @@ -43401,12 +40179,11 @@ Structure file processing - bioinformatics - operations beta12orEarlier - edam Perform basic (non-analytical) operations on a file of molecular tertiary structural data. - operation + + + @@ -43416,16 +40193,13 @@ Data retrieval (sequence profile) + beta12orEarlier This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. beta13 true - bioinformatics - operation - edam - beta12orEarlier - operations Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. + @@ -43434,16 +40208,12 @@ Statistical calculation - - beta12orEarlier - edam - true + beta12orEarlier - operations - bioinformatics Perform a statistical data operation of some type, e.g. calibration or validation. - operation - + + + @@ -43456,23 +40226,22 @@ - - + + - - + + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. - operation - operations - bioinformatics A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. beta12orEarlier - edam + + + @@ -43485,22 +40254,21 @@ - - + + - - + + - operations beta12orEarlier - bioinformatics - operation Visualise transmembrane proteins, typically the transmembrane regions within a sequence. - edam + + + @@ -43511,13 +40279,10 @@ Demonstration beta13 - bioinformatics - edam - operation - operations An operation performing purely illustrative (pedagogical) purposes. true beta12orEarlier + @@ -43527,15 +40292,12 @@ Data retrieval (pathway or network) - operation - true - beta12orEarlier beta13 Query a biological pathways database and retrieve annotation on one or more pathways. - bioinformatics - operations - edam + true + beta12orEarlier + @@ -43545,15 +40307,12 @@ Data retrieval (identifier) - edam true beta13 - bioinformatics Query a database and retrieve one or more data identifiers. beta12orEarlier - operation - operations + @@ -43563,12 +40322,11 @@ Nucleic acid density plotting - edam - operation - operations Calculate a density plot (of base composition) for a nucleotide sequence. - bioinformatics beta12orEarlier + + + @@ -43580,8 +40338,8 @@ - - + + @@ -43592,17 +40350,16 @@ - - + + - operations - edam - operation - bioinformatics Sequence analysis (general) beta12orEarlier Analyse one or more known molecular sequences. + + + @@ -43619,11 +40376,10 @@ beta12orEarlier - operation Process (read and / or write) molecular sequence motifs. - operations - bioinformatics - edam + + + @@ -43639,12 +40395,11 @@ - operations - bioinformatics beta12orEarlier - operation - edam Process (read and / or write) protein interaction data. + + + @@ -43667,13 +40422,12 @@ - operation - bioinformatics beta12orEarlier Structure analysis (protein) Analyse protein tertiary structural data. - edam - operations + + + @@ -43683,15 +40437,12 @@ Annotation processing - bioinformatics - edam + Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. beta12orEarlier beta12orEarlier true - operation - operations - Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. + @@ -43702,14 +40453,11 @@ Sequence feature analysis beta12orEarlier - operation - operations + Analyse features in molecular sequences. true beta12orEarlier - Analyse features in molecular sequences. - bioinformatics - edam + @@ -43726,14 +40474,13 @@ Data file processing - operations File handling - bioinformatics - edam - operation Report handling beta12orEarlier Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations. + + + @@ -43743,15 +40490,12 @@ Gene expression analysis + beta12orEarlier true - operations Analyse gene expression and regulation data. - beta12orEarlier - bioinformatics beta12orEarlier - edam - operation + @@ -43767,12 +40511,11 @@ - operations - bioinformatics - operation - edam Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. beta12orEarlier + + + @@ -43782,13 +40525,12 @@ Data index processing - bioinformatics beta12orEarlier Process (read and / or write) an index of (typically a file of) biological data. - edam - operations - operation Database index processing + + + @@ -43804,12 +40546,11 @@ - bioinformatics - operation - operations Process (read and / or write) some type of sequence profile. beta12orEarlier - edam + + + @@ -43825,13 +40566,12 @@ - edam - operations beta12orEarlier Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. This is a broad concept and is used a placeholder for other, more specific concepts. - operation - bioinformatics + + + @@ -43855,13 +40595,12 @@ beta12orEarlier - edam - operation Protein folding modelling Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. This is a broad concept and is used a placeholder for other, more specific concepts. - bioinformatics - operations + + + @@ -43883,13 +40622,12 @@ - operation - edam - Analyse known protein secondary structure data. - operations - bioinformatics Secondary structure analysis (protein) beta12orEarlier + Analyse known protein secondary structure data. + + + @@ -43899,15 +40637,12 @@ Physicochemical property data processing - bioinformatics beta12orEarlier Process (read and / or write) data on the physicochemical property of a molecule. true - operations beta13 - edam - operation + @@ -43924,13 +40659,12 @@ - bioinformatics - operations - Primer and probe prediction Predict oligonucleotide primers or probes. - operation beta12orEarlier - edam + Primer and probe prediction + + + @@ -43940,14 +40674,13 @@ Analysis and processing - operation - operations beta12orEarlier Process (read and / or write) data of a specific type, for example applying analytical methods. - edam - bioinformatics Calculation Computation + + + @@ -43966,11 +40699,10 @@ 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. - operations - bioinformatics - operation beta12orEarlier - edam + + + @@ -43987,12 +40719,11 @@ Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. - edam - operations beta12orEarlier - operation - bioinformatics Information retrieval + + + @@ -44002,12 +40733,11 @@ Prediction, detection and recognition - operations - edam Predict, recognise, detect or identify some properties of a biomolecule. - bioinformatics beta12orEarlier - operation + + + @@ -44018,11 +40748,10 @@ Comparison Compare two or more things to identify similarities. - edam - bioinformatics - operation - operations beta12orEarlier + + + @@ -44032,12 +40761,11 @@ Optimisation and refinement - operation - bioinformatics - edam Refine or optimise some data model. beta12orEarlier - operations + + + @@ -44054,11 +40782,10 @@ Model or simulate some biological entity or system. - edam - operation - operations beta12orEarlier - bioinformatics + + + @@ -44069,14 +40796,11 @@ Data handling beta12orEarlier - operation - true - edam - operations Perform basic operations on some data or a database. - bioinformatics beta12orEarlier + true + @@ -44086,13 +40810,12 @@ Evaluation and validation - edam Validate or standardise some data. Validation and standardisation - operation - bioinformatics - operations beta12orEarlier + + + @@ -44105,22 +40828,21 @@ - + - + - operations - Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. - operation - bioinformatics beta12orEarlier - edam + Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. This is a broad concept and is used a placeholder for other, more specific concepts. + + + @@ -44130,15 +40852,12 @@ Design - beta13 - operations - bioinformatics - edam true Design a biological entity (typically a molecular sequence or structure) with specific properties. - operation + beta13 beta12orEarlier + @@ -44148,15 +40867,12 @@ Microarray data processing - bioinformatics true beta12orEarlier - edam - operation - operations Process (read and / or write) microarray data. beta12orEarlier + @@ -44167,11 +40883,10 @@ Codon usage table processing beta12orEarlier - bioinformatics - operations Process (read and / or write) a codon usage table. - operation - edam + + + @@ -44182,14 +40897,11 @@ Data retrieval (codon usage table) beta13 - operations - edam true - bioinformatics beta12orEarlier Retrieve a codon usage table and / or associated annotation. - operation + @@ -44199,12 +40911,11 @@ Gene expression profile processing - bioinformatics beta12orEarlier - operations Process (read and / or write) a gene expression profile. - operation - edam + + + @@ -44222,11 +40933,10 @@ Annotate a gene expression profile with concepts from an ontology of gene functions. - operation - bioinformatics beta12orEarlier - operations - edam + + + @@ -44244,11 +40954,10 @@ beta12orEarlier - operation Predict a network of gene regulation. - edam - operations - bioinformatics + + + @@ -44264,12 +40973,11 @@ - edam beta12orEarlier - operation Generate, analyse or handle a biological pathway or network. - bioinformatics - operations + + + @@ -44286,12 +40994,11 @@ - operations Process (read and / or write) RNA secondary structure data. - edam - bioinformatics - operation beta12orEarlier + + + @@ -44304,12 +41011,9 @@ true beta13 beta12orEarlier - operation - bioinformatics - operations - edam Process (read and / or write) RNA tertiary structure data. + @@ -44327,10 +41031,9 @@ Predict RNA tertiary structure. beta12orEarlier - bioinformatics - edam - operation - operations + + + @@ -44346,12 +41049,11 @@ - bioinformatics beta12orEarlier Predict DNA tertiary structure. - operation - edam - operations + + + @@ -44367,12 +41069,11 @@ - edam Process (read and / or write) a phylogenetic tree. - bioinformatics beta12orEarlier - operation - operations + + + @@ -44389,12 +41090,11 @@ - edam - bioinformatics beta12orEarlier - operations - operation Process (read and / or write) protein secondary structure data. + + + @@ -44411,12 +41111,11 @@ - edam - operation Process (read and / or write) a network of protein interactions. - bioinformatics beta12orEarlier - operations + + + @@ -44426,13 +41125,12 @@ Sequence processing - edam beta12orEarlier Process (read and / or write) one or more molecular sequences and associated annotation. - operation - operations - bioinformatics Sequence processing (general) + + + @@ -44443,12 +41141,11 @@ Sequence processing (protein) - operations - edam - bioinformatics - operation beta12orEarlier Process (read and / or write) a protein sequence and associated annotation. + + + @@ -44459,12 +41156,11 @@ Sequence processing (nucleic acid) - operations - edam - operation Process (read and / or write) a nucleotide sequence and associated annotation. - bioinformatics beta12orEarlier + + + @@ -44477,14 +41173,14 @@ - - + + - - + + @@ -44494,11 +41190,10 @@ beta12orEarlier - edam - operations - bioinformatics Compare two or more molecular sequences. - operation + + + @@ -44514,12 +41209,11 @@ - operation - bioinformatics beta12orEarlier - edam - operations Process (read and / or write) a sequence cluster. + + + @@ -44531,34 +41225,33 @@ - - + + - - + + - - + + - - + + - operations beta12orEarlier - operation - edam - bioinformatics Process (read and / or write) a sequence feature table. + + + @@ -44570,23 +41263,22 @@ - - + + - - + + Gene finding - bioinformatics - operations - beta12orEarlier - operation - edam Detect, predict and identify genes or components of genes in DNA sequences. + beta12orEarlier + + + @@ -44603,13 +41295,12 @@ - edam Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - beta12orEarlier - operations - bioinformatics - operation G protein-coupled receptor (GPCR) classification + beta12orEarlier + + + @@ -44627,12 +41318,11 @@ - operation - edam - operations beta12orEarlier - bioinformatics Predict G-protein coupled receptor (GPCR) coupling selectivity. + + + @@ -44650,11 +41340,10 @@ Process (read and / or write) a protein tertiary structure. - operation beta12orEarlier - bioinformatics - edam - operations + + + @@ -44664,13 +41353,12 @@ Protein atom surface calculation - operation - edam - operations beta12orEarlier Calculate the solvent accessibility for each atom in a structure. - bioinformatics Waters are not considered. + + + @@ -44680,12 +41368,11 @@ Protein residue surface calculation - operation Calculate the solvent accessibility for each residue in a structure. - edam - operations beta12orEarlier - bioinformatics + + + @@ -44695,12 +41382,11 @@ Protein surface calculation - operations - edam beta12orEarlier Calculate the solvent accessibility of a structure as a whole. - operation - bioinformatics + + + @@ -44716,12 +41402,11 @@ - bioinformatics Process (read and / or write) a molecular sequence alignment. - edam - operations beta12orEarlier - operation + + + @@ -44733,22 +41418,21 @@ - - + + - - + + - bioinformatics - operations beta12orEarlier - edam Identify or predict protein-protein interactions, interfaces, binding sites etc. - operation + + + @@ -44759,11 +41443,10 @@ Structure processing beta12orEarlier - bioinformatics Process (read and / or write) a molecular tertiary structure. - operations - operation - edam + + + @@ -44776,22 +41459,21 @@ - + - + - edam - bioinformatics - Annotate a DNA map of some type with terms from a controlled vocabulary. - operations - operation beta12orEarlier + Annotate a DNA map of some type with terms from a controlled vocabulary. + + + @@ -44801,16 +41483,13 @@ Data retrieval (protein annotation) - operation + beta12orEarlier Protein information retrieval true - edam - bioinformatics - beta12orEarlier - operations beta13 Retrieve information on a protein. + @@ -44820,15 +41499,12 @@ Data retrieval (phylogenetic tree) - operations - bioinformatics - operation - beta13 true Retrieve a phylogenetic tree from a data resource. - edam + beta13 beta12orEarlier + @@ -44838,15 +41514,12 @@ Data retrieval (protein interaction annotation) - operations - beta13 - Retrieve information on a protein interaction. - operation - edam beta12orEarlier - bioinformatics + beta13 true + Retrieve information on a protein interaction. + @@ -44856,16 +41529,13 @@ Data retrieval (protein family annotation) - operation - operations - Retrieve information on a protein family. - edam - beta12orEarlier true - bioinformatics + Retrieve information on a protein family. beta13 Protein family information retrieval + beta12orEarlier + @@ -44877,14 +41547,11 @@ beta13 beta12orEarlier - operations RNA family information retrieval - operation - Retrieve information on an RNA family. true - edam - bioinformatics + Retrieve information on an RNA family. + @@ -44894,16 +41561,13 @@ Data retrieval (gene annotation) - bioinformatics beta13 Retrieve information on a specific gene. + true Gene information retrieval beta12orEarlier - operations - true - edam - operation + @@ -44914,15 +41578,12 @@ Data retrieval (genotype and phenotype annotation) true - bioinformatics - operations - Retrieve information on a specific genotype or phenotype. beta13 beta12orEarlier Genotype and phenotype information retrieval - edam - operation + Retrieve information on a specific genotype or phenotype. + @@ -44933,18 +41594,11 @@ Protein architecture comparison - - - - - - beta12orEarlier - operation - bioinformatics Compare the architecture of two or more protein structures. - operations - edam + + + @@ -44956,18 +41610,12 @@ - - - - - - - operation Identify the architecture of a protein structure. - edam - operations - bioinformatics + 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. beta12orEarlier + + + @@ -44981,14 +41629,14 @@ - - + + - - + + @@ -44997,12 +41645,11 @@ - edam Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - bioinformatics - operation - operations beta12orEarlier + + + @@ -45025,13 +41672,12 @@ - operations - edam - bioinformatics Sequence analysis (nucleic acid) beta12orEarlier - operation Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). + + + @@ -45044,23 +41690,22 @@ - - + + - - + + - operations beta12orEarlier Sequence analysis (protein) - operation - edam Analyse a protein sequence (using methods that are only applicable to protein sequences). - bioinformatics + + + @@ -45072,14 +41717,14 @@ - - + + - - + + @@ -45088,12 +41733,11 @@ - operations Analyse known molecular tertiary structures. - operation - edam - bioinformatics beta12orEarlier + + + @@ -45116,12 +41760,11 @@ - operations - operation - edam - bioinformatics beta12orEarlier Analyse nucleic acid tertiary structural data. + + + @@ -45138,11 +41781,10 @@ beta12orEarlier - edam Process (read and / or write) a molecular secondary structure. - bioinformatics - operations - operation + + + @@ -45160,11 +41802,10 @@ Compare two or more molecular tertiary structures. - operation - bioinformatics - operations beta12orEarlier - edam + + + @@ -45181,11 +41822,10 @@ Render a helical wheel representation of protein secondary structure. - operation - operations beta12orEarlier - bioinformatics - edam + + + @@ -45201,12 +41841,11 @@ - bioinformatics - operations - edam Render a topology diagram of protein secondary structure. beta12orEarlier - operation + + + @@ -45232,12 +41871,11 @@ Compare protein tertiary structures. beta12orEarlier - operations Methods might identify structural neighbors, find structural similarities or define a structural core. Structure comparison (protein) - operation - edam - bioinformatics + + + @@ -45255,14 +41893,13 @@ - edam - bioinformatics - operation Compare protein secondary structures. beta12orEarlier Protein secondary structure Secondary structure comparison (protein) - operations + + + @@ -45279,14 +41916,13 @@ - bioinformatics Predict the subcellular localization of a protein sequence. The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. beta12orEarlier - operations Protein targeting prediction - edam - operation + + + @@ -45296,12 +41932,11 @@ Residue contact calculation (residue-residue) - operation Calculate contacts between residues in a protein structure. - operations - bioinformatics - edam beta12orEarlier + + + @@ -45313,11 +41948,10 @@ beta12orEarlier - operations - bioinformatics Identify potential hydrogen bonds between amino acid residues. - operation - edam + + + @@ -45334,12 +41968,11 @@ - edam beta12orEarlier - operations - operation - bioinformatics Predict the interactions of proteins with other molecules. + + + @@ -45349,15 +41982,12 @@ Codon usage data processing - edam - bioinformatics - beta13 - beta12orEarlier true - operation - operations Process (read and / or write) codon usage data. + beta13 + beta12orEarlier + @@ -45374,13 +42004,12 @@ Process (read and / or write) gene expression (typically microarray) data. - bioinformatics - operations Microarray data processing - beta12orEarlier - operation - edam Gene expression (microarray) data processing + beta12orEarlier + + + @@ -45396,12 +42025,11 @@ - operations - operation - bioinformatics Process (read and / or write) a network of gene regulation. beta12orEarlier - edam + + + @@ -45413,24 +42041,23 @@ - - + + - - + + beta12orEarlier Network analysis - edam Analyse a known biological pathway or network. - bioinformatics - operations Pathway analysis - operation + + + @@ -45440,15 +42067,12 @@ Sequencing-based expression profile data analysis - operations - operation - beta12orEarlier - Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. - edam - bioinformatics true beta12orEarlier + beta12orEarlier + Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. + @@ -45472,13 +42096,12 @@ - operations beta12orEarlier Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences. - operation - edam Splicing modelling - bioinformatics + + + @@ -45488,15 +42111,12 @@ Microarray raw data analysis - bioinformatics - operations Analyse raw microarray data. - beta12orEarlier true + beta12orEarlier beta12orEarlier - edam - operation + @@ -45514,10 +42134,9 @@ beta12orEarlier Process (read and / or write) nucleic acid sequence or structural data. - operation - bioinformatics - operations - edam + + + @@ -45533,12 +42152,11 @@ - bioinformatics - operation Process (read and / or write) protein sequence or structural data. - operations beta12orEarlier - edam + + + @@ -45548,14 +42166,11 @@ Sequence data processing - operation true - edam beta13 beta12orEarlier Process (read and / or write) molecular sequence data. - operations - bioinformatics + @@ -45565,15 +42180,12 @@ Structural data processing - operations - edam - bioinformatics - beta13 beta12orEarlier true - operation + beta13 Process (read and / or write) molecular structural data. + @@ -45583,12 +42195,11 @@ Text processing - edam Process (read and / or write) text. - operations beta12orEarlier - operation - bioinformatics + + + @@ -45612,12 +42223,11 @@ - operation - edam - operations beta12orEarlier - bioinformatics Analyse a protein sequence alignment, typically to detect features or make predictions. + + + @@ -45642,11 +42252,10 @@ Analyse a protein sequence alignment, typically to detect features or make predictions. - operations beta12orEarlier - edam - bioinformatics - operation + + + @@ -45658,13 +42267,12 @@ - operation beta12orEarlier Compare two or more nucleic acid sequences. - operations - bioinformatics Sequence comparison (nucleic acid) - edam + + + @@ -45676,13 +42284,12 @@ - operations - operation Compare two or more protein sequences. - bioinformatics Sequence comparison (protein) - edam beta12orEarlier + + + @@ -45699,11 +42306,10 @@ Back-translate a protein sequence into DNA. - operation beta12orEarlier - operations - edam - bioinformatics + + + @@ -45715,11 +42321,10 @@ beta12orEarlier - bioinformatics Edit or change a nucleic acid sequence, either randomly or specifically. - operations - edam - operation + + + @@ -45731,11 +42336,10 @@ beta12orEarlier - operation - edam - operations Edit or change a protein sequence, either randomly or specifically. - bioinformatics + + + @@ -45752,12 +42356,11 @@ - operations - bioinformatics - operation beta12orEarlier Generate a nucleic acid sequence by some means. - edam + + + @@ -45774,12 +42377,11 @@ - edam - operation - bioinformatics - operations beta12orEarlier Generate a protein sequence by some means. + + + @@ -45796,13 +42398,12 @@ - Visualise, format or render a nucleic acid sequence. beta12orEarlier - edam Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - operations - operation - bioinformatics + Visualise, format or render a nucleic acid sequence. + + + @@ -45813,13 +42414,14 @@ Sequence rendering (protein) + Protein sequence visualisation + beta12orEarlier Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - edam - operation - bioinformatics + Protein sequence rendering Visualise, format or render a protein sequence. - beta12orEarlier - operations + + + @@ -45831,13 +42433,12 @@ - operation - bioinformatics - operations - edam Structure comparison (nucleic acid) beta12orEarlier Compare nucleic acid tertiary structures. + + + @@ -45855,11 +42456,10 @@ Process (read and / or write) nucleic acid tertiary structure data. - operation - edam beta12orEarlier - bioinformatics - operations + + + @@ -45876,12 +42476,11 @@ - edam Generate a map of a DNA sequence annotated with positional or non-positional features of some type. beta12orEarlier - bioinformatics - operation - operations + + + @@ -45897,13 +42496,12 @@ - operations beta12orEarlier - edam Process (read and / or write) a DNA map of some type. - operation DNA map data processing - bioinformatics + + + @@ -45915,22 +42513,21 @@ - - + + - - + + - operations Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). - operation - bioinformatics - edam beta12orEarlier + + + @@ -45949,22 +42546,21 @@ - + - + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. - operations - edam - bioinformatics beta12orEarlier - operation Ligand-binding and active site prediction + + + @@ -45980,14 +42576,13 @@ - 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. - bioinformatics Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). - edam + 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. beta12orEarlier Sequence mapping - operations - operation + + + @@ -46005,11 +42600,10 @@ beta12orEarlier Alignment - bioinformatics - edam - operations - operation Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. + + + @@ -46022,10 +42616,9 @@ Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. beta12orEarlier - edam - bioinformatics - operation - operations + + + @@ -46043,10 +42636,9 @@ beta12orEarlier Compare the physicochemical properties of two or more proteins (or reference data). - bioinformatics - operations - operation - edam + + + @@ -46074,12 +42666,11 @@ - operation beta12orEarlier Compare two or more molecular secondary structures. - edam - bioinformatics - operations + + + @@ -46089,12 +42680,11 @@ Hopp and Woods plotting - edam - bioinformatics - operations Generate a Hopp and Woods plot of antigenicity of a protein. beta12orEarlier - operation + + + @@ -46104,12 +42694,11 @@ Microarray cluster textual view rendering - edam - operations - bioinformatics - operation Visualise gene clusters with gene names. beta12orEarlier + + + @@ -46119,14 +42708,13 @@ Microarray wave graph rendering - edam 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. - bioinformatics - operations - operation beta12orEarlier Microarray cluster temporal graph rendering + + + @@ -46136,14 +42724,13 @@ Microarray dendrograph rendering - operations Microarray view rendering Microarray checks view rendering - operation - edam beta12orEarlier Generate a dendrograph of raw, preprocessed or clustered microarray data. - bioinformatics + + + @@ -46153,13 +42740,12 @@ Microarray proximity map rendering - bioinformatics - operations Generate a plot of distances (distance matrix) between genes. - operation - edam Microarray distance map rendering beta12orEarlier + + + @@ -46171,12 +42757,11 @@ Microarray matrix tree plot rendering Microarray 2-way dendrogram rendering - edam - operations Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. beta12orEarlier - operation - bioinformatics + + + @@ -46187,11 +42772,10 @@ Microarray principal component rendering Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. - edam - bioinformatics - operations beta12orEarlier - operation + + + @@ -46201,12 +42785,11 @@ Microarray scatter plot rendering - operations - operation - edam beta12orEarlier - bioinformatics Generate a scatter plot of microarray data, typically after principal component analysis. + + + @@ -46217,11 +42800,10 @@ Whole microarray graph view rendering beta12orEarlier - edam - bioinformatics Visualise gene expression data where each band (or line graph) corresponds to a sample. - operations - operation + + + @@ -46231,12 +42813,11 @@ Microarray tree-map rendering - operation Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. - operations beta12orEarlier - edam - bioinformatics + + + @@ -46246,12 +42827,11 @@ Microarray Box-Whisker plot rendering - bioinformatics - edam - operation Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. - operations beta12orEarlier + + + @@ -46273,12 +42853,11 @@ - operation - operations - edam - bioinformatics 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. beta12orEarlier + + + @@ -46289,15 +42868,12 @@ Analysis beta12orEarlier - edam + true beta12orEarlier For non-analytical operations, see the 'Processing' branch. - true - bioinformatics - operations - operation Apply analytical methods to existing data of a specific type. + @@ -46320,11 +42896,10 @@ Analyse an existing alignment of two or more molecular sequences, structures or derived data. - operation - operations beta12orEarlier - edam - bioinformatics + + + @@ -46336,8 +42911,8 @@ - - + + @@ -46348,16 +42923,15 @@ - - + + beta12orEarlier - bioinformatics - operations - operation - edam Analyse a body of scientific text (typically a full text article from a scientific journal.) + + + @@ -46367,14 +42941,11 @@ Molecular interaction analysis - bioinformatics true beta13 - edam - operation - operations beta12orEarlier Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. + @@ -46391,11 +42962,10 @@ Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. - operations - edam - operation - bioinformatics beta12orEarlier + + + @@ -46405,12 +42975,11 @@ Residue contact calculation - bioinformatics - edam Calculate contacts between residues and some other group in a protein structure. beta12orEarlier - operations - operation + + + @@ -46421,11 +42990,10 @@ Alignment processing beta12orEarlier - edam Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. - operation - bioinformatics - operations + + + @@ -46441,12 +43009,11 @@ - bioinformatics beta12orEarlier Process (read and / or write) a molecular tertiary (3D) structure alignment. - operations - operation - edam + + + @@ -46462,12 +43029,11 @@ - operations - edam beta12orEarlier - bioinformatics Calculate codon usage bias. - operation + + + @@ -46483,12 +43049,11 @@ - bioinformatics - operation - edam - operations Generate a codon usage bias plot. beta12orEarlier + + + @@ -46504,12 +43069,11 @@ - operations - edam - bioinformatics beta12orEarlier Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. - operation + + + @@ -46525,12 +43089,11 @@ - operations Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. - bioinformatics - edam beta12orEarlier - operation + + + @@ -46541,13 +43104,10 @@ Molecular interaction data processing Process (read and / or write) molecular interaction data. - edam - bioinformatics - operation - operations beta12orEarlier true beta13 + @@ -46558,12 +43118,11 @@ Sequence classification - operation - bioinformatics Assign molecular sequence(s) to a group or category. - edam - operations beta12orEarlier + + + @@ -46574,12 +43133,11 @@ Structure classification - operations - edam - bioinformatics beta12orEarlier Assign molecular structure(s) to a group or category. - operation + + + @@ -46590,11 +43148,10 @@ Protein comparison beta12orEarlier - edam - bioinformatics - operation Compare two or more proteins (or some aspect) to identify similarities. - operations + + + @@ -46606,10 +43163,9 @@ Compare two or more nucleic acids to identify similarities. beta12orEarlier - operation - bioinformatics - operations - edam + + + @@ -46619,12 +43175,11 @@ Prediction, detection and recognition (protein) - operations Predict, recognise, detect or identify some properties of proteins. - bioinformatics beta12orEarlier - operation - edam + + + @@ -46635,11 +43190,10 @@ Prediction, detection and recognition (nucleic acid) Predict, recognise, detect or identify some properties of nucleic acids. - edam - operation - operations - bioinformatics beta12orEarlier + + + @@ -46658,10 +43212,9 @@ beta13 Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. - edam - operations - bioinformatics - operation + + + @@ -46672,12 +43225,11 @@ Sequence alignment editing - operation - bioinformatics - operations beta13 - edam Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. + + + @@ -46695,11 +43247,10 @@ beta13 - bioinformatics - operation - edam - operations Render (visualise) a biological pathway or network. + + + @@ -46719,11 +43270,10 @@ Predict general (non-positional) functional properties of a protein from analysing its sequence. For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. - edam - operation - bioinformatics - operations beta13 + + + @@ -46734,13 +43284,12 @@ Protein site detection - bioinformatics beta13 - operations - edam name: Sequence motif recognition (protein) Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. - operation + + + @@ -46751,12 +43300,11 @@ Protein property calculation (from sequence) - edam - bioinformatics - operations - operation Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. beta13 + + + @@ -46768,11 +43316,10 @@ Predict, recognise and identify positional features in proteins from analysing protein structure. - operations - operation beta13 - bioinformatics - edam + + + @@ -46802,12 +43349,11 @@ - operations - operation - edam beta13 Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. - bioinformatics + + + @@ -46817,12 +43363,11 @@ Sequence screening - bioinformatics beta13 Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - edam - operations - operation + + + @@ -46838,12 +43383,11 @@ - operations Predict a network of protein interactions. - edam - bioinformatics - operation beta13 + + + @@ -46853,12 +43397,11 @@ Nucleic acid design - operations Design (or predict) nucleic acid sequences with specific chemical or physical properties. - bioinformatics beta13 - edam - operation + + + @@ -46869,11 +43412,10 @@ Editing Edit, convert or otherwise change a data entity, either randomly or specifically. - bioinformatics - edam - operation beta13 - operations + + + @@ -46887,14 +43429,14 @@ - - + + - - + + @@ -46903,12 +43445,11 @@ - bioinformatics - edam - operations 1.1 Evaluate a DNA sequence assembly, typically for purposes of quality control. - operation + + + @@ -46920,11 +43461,10 @@ Genome alignment 1.1 - edam - operations Align two or more (tpyically huge) molecular sequences that represent genomes. - bioinformatics - operation + + + @@ -46934,12 +43474,11 @@ Localized reassembly - operation 1.1 - operations - bioinformatics Reconstruction of a sequence assembly in a localised area. - edam + + + @@ -46950,14 +43489,13 @@ Sequence assembly rendering Assembly visualisation - edam - operations 1.1 - bioinformatics - operation Render and visualise a DNA sequence assembly. Assembly rendering Sequence assembly visualisation + + + @@ -46974,14 +43512,13 @@ Base calling - operation - operations 1.1 Phred base calling Phred base-calling - bioinformatics Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. - edam + + + @@ -46991,15 +43528,14 @@ Bisulfite mapping + Bisulfite sequence mapping Bisulfite sequence alignment The mapping of methylation sites in a DNA (genome) sequence. - bioinformatics - Bisulfite sequence mapping - operations - edam - operation 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. 1.1 + + + @@ -47016,11 +43552,10 @@ Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. - operations - operation beta12orEarlier - bioinformatics - edam + + + @@ -47030,13 +43565,12 @@ Trim ends - bioinformatics For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - operation - operations 1.1 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. - edam + + + @@ -47046,12 +43580,11 @@ Trim vector - operations - edam 1.1 - operation - bioinformatics Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + + + @@ -47061,12 +43594,11 @@ Trim to reference - operation Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. - bioinformatics - edam 1.1 - operations + + + @@ -47076,12 +43608,11 @@ Sequence trimming - bioinformatics - operations - edam Cut (remove) the end from a molecular sequence. - operation 1.1 + + + @@ -47094,10 +43625,9 @@ 1.1 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. - bioinformatics - operation - edam - operations + + + @@ -47113,14 +43643,13 @@ + Detect errors in DNA sequences generated from sequencing projects). beta12orEarlier Short-read error correction - operation - Detect errors in DNA sequences generated from sequencing projects). - operations - edam - bioinformatics Short read error correction + + + @@ -47130,13 +43659,12 @@ Genotyping - edam 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. - operations 1.1 - bioinformatics - operation + + + @@ -47153,14 +43681,13 @@ Genetic variation annotation - edam - operation - bioinformatics 1.1 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. Sequence variation analysis - operations + + + @@ -47168,10 +43695,9 @@ - Oligonucleotide alignment construction + Read mapping - operation - operations + Short sequence read mapping Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. Short read alignment @@ -47179,12 +43705,13 @@ Read alignment 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. Oligonucleotide alignment - edam + Oligonucleotide alignment construction Short read mapping - bioinformatics - Read mapping Oligonucleotide mapping Short oligonucleotide alignment + + + @@ -47194,12 +43721,11 @@ Split read mapping - operations - operation 1.1 - edam - bioinformatics A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. + + + @@ -47210,12 +43736,11 @@ DNA barcoding Sample barcoding - operation 1.1 - edam - operations - bioinformatics Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + + + @@ -47225,13 +43750,12 @@ SNP calling - bioinformatics - edam - operation 1.1 Operations usually score confidence in the prediction or some other statistical measure of evidence. - operations 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. + + + @@ -47241,13 +43765,12 @@ Mutation detection - operations - bioinformatics - edam 1.1 - operation Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. Polymorphism detection + + + @@ -47257,13 +43780,12 @@ Chromatogram visualisation - edam - operations 1.1 - operation Chromatogram viewing Visualise, format or render an image of a Chromatogram. - bioinformatics + + + @@ -47273,12 +43795,11 @@ Methylation analysis - bioinformatics Determine cytosine methylation states in nucleic acid sequences. 1.1 - edam - operation - operations + + + @@ -47288,12 +43809,11 @@ Methylation calling - bioinformatics Determine cytosine methylation status of specific positions in a nucleic acid sequences. - edam - operations 1.1 - operation + + + @@ -47303,13 +43823,12 @@ Methylation level analysis (global) - operations Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. - bioinformatics - operation - edam Global methylation analysis 1.1 + + + @@ -47319,14 +43838,13 @@ Methylation level analysis (gene-specific) - bioinformatics - operation - operations Many different techniques are available for this. Measure the level of methyl cytosines in specific genes. - edam 1.1 Gene-specific methylation analysis + + + @@ -47337,15 +43855,14 @@ Genome rendering Genome browsing - bioinformatics Genome viewing - operation - edam Genome visualisation Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. - 1.1 - operations Genome visualization + 1.1 + + + @@ -47355,13 +43872,12 @@ Genome comparison - bioinformatics Genomic region matching 1.1 - edam - operations - operation Compare the sequence or features of two or more genomes, for example, to find matching regions. + + + @@ -47378,12 +43894,11 @@ 1.1 - bioinformatics Generate an index of a genome sequence. - operations Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. - operation - edam + + + @@ -47393,13 +43908,12 @@ Genome indexing (Burrows-Wheeler) - operations - operation 1.1 Generate an index of a genome sequence using the Burrows-Wheeler algorithm. - edam - bioinformatics The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. + + + @@ -47409,14 +43923,13 @@ Genome indexing (suffix arrays) - bioinformatics - operations A suffix array consists of the lexicographically sorted list of suffixes of a genome. - operation - edam suffix arrays Generate an index of a genome sequence using a suffix arrays algorithm. 1.1 + + + @@ -47427,13 +43940,12 @@ Spectrum analysis Mass spectrum analysis - operation Analyse a spectrum from a mass spectrometry (or other) experiment. - edam - bioinformatics - Spectral analysis 1.1 - operations + Spectral analysis + + + @@ -47449,13 +43961,12 @@ - operation - operations - edam Identify peaks in a spectrum from a mass spectrometry experiment. - bioinformatics Peak finding 1.1 + + + @@ -47467,14 +43978,13 @@ - operation Scaffold may be positioned along a chromosome physical map to create a "golden path". 1.1 - edam - operations - bioinformatics 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 + + + @@ -47486,13 +43996,12 @@ - bioinformatics - 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. - operations 1.1 - operation + 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. Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. - edam + + + @@ -47503,14 +44012,13 @@ Sequencing quality control - bioinformatics - operations - operation - Sequencing QC - Raw sequence data quality control. - edam Analyse raw sequence data from a sequencing pipeline and identify problems. 1.1 + Sequencing QC + Raw sequence data quality control. + + + @@ -47521,13 +44029,12 @@ Read pre-processing 1.1 - operations Pre-process sequence reads to ensure (or improve) quality and reliability. - operation - bioinformatics This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. - edam Sequence read pre-processing + + + @@ -47545,10 +44052,9 @@ 1.1 Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. - operations - bioinformatics - operation - edam + + + @@ -47561,11 +44067,10 @@ 1.1 Protein binding peak detection Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. - bioinformatics 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'). - edam - operations - operation + + + @@ -47575,14 +44080,13 @@ Differential expression analysis - operations - operation 1.1 Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. - edam Differentially expressed gene identification - bioinformatics Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. + + + @@ -47592,13 +44096,12 @@ Gene set testing - edam 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. - bioinformatics Gene sets can be defined beforehand by biological function, chromosome locations and so on. - operations 1.1 - operation + + + @@ -47609,13 +44112,12 @@ Variant classification - operations - edam 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.) - operation - bioinformatics 1.1 Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. + + + @@ -47625,13 +44127,12 @@ Variant prioritization - edam - bioinformatics 1.1 - operation - operations Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + + + @@ -47641,14 +44142,13 @@ Variant mapping - bioinformatics - operations Variant calling Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. - edam Methods often utilise a database of aligned reads. - operation 1.1 + + + @@ -47658,13 +44158,12 @@ Structural variation discovery - operations Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. - bioinformatics - operation 1.1 - edam Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). + + + @@ -47675,14 +44174,13 @@ Exome analysis Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. + Exome sequence analysis Exome sequencing is considered a cheap alternative to whole genome sequencing. - bioinformatics Targeted exome capture 1.1 - edam - Exome sequence analysis - operation - operations + + + @@ -47694,10 +44192,9 @@ Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. 1.1 - operations - bioinformatics - operation - edam + + + @@ -47713,15 +44210,14 @@ - operation - operations - bioinformatics 1.1 - edam expression quantitative trait loci profiling expression QTL 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. eQTL profiling + + + @@ -47731,14 +44227,13 @@ Copy number estimation - operation Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. - bioinformatics - edam 1.1 - operations Transcript copy number estimation 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). + + + @@ -47749,12 +44244,11 @@ Primer removal - bioinformatics Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). - operations - operation 1.2 - edam + + + @@ -47768,22 +44262,21 @@ - - + + - - + + - edam Infer a transcriptome sequence by analysis of short sequence reads. - operations - operation 1.2 - bioinformatics + + + @@ -47793,13 +44286,12 @@ Transcriptome assembly (de novo) - operations Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. 1.2 - operation - edam de novo transcriptome assembly - bioinformatics + + + @@ -47809,12 +44301,11 @@ Transcriptome assembly (mapping) - bioinformatics 1.2 - operation Infer a transcriptome sequence by mapping short reads to a reference genome. - operations - edam + + + @@ -47826,22 +44317,21 @@ - + - + - operations - edam 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. 1.3 - bioinformatics - operation + + + @@ -47851,12 +44341,11 @@ Document similarity calculation - operation 1.3 - edam - operations - bioinformatics Calculate similarity between 2 or more documents. + + + @@ -47867,11 +44356,10 @@ Document clustering 1.3 - operations - operation Cluster (group) documents on the basis of their calculated similarity. - edam - bioinformatics + + + @@ -47881,12 +44369,11 @@ Named entity recognition - edam - operations - operation Recognise named entities (text tokens) within documents. 1.3 - bioinformatics + + + @@ -47896,14 +44383,13 @@ ID mapping - operations Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. - operation Accession mapping - edam - bioinformatics 1.3 Identifier mapping + + + @@ -47913,13 +44399,12 @@ Data anonymisation - edam 1.3 - bioinformatics Data anonymization - operation Process data in such a way that makes it hard to trace to the person which the data concerns. - operations + + + @@ -47937,16 +44422,164 @@ 1.3 Search for and retrieve a data identifier of some kind, e.g. a database entry accession. - edam Accession retrieval - bioinformatics - operation Data retrieval (id) Identifier retrieval Data retrieval (ID) Data retrieval (accession) - operations id retrieval + + + + + + + + + + + Sequence checksum generation + + + + + + + + + + + + + + 1.4 + Generate a checksum of a molecular sequence. + + + + + + + + + + + Bibliography construction + + 1.4 + Construct a bibliography from the scientific literature. + + + + + + + + + + + Protein quaternary structure prediction + + Predict the structure of a multi-subunit protein and particularly how the subunits fit together. + 1.4 + + + + + + + + + + + Protein surface analysis + + Analyse the surface properties of proteins. + 1.4 + + + + + + + + + + + Ontology comparison + + Compare two or more ontologies, e.g. identify differences. + 1.4 + + + + + + + + + + + Semantic analysis + + Analyse set(s) of terms from a controlled vocabulary to make scientific inferences. + Compare two or more ontologies, e.g. identify differences. + 1.4 + + + + + + + + + + + Format detection + + + + + + + + + + + + + + Format inference + '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. + Format recognition + Format identification + 1.4 + Recognition of which format the given data is in. + + + + + + + The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. + + + + + + + + + + + File splitting + + 1.4 + split a file containing multiple data items into many files, each +containing one item + + + @@ -47959,12 +44592,11 @@ sumo:FieldOfStudy beta12orEarlier 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. - bioinformatics - edam - topic - topics + + + @@ -47979,10 +44611,10 @@ - GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. + Topic can be a quality of an entity. - + GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. @@ -47991,10 +44623,10 @@ - Topic can be a quality of an entity. + GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. - + @@ -48004,19 +44636,18 @@ Nucleic acids - edam - Nucleic acid analysis + Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. beta12orEarlier - bioinformatics Nucleic acid physicochemistry - Processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid properties - topic - topics Nucleic acid informatics + Nucleic acid analysis Nucleic acid bioinformatics + + + @@ -48027,18 +44658,15 @@ Proteins beta12orEarlier - Protein data resources + Protein analysis Protein databases Protein bioinformatics - bioinformatics - edam - Protein analysis Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. - Proteins - topic Protein informatics - topics + + + @@ -48049,13 +44677,12 @@ Metabolites beta12orEarlier - bioinformatics This concept excludes macromolecules such as proteins and nucleic acids. - topics Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Metabolite structures - topic - edam + + + @@ -48065,17 +44692,16 @@ Sequence analysis - events - bioinformatics - topic BioCatalogue:Sequence Analysis - topics Sequences Sequence databases Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. - edam beta12orEarlier + + + + @@ -48086,19 +44712,18 @@ Structure analysis beta12orEarlier - topics Structure data resources This includes related concepts such as structural properties, alignments and structural motifs. Structure databases - edam Structural bioinformatics - topic Structure analysis - bioinformatics - events Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. Computational structural biology + + + + @@ -48108,12 +44733,11 @@ Structure prediction - bioinformatics - topic - edam beta12orEarlier Topic concerning the prediction of molecular (secondary or tertiary) structure. - topics + + + @@ -48123,17 +44747,14 @@ Alignment - edam - Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). - beta12orEarlier beta12orEarlier - topic - topics + Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). true - bioinformatics + beta12orEarlier + @@ -48144,21 +44765,22 @@ Phylogeny BioCatalogue:Evolutionary Distance Measurements - Phylogenetic clocks, dating and stratigraphy 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. - bioinformatics BioCatalogue:Phylogeny - edam Phylogenetic simulation BioCatalogue:Statistical Robustness - topics - events - topic Topic concerning the study of evolutionary relationships amongst organisms. + Phylogenetic clocks + Phylogenetic dating beta12orEarlier BioCatalogue:Tree Inference + Phylogenetic stratigraphy Phylogeny reconstruction + + + + @@ -48170,14 +44792,12 @@ BioCatalogue:Functional Genomics - topic - Genome annotation - bioinformatics - topics - edam - events Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. beta12orEarlier + + + + @@ -48186,19 +44806,20 @@ Ontology and terminology - - topics + + Ontologies BioCatalogue:Ontology Lookup - bioinformatics Topic concerning 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. - events + Ontology Applied ontology beta12orEarlier - Ontologies - topic - edam + Terminology BioCatalogue:Ontology + + + + @@ -48212,16 +44833,16 @@ Data query BioCatalogue:Structure Retrieval BioCatalogue:Image Retrieval - bioinformatics - edam BioCatalogue:Sequence Retrieval BioCatalogue:Data Retrieval BioCatalogue:Identifier Retrieval - topic + Data search This includes, for example, search, query and retrieval of molecular sequences and associated data. - topics Data retrieval beta12orEarlier + + + @@ -48232,18 +44853,14 @@ Bioinformatics - topics - bioinformatics - events This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. - Information science - Data handling Topic concerning the archival, curation, processing and analysis of complex biological data. beta12orEarlier - edam - Informatics - topic + + + + @@ -48253,15 +44870,14 @@ Data visualisation - edam - bioinformatics - Data rendering and visualisation - Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data. beta12orEarlier - topic + Data rendering and visualisation Data rendering Data plotting - topics + Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data. + + + @@ -48271,11 +44887,11 @@ Nucleic acid thermodynamics - topics 1.3 true Topic concerning the study of the thermodynamic properties of a nucleic acid. + @@ -48290,15 +44906,14 @@ Nucleic acid thermodynamics beta12orEarlier RNA structure alignment - bioinformatics Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. - edam - topic RNA alignment Nucleic acid denaturation - topics DNA melting Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. + + + @@ -48309,11 +44924,10 @@ RNA Topic concerning RNA sequences and structures. - topic - edam - bioinformatics - topics beta12orEarlier + + + @@ -48323,15 +44937,12 @@ Nucleic acid restriction - bioinformatics true - edam Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. - 1.3 - topics - topic beta12orEarlier + 1.3 + @@ -48341,15 +44952,15 @@ Mapping - topic - edam 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. beta12orEarlier - topics - bioinformatics Linkage mapping + Linkage Genetic linkage Topic concerning the mapping of complete (typically nucleotide) sequences. + + + @@ -48361,11 +44972,11 @@ Codon usage analysis 1.3 - topics Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. true beta12orEarlier + @@ -48375,14 +44986,13 @@ Protein expression - bioinformatics beta12orEarlier - topic - events Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. - edam Translation - topics + + + + @@ -48393,18 +45003,15 @@ Gene finding BioCatalogue:Gene Prediction - bioinformatics - edam Gene discovery Topic 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. 1.3 true Gene prediction - topics beta12orEarlier - topic + @@ -48414,15 +45021,12 @@ Transcription - beta12orEarlier - topic - topics true - bioinformatics + beta12orEarlier Topic concerning the transcription of DNA into mRNA. - edam 1.3 + @@ -48432,16 +45036,13 @@ Promoters - topic - edam + beta13 Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). BioCatalogue:Promoter Prediction - topics - beta13 - bioinformatics beta12orEarlier true + @@ -48455,11 +45056,8 @@ Topic concerning the folding (in 3D space) of nucleic acid molecules. true beta12orEarlier - edam - topic - bioinformatics - topics + @@ -48469,15 +45067,12 @@ Gene structure - topics Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion. - topic - RNA splicing - Gene structure beta12orEarlier - bioinformatics - edam This includes the study of promoters, coding regions etc. + + + @@ -48486,20 +45081,19 @@ Proteomics - + BioCatalogue:Proteomics Protein expression Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. - bioinformatics - edam 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 expression data, for example in different cells or tissues. Peptide identification Protein and peptide identification beta12orEarlier - events - topic - topics + + + + @@ -48510,14 +45104,13 @@ Structural genomics - edam Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. - BioCatalogue:Structural Genomics - topic - events - bioinformatics beta12orEarlier - topics + BioCatalogue:Structural Genomics + + + + @@ -48527,14 +45120,13 @@ Protein properties - topics beta12orEarlier - Topic for 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 - topic - edam - bioinformatics + Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. + + + @@ -48545,20 +45137,19 @@ Protein interactions - topics BioCatalogue:Protein Interaction Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. Protein-DNA interaction BioCatalogue:Ligand Interaction Protein-ligand interactions beta12orEarlier - edam - bioinformatics Protein-protein interactions This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. Protein-nucleic acid interactions Protein-RNA interaction - topic + + + @@ -48569,14 +45160,15 @@ Protein folding, stability and design Rational protein design - bioinformatics - edam + Protein stability + Protein folding Protein design Protein residue interactions beta12orEarlier - topic Topic concerning 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. - topics + + + @@ -48586,15 +45178,12 @@ Two-dimensional gel electrophoresis - topics true beta12orEarlier beta13 - topic - edam - bioinformatics Topic concerning two-dimensional gel electrophoresis image and related data. + @@ -48603,16 +45192,12 @@ Mass spectrometry - - topics - beta13 + + Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. beta12orEarlier - topic - Topic concerning mass spectrometry and related data. - true - edam - bioinformatics - + + + @@ -48623,15 +45208,12 @@ Protein microarrays beta13 - edam beta12orEarlier - bioinformatics true - topics - topic Topic concerning protein microarray data. + @@ -48643,10 +45225,10 @@ 1.3 true - topics beta12orEarlier Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. + @@ -48656,13 +45238,14 @@ Protein targeting and localization - edam beta12orEarlier - topic - topics - bioinformatics - Protein sorting - Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + Protein localization + Protein targeting + Protein sorting + Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + + + @@ -48672,15 +45255,12 @@ Protein cleavage sites and proteolysis - bioinformatics - topic - edam - topics + 1.3 beta12orEarlier Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. true - 1.3 + @@ -48691,16 +45271,13 @@ Protein structure comparison beta12orEarlier - topics - Use this concept for methods that are exclusively for protein structure. true + Use this concept for methods that are exclusively for protein structure. beta12orEarlier - bioinformatics - topic Topic concerning the comparison of two or more protein structures. - edam + @@ -48710,16 +45287,13 @@ Protein residue interactions - bioinformatics + beta12orEarlier 1.3 Protein residue interactions - edam - beta12orEarlier true - topic - topics The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. + @@ -48734,8 +45308,8 @@ beta12orEarlier true Protein interaction networks - topics + @@ -48747,10 +45321,10 @@ 1.3 true - topics Topic concerning protein-ligand (small molecule) interactions. beta12orEarlier + @@ -48760,12 +45334,12 @@ Protein-nucleic acid interactions - topics true 1.3 Topic concerning protein-DNA/RNA interactions. beta12orEarlier + @@ -48776,12 +45350,11 @@ Protein design true - bioinformatics Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - topics beta12orEarlier 1.3 + @@ -48792,14 +45365,11 @@ G protein-coupled receptors (GPCR) beta12orEarlier - edam - topics beta12orEarlier Topic concerning G-protein coupled receptors (GPCRs). - bioinformatics - topic true + @@ -48809,12 +45379,11 @@ Carbohydrates - edam Topic concerning carbohydrates, typically including structural information. - topics - bioinformatics beta12orEarlier - topic + + + @@ -48824,12 +45393,11 @@ Lipids - edam - topics Topic concerning lipids and their structures. beta12orEarlier - bioinformatics - topic + + + @@ -48839,14 +45407,13 @@ Small molecules - edam - topic beta12orEarlier CHEBI:23367 Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. - bioinformatics Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. - topics + + + @@ -48858,14 +45425,11 @@ beta12orEarlier Edit, convert or otherwise change a molecular sequence, either randomly or specifically. - beta12orEarlier - edam - bioinformatics - topic true - topics + beta12orEarlier + @@ -48878,15 +45442,14 @@ BioCatalogue:Repeats Sequence composition Topic concerning 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. - bioinformatics Sequence repeats Low complexity sequences Sequence complexity - topic - topics beta12orEarlier Repeat sequences - edam + + + @@ -48896,16 +45459,13 @@ Sequence motifs - topics - bioinformatics + Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. 1.3 true - Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. - topic Motifs - edam beta12orEarlier + @@ -48915,15 +45475,14 @@ Sequence comparison - topic - bioinformatics - topics + beta12orEarlier + BioCatalogue:Protein Sequence Similarity BioCatalogue:Nucleotide Sequence Similarity The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. Topic concerning the comparison of two or more molecular sequences. - edam - beta12orEarlier - BioCatalogue:Protein Sequence Similarity + + + @@ -48940,15 +45499,14 @@ Protein sequence features Topic concerning 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. - edam Sequence feature detection Sequence motifs Functional sites - topic Protein functional sites - bioinformatics - topics Sequence features + + + @@ -48958,16 +45516,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence database search - true - beta12orEarlier - topic - edam The query is a sequence-based entity such as another sequence, a motif or profile. + true beta12orEarlier Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). - topics - bioinformatics + beta12orEarlier + @@ -48979,12 +45534,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence clusters Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. - topics - bioinformatics - topic beta12orEarlier - edam This includes systems that generate, process and analyse sequence clusters. + + + @@ -48993,18 +45547,17 @@ positional features such as functional and other key sites, in molecular sequenc Protein structural motifs and surfaces - - topic - topics - Protein surfaces - bioinformatics + + Protein surfaces + Protein structural motifs beta12orEarlier Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. - Structural motifs - Protein structural features - Protein structural motifs - edam + Protein structural features + Structural motifs + + + @@ -49014,16 +45567,13 @@ positional features such as functional and other key sites, in molecular sequenc Structural (3D) profiles - edam - 1.3 Structural profiles + 1.3 beta12orEarlier - bioinformatics - topics true 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. - topic + @@ -49035,12 +45585,11 @@ positional features such as functional and other key sites, in molecular sequenc BioCatalogue:Protein Structure Prediction - edam - topic - topics Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. beta12orEarlier - bioinformatics + + + @@ -49053,16 +45602,16 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. Nucleic acid folding - topic BioCatalogue:Nucleotide Structure Prediction BioCatalogue:Nucleotide Tertiary Structure - bioinformatics - edam BioCatalogue:Nucleotide Secondary Structure beta12orEarlier - topics + RNA structure prediction Nucleic acid design - RNA/DNA structure prediction + DNA structure prediction + + + @@ -49073,12 +45622,11 @@ positional features such as functional and other key sites, in molecular sequenc Ab initio structure prediction beta12orEarlier - bioinformatics de novo protein structure prediction - edam - Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. - topics - topic + Topic concerning 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. + + + @@ -49087,14 +45635,13 @@ positional features such as functional and other key sites, in molecular sequenc Homology modelling - - topics + + Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data. beta12orEarlier - topic - edam - Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data. - bioinformatics - Comparative modelling + true + 1.4 + + @@ -49103,16 +45650,15 @@ positional features such as functional and other key sites, in molecular sequenc Molecular dynamics - - bioinformatics + beta12orEarlier + Molecular motions + Molecular flexibility Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - Molecular flexibility - edam - Molecular motions - topics This includes resources concerning flexibility and motion in protein and other molecular structures. - topic + + + @@ -49121,13 +45667,12 @@ positional features such as functional and other key sites, in molecular sequenc Molecular docking - - Topic for modelling the structure of proteins in complex with small molecules or other macromolecules. - topics - bioinformatics - edam - topic + + Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. beta12orEarlier + + + @@ -49141,9 +45686,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier 1.3 Topic concerning the prediction of secondary or supersecondary structure of protein sequences. - topics + @@ -49157,10 +45702,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier true 1.3 - topic - topics + @@ -49169,14 +45713,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein fold recognition - - topic + beta12orEarlier - bioinformatics Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). - edam - topics For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + + + @@ -49186,20 +45729,19 @@ positional features such as functional and other key sites, in molecular sequenc Sequence alignment - bioinformatics BioCatalogue:Protein Multiple Alignment Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). - topic BioCatalogue:Protein Pairwise Alignment - edam beta12orEarlier 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. BioCatalogue:Nucleotide Multiple Alignment BioCatalogue:Protein Sequence Alignment - topics BioCatalogue:Nucleotide Pairwise Alignment BioCatalogue:Nucleotide Sequence Alignment + + + @@ -49210,13 +45752,12 @@ positional features such as functional and other key sites, in molecular sequenc Structure alignment beta12orEarlier - bioinformatics - topic This includes the generation, storage, analysis, rendering etc. of structure alignments. - edam Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). - topics Structure alignment generation + + + @@ -49227,15 +45768,12 @@ positional features such as functional and other key sites, in molecular sequenc Threading true - edam - Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). beta12orEarlier + Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). 1.3 - topics - bioinformatics - topic Sequence-structure alignment + @@ -49246,15 +45784,12 @@ positional features such as functional and other key sites, in molecular sequenc Sequence profiles and HMMs Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. - beta12orEarlier 1.3 - topics - topic - bioinformatics + beta12orEarlier Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. - edam true + @@ -49264,18 +45799,15 @@ positional features such as functional and other key sites, in molecular sequenc Phylogeny reconstruction - topic BioCatalogue:Tree Inference Currently too specific for the topic sub-ontology (but might be unobsoleted). - topics Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. BioCatalogue:Evolutionary Distance Measurements - bioinformatics beta12orEarlier - edam true 1.3 http://edamontology.org/topic_0084 + @@ -49286,13 +45818,12 @@ positional features such as functional and other key sites, in molecular sequenc Phylogenomics - topics - edam - events - topic Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. - bioinformatics beta12orEarlier + + + + @@ -49303,16 +45834,13 @@ positional features such as functional and other key sites, in molecular sequenc Virtual PCR Topic concerning simulated polymerase chain reaction (PCR). - topic true - edam - topics PCR beta12orEarlier - bioinformatics - beta13 Polymerase chain reaction + beta13 + @@ -49322,13 +45850,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly - bioinformatics Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. beta12orEarlier This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - topic - edam - topics + Assembly + + + @@ -49338,15 +45866,15 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation - edam - Mutation and polymorphism DNA variation - bioinformatics - topics beta12orEarlier + Polymorphism + Mutation Topic concerning DNA sequence variation (mutation and polymorphism) data. - topic + + + @@ -49357,17 +45885,14 @@ positional features such as functional and other key sites, in molecular sequenc Microarrays beta12orEarlier - topics Topic concerning microarrays, for example, to process microarray data or design probes and experiments. 1.3 - topic BioCatalogue:Microarrays - bioinformatics DNA microarrays true - edam + @@ -49377,15 +45902,14 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacology - edam - events - beta12orEarlier - topic - bioinformatics Topic concerning the study of drugs and their effects or responses in living systems. Pharmacoinformatics - topics + beta12orEarlier Computational pharmacology + + + + @@ -49395,24 +45919,22 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression - Gene expression resources - Gene expression profiling Codon usage - Expression profiling - edam DNA microarrays Gene expression analysis - events - bioinformatics 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. http://edamontology.org/topic_0197 - topic - topics Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. beta12orEarlier + Expression profiling + Gene expression profiling BioCatalogue:Microarrays This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. + + + + @@ -49422,13 +45944,11 @@ positional features such as functional and other key sites, in molecular sequenc Gene regulation - Gene regulation resources - bioinformatics beta12orEarlier - topic - edam Topic concerning primarily the regulation of gene expression. - topics + + + @@ -49439,14 +45959,12 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacogenomics - topics Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. - edam beta12orEarlier - Pharmacogenetics - bioinformatics - events - topic + + + + @@ -49454,15 +45972,17 @@ positional features such as functional and other key sites, in molecular sequenc - Drug design + Medicinal chemistry - edam - bioinformatics + + Drug design beta12orEarlier - topic - Topic concerning the design of drugs or potential drug compounds. + Topic concerning 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. - topics + + + + @@ -49474,10 +45994,10 @@ positional features such as functional and other key sites, in molecular sequenc 1.3 true - topics Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. beta12orEarlier + @@ -49487,12 +46007,12 @@ positional features such as functional and other key sites, in molecular sequenc Flies - topics beta12orEarlier true 1.3 Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. + @@ -49504,11 +46024,11 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. 1.3 - topics beta12orEarlier true The resource may be specific to a group of mice / rats or all mice / rats. + @@ -49519,11 +46039,11 @@ positional features such as functional and other key sites, in molecular sequenc Worms beta12orEarlier - topics 1.3 true Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. + @@ -49534,14 +46054,11 @@ positional features such as functional and other key sites, in molecular sequenc Literature analysis true - topic - topics + The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. 1.3 beta12orEarlier - The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. - bioinformatics - edam + @@ -49553,18 +46070,17 @@ positional features such as functional and other key sites, in molecular sequenc BioCatalogue:Document Clustering BioCatalogue:Document Similarity - edam Text data mining - topic BioCatalogue:Text Mining beta12orEarlier Topic concerning the analysis of the biomedical and informatics literature. Literature mining - bioinformatics - events - Literature analysis - topics + Literature analysis BioCatalogue:Named Entity Recognition + + + + @@ -49573,19 +46089,19 @@ positional features such as functional and other key sites, in molecular sequenc Data curation and annotation - - edam - bioinformatics - events + Annotation Ontology annotation Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary. BioCatalogue:Ontology Annotation - topics BioCatalogue:Genome Annotation Genome annotation beta12orEarlier - topic + Curation + + + + @@ -49595,19 +46111,18 @@ positional features such as functional and other key sites, in molecular sequenc Data processing and validation - topic beta12orEarlier Data file handling Report processing Datatypes - topics Data types Report handling - bioinformatics This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - edam Topic concerning basic manipulations of files or reports of generic biological data. File handling + + + @@ -49617,15 +46132,12 @@ positional features such as functional and other key sites, in molecular sequenc Sequence annotation - edam Annotate a molecular sequence. - bioinformatics + true beta12orEarlier beta12orEarlier - topics - true - topic + @@ -49635,17 +46147,14 @@ positional features such as functional and other key sites, in molecular sequenc Genome annotation - topic - topics + BioCatalogue:Genome Annotation Annotate a genome. beta12orEarlier - beta12orEarlier - bioinformatics - BioCatalogue:Genome Annotation true - edam + beta12orEarlier + @@ -49653,17 +46162,17 @@ positional features such as functional and other key sites, in molecular sequenc - NMR - - edam - beta13 - topics + NMR spectroscopy + + + Topic concerning 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. + Spectroscopy + Nuclear magnetic resonance spectroscopy beta12orEarlier - Topic concerning raw NMR data. - bioinformatics - topic - true - + NMR + + + @@ -49674,13 +46183,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence classification Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. - topics Topic concerning the classification of molecular sequences based on some measure of their similarity. beta12orEarlier - topic - edam - bioinformatics - Sequence classification + + + @@ -49690,15 +46197,12 @@ positional features such as functional and other key sites, in molecular sequenc Protein classification - bioinformatics - true - 1.3 - topics beta12orEarlier - topic - edam Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. + true + 1.3 + @@ -49710,15 +46214,12 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. beta12orEarlier - edam This includes comparison, discovery, recognition etc. of sequence motifs. true - topics - bioinformatics - topic beta12orEarlier + @@ -49728,16 +46229,15 @@ positional features such as functional and other key sites, in molecular sequenc Protein modifications - bioinformatics beta12orEarlier MOD:00000 - topic - edam 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) - topics Protein post-translational modification Topic concerning protein chemical modifications, e.g. post-translational modifications. GO:0006464 + + + @@ -49748,20 +46248,19 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks BioCatalogue:Pathways - edam http://edamontology.org/topic_3076 Topic concerning molecular interactions, biological pathways, networks and other models. Biological pathways Biological models Molecular interactions - events beta13 - bioinformatics Network or pathway analysis Biological networks BioCatalogue:Pathway Retrieval - topic - topics + + + + @@ -49771,15 +46270,12 @@ positional features such as functional and other key sites, in molecular sequenc Informatics - bioinformatics - topic - A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. - true - topics beta12orEarlier beta12orEarlier - edam + A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. + true + @@ -49789,15 +46285,12 @@ positional features such as functional and other key sites, in molecular sequenc Literature data resources - topics - true 1.3 beta12orEarlier - topic - edam + true Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. - bioinformatics + @@ -49807,15 +46300,14 @@ positional features such as functional and other key sites, in molecular sequenc Laboratory information management - edam - bioinformatics - events Laboratory resources - topic beta12orEarlier Topic concerning 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. - topics + + + + @@ -49827,15 +46319,12 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Cell culture - topics - edam - bioinformatics Topic concerning general cell culture or data on a specific cell lines. - 1.3 true - topic + 1.3 Tissue culture + @@ -49847,16 +46336,15 @@ positional features such as functional and other key sites, in molecular sequenc Environmental science Ecoinformatics - edam Computational ecology beta12orEarlier - bioinformatics - topic Ecological informatics Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). - topics - events + + + + @@ -49865,16 +46353,13 @@ positional features such as functional and other key sites, in molecular sequenc Electron microscopy - - edam - true + + + Topic concerning the use of electrons to analyse structures at resolutions higher than can be achieved using light. beta12orEarlier - topics - Topic concerning electron microscopy data. - bioinformatics - beta13 - topic - + + + @@ -49884,15 +46369,12 @@ positional features such as functional and other key sites, in molecular sequenc Cell cycle - topic - Topic concerning the cell cycle including key genes and proteins. true beta12orEarlier - topics - edam + Topic concerning the cell cycle including key genes and proteins. beta13 - bioinformatics + @@ -49902,12 +46384,13 @@ positional features such as functional and other key sites, in molecular sequenc Peptides and amino acids - bioinformatics - topics - edam + Peptides + Amino acids Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. - topic beta12orEarlier + + + @@ -49918,25 +46401,22 @@ positional features such as functional and other key sites, in molecular sequenc Organelles 1.3 - bioinformatics Rough endoplasmic reticulum Golgi apparatus Mitochondria true Nucleus Ribosome - Centriole Lysosome + Centriole beta12orEarlier - topics - edam - topic Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). Smooth endoplasmic reticulum Cell membrane - Organelle genes and proteins Cytoplasm + Organelle genes and proteins + @@ -49948,11 +46428,11 @@ positional features such as functional and other key sites, in molecular sequenc true 1.3 - topics Topic concerning ribosomes, typically of ribosome-related genes and proteins. Ribosome genes and proteins beta12orEarlier + @@ -49964,13 +46444,10 @@ positional features such as functional and other key sites, in molecular sequenc true beta13 - edam beta12orEarlier - topic A database about scents. - topics - bioinformatics + @@ -49978,16 +46455,17 @@ positional features such as functional and other key sites, in molecular sequenc - Drugs and targets + Drugs and target structures - topic - edam - Drug and target structures - topics + Target structures beta12orEarlier Topic concerning the structures of drugs, drug target, their interactions and binding affinities. - bioinformatics + Drug structures + + + + @@ -49997,15 +46475,14 @@ positional features such as functional and other key sites, in molecular sequenc Organisms - topic - topics Model organisms - events + Topic concerning 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. beta12orEarlier - edam - bioinformatics - Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. + + + + @@ -50014,16 +46491,15 @@ positional features such as functional and other key sites, in molecular sequenc Genomics - - events + beta12orEarlier Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. - bioinformatics - topic - topics BioCatalogue:Genomics - edam + + + + @@ -50034,17 +46510,16 @@ positional features such as functional and other key sites, in molecular sequenc Gene families - bioinformatics Genes, gene family or system - events Gene and protein families - topics - edam Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. - Genes and proteins resources + Gene system Gene family - topic beta12orEarlier + + + + @@ -50054,12 +46529,11 @@ positional features such as functional and other key sites, in molecular sequenc Chromosomes - edam Topic concerning chromosomes. beta12orEarlier - bioinformatics - topics - topic + + + @@ -50069,15 +46543,14 @@ positional features such as functional and other key sites, in molecular sequenc Genotype and phenotype - topics - edam + beta12orEarlier Genotyping Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotype and phenotype resources - topic - bioinformatics - beta12orEarlier - events + + + + @@ -50087,16 +46560,13 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression and microarray - topic beta12orEarlier - bioinformatics - edam + true beta12orEarlier - topics Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. - true + @@ -50106,20 +46576,19 @@ positional features such as functional and other key sites, in molecular sequenc Sequence design - edam beta12orEarlier - Probe design Primers - topics + Primer design in silico cloning Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). - topic + Probe design Gene design - bioinformatics This includes the design of primers for PCR and DNA amplification or the design of molecular probes. - Primer design Probes + + + @@ -50129,15 +46598,13 @@ positional features such as functional and other key sites, in molecular sequenc Pathology + Diseases beta12orEarlier - events - edam Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. - Diseases - topics - bioinformatics - topic - Disease + + + + @@ -50147,16 +46614,13 @@ positional features such as functional and other key sites, in molecular sequenc Specific protein resources - topic + beta12orEarlier Specific protein true - edam 1.3 - bioinformatics - beta12orEarlier - topics Topic concerning a particular protein, protein family or other group of proteins. + @@ -50169,9 +46633,9 @@ positional features such as functional and other key sites, in molecular sequenc 1.3 true Topic concerning organism classification, identification and naming. - topics beta12orEarlier + @@ -50182,13 +46646,12 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence analysis Protein sequences - topic - topics Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. BioCatalogue:Protein Sequence Analysis - edam beta12orEarlier - bioinformatics + + + @@ -50199,12 +46662,11 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence analysis Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. - topic - topics - edam - bioinformatics BioCatalogue:Nucleotide Sequence Analysis beta12orEarlier + + + @@ -50215,11 +46677,11 @@ positional features such as functional and other key sites, in molecular sequenc Repeat sequences 1.3 - topics Topic concerning the repetitive nature of molecular sequences. beta12orEarlier true + @@ -50229,12 +46691,12 @@ positional features such as functional and other key sites, in molecular sequenc Low complexity sequences - topics beta12orEarlier 1.3 Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. true + @@ -50245,14 +46707,11 @@ positional features such as functional and other key sites, in molecular sequenc Proteome true - Topic concerning a specific proteome including protein sequences and annotation. - edam - bioinformatics beta13 - topics beta12orEarlier - topic + Topic concerning a specific proteome including protein sequences and annotation. + @@ -50262,14 +46721,13 @@ positional features such as functional and other key sites, in molecular sequenc DNA - topic The DNA sequences might be coding or non-coding sequences. - bioinformatics Topic concerning DNA sequences and structure, including processes such as methylation and replication. - topics - edam beta12orEarlier DNA analysis + + + @@ -50280,12 +46738,13 @@ positional features such as functional and other key sites, in molecular sequenc Coding RNA beta12orEarlier - topic - edam - bioinformatics - mRNA, EST or cDNA - topics + mRNA + cDNA Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + EST + + + @@ -50295,16 +46754,15 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA - bioinformatics - topic beta12orEarlier - edam - Non-coding RNA - Functional RNA Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). - topics 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). Regulatory RNA + Functional RNA + Non-coding RNA + + + @@ -50314,11 +46772,11 @@ positional features such as functional and other key sites, in molecular sequenc rRNA - topics Topic concerning one or more ribosomal RNA (rRNA) sequences. true 1.3 + @@ -50331,8 +46789,8 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning one or more transfer RNA (tRNA) sequences. 1.3 true - topics + @@ -50345,12 +46803,11 @@ positional features such as functional and other key sites, in molecular sequenc This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. BioCatalogue:Protein Secondary Structure Topic concerning protein secondary structure or secondary structure alignments. + Protein secondary structure analysis beta12orEarlier - topics - Protein secondary structure analysis - bioinformatics - topic - edam + + + @@ -50363,9 +46820,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier true Topic concerning RNA secondary or tertiary structure and alignments. - topics 1.3 + @@ -50375,14 +46832,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure - topics beta12orEarlier Protein tertiary structure analysis Topic concerning protein tertiary structures. - edam - topic - bioinformatics BioCatalogue:Protein Tertiary Structure + + + @@ -50393,14 +46849,11 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid classification beta12orEarlier - bioinformatics - topics Topic concerning classification of nucleic acid sequences and structures. - topic true 1.3 - edam + @@ -50412,15 +46865,14 @@ positional features such as functional and other key sites, in molecular sequenc A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. + Protein secondary databases + Protein sequence classification beta12orEarlier - events - topics - Protein sequence classification - Protein secondary - topic - edam - bioinformatics Topic concerning 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. + + + + @@ -50429,14 +46881,15 @@ positional features such as functional and other key sites, in molecular sequenc Protein domains and folds - - topic + BioCatalogue:Domains - topics - edam - bioinformatics + Protein domains + Protein folds Topic concerning protein tertiary structural domains and folds. beta12orEarlier + + + @@ -50446,15 +46899,12 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence alignment - bioinformatics - true - beta12orEarlier - topic 1.3 Topic concerning nucleotide sequence alignments. - edam - topics + true + beta12orEarlier + @@ -50464,16 +46914,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence alignment - Topic concerning protein sequence alignments. - edam - 1.3 - topics - topic A sequence profile typically represents a sequence alignment. + Topic concerning protein sequence alignments. true - bioinformatics beta12orEarlier + 1.3 + @@ -50483,7 +46930,6 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sites and features - topics Topic concerning the archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences. true @@ -50491,6 +46937,7 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier + @@ -50503,10 +46950,10 @@ positional features such as functional sites in nucleotide sequences.true Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. 1.3 - topics beta12orEarlier + @@ -50517,17 +46964,16 @@ positional features such as functional sites in nucleotide sequences.Transcription factors and regulatory sites + Transcription factor binding sites beta12orEarlier - Transcriptional regulatory sites + Transcription factors + Transcriptional regulatory sites Topic concerning 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. - bioinformatics - Transcription factor and binding site - Transcription factors BioCatalogue:Transcription Factors - edam 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. - topic - topics + + + @@ -50539,14 +46985,11 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. - edam - topic - topics - bioinformatics true 1.0 + @@ -50556,12 +46999,11 @@ positional features such as functional sites in nucleotide sequences. Metabolic pathways - topic Topic concerning metabolic pathways. - edam - bioinformatics beta12orEarlier - topics + + + @@ -50571,12 +47013,11 @@ positional features such as functional sites in nucleotide sequences. Signaling pathways - topic beta12orEarlier - topics Topic concerning signaling pathways. - edam - bioinformatics + + + @@ -50590,6 +47031,7 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier 1.3 + @@ -50599,14 +47041,11 @@ positional features such as functional sites in nucleotide sequences. Workflows - topics 1.0 - bioinformatics beta12orEarlier true Topic concerning biological or biomedical analytical workflows or pipelines. - topic - edam + @@ -50617,14 +47056,11 @@ positional features such as functional sites in nucleotide sequences.Data types and objects true - beta12orEarlier - edam - topics 1.0 - topic - bioinformatics + beta12orEarlier Topic concerning structuring data into basic types and (computational) objects. + @@ -50637,6 +47073,7 @@ positional features such as functional sites in nucleotide sequences.true 1.3 + @@ -50647,11 +47084,11 @@ positional features such as functional sites in nucleotide sequences.Mitochondria 1.3 - topics Topic concerning mitochondria, typically of mitochondrial genes and proteins. true beta12orEarlier + @@ -50664,13 +47101,12 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Plant - bioinformatics - topics Botany Plant biology - topic - edam The resource may be specific to a plant, a group of plants or all plants. + + + @@ -50681,14 +47117,12 @@ positional features such as functional sites in nucleotide sequences.Viruses The resource may be specific to a virus, a group of viruses or all viruses. - topics - topic - bioinformatics beta12orEarlier - Virus Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. - edam Virology + + + @@ -50698,14 +47132,13 @@ positional features such as functional sites in nucleotide sequences. Fungi - topics The resource may be specific to a fungus, a group of fungi or all fungi. - bioinformatics Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. - edam - topic beta12orEarlier Mycology + + + @@ -50716,13 +47149,11 @@ positional features such as functional sites in nucleotide sequences.Pathogens Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - edam - bioinformatics The resource may be specific to a pathogen, a group of pathogens or all pathogens. beta12orEarlier - topics - topic - Pathogen + + + @@ -50732,15 +47163,12 @@ positional features such as functional sites in nucleotide sequences. Arabidopsis - beta12orEarlier - Topic concerning Arabidopsis-specific data. - topics - topic 1.3 true - bioinformatics - edam + beta12orEarlier + Topic concerning Arabidopsis-specific data. + @@ -50752,10 +47180,10 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Topic concerning rice-specific data. - topics 1.3 true + @@ -50766,16 +47194,13 @@ positional features such as functional sites in nucleotide sequences.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. - topics Genetic linkage - topic - bioinformatics true - edam 1.3 beta12orEarlier Linkage mapping + @@ -50786,13 +47211,12 @@ positional features such as functional sites in nucleotide sequences.Comparative genomics BioCatalogue:Comparative Genomics - bioinformatics - topic - edam beta12orEarlier - events - topics Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. + + + + @@ -50802,12 +47226,11 @@ positional features such as functional sites in nucleotide sequences. Mobile genetic elements - edam - bioinformatics Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. beta12orEarlier - topic - topics + + + @@ -50818,14 +47241,11 @@ positional features such as functional sites in nucleotide sequences.Human disease Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. - edam beta12orEarlier - topics true beta13 - bioinformatics - topic + @@ -50835,17 +47255,16 @@ positional features such as functional sites in nucleotide sequences. Immunology - edam - Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. - topics - bioinformatics Computational immunology beta12orEarlier - events Immunoinformatics - topic + Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + + + + @@ -50856,12 +47275,13 @@ positional features such as functional sites in nucleotide sequences.Membrane and lipoproteins Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. - topics - bioinformatics - Transmembrane proteins - topic + Lipoproteins + Transmembrane proteins beta12orEarlier - edam + Membrane proteins + + + @@ -50871,14 +47291,12 @@ positional features such as functional sites in nucleotide sequences. Enzymes - topics - Enzymes and reactions - bioinformatics Enzymology - edam beta12orEarlier Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. - topic + + + @@ -50889,17 +47307,16 @@ positional features such as functional sites in nucleotide sequences.Structural biology Structural determination - A topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. - events 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. 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. - topics 1.3 Structure determination Structural assignment - topic - bioinformatics - edam + Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + + + + @@ -50910,13 +47327,12 @@ positional features such as functional sites in nucleotide sequences.Structure comparison beta12orEarlier - events - bioinformatics Topic concerning the comparison of two or more molecular structures. - topics This might involve comparison of secondary or tertiary (3D) structural information. - edam - topic + + + + @@ -50926,16 +47342,15 @@ positional features such as functional sites in nucleotide sequences. Function analysis - edam - topics - topic - events + Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. beta12orEarlier - bioinformatics Protein function analysis - Topic for the study of gene and protein function including the prediction of functional properties of a protein. BioCatalogue:Function Prediction Protein function prediction + + + + @@ -50945,14 +47360,12 @@ positional features such as functional sites in nucleotide sequences. Prokaryotes and archae - Prokaryote and archae Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. beta12orEarlier - topic - topics - bioinformatics - edam The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. + + + @@ -50962,16 +47375,13 @@ positional features such as functional sites in nucleotide sequences. Protein databases - topics - topic - true - beta12orEarlier - Topic concerning protein data resources. Protein data resources - bioinformatics - edam + Topic concerning protein data resources. + beta12orEarlier 1.3 + true + @@ -50983,10 +47393,10 @@ positional features such as functional sites in nucleotide sequences. 1.3 true - topics Topic concerning 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. beta12orEarlier + @@ -50997,11 +47407,10 @@ positional features such as functional sites in nucleotide sequences.Cell biology Topic concerning cells, such as key genes and proteins involved in the cell cycle. - bioinformatics - edam - topic - topics beta12orEarlier + + + @@ -51011,15 +47420,12 @@ positional features such as functional sites in nucleotide sequences. Classification - edam - beta12orEarlier - topics true Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. - bioinformatics - topic + beta12orEarlier beta13 + @@ -51029,13 +47435,12 @@ positional features such as functional sites in nucleotide sequences. Lipoproteins - topics beta12orEarlier Topic concerning lipoproteins (protein-lipid assemblies). - bioinformatics 1.3 true + @@ -51045,16 +47450,13 @@ positional features such as functional sites in nucleotide sequences. Phylogeny visualisation - bioinformatics - edam - topics - true beta12orEarlier - topic beta12orEarlier - Visualise a phylogeny, for example, render a phylogenetic tree. BioCatalogue:Tree Display + Visualise a phylogeny, for example, render a phylogenetic tree. + true + @@ -51065,16 +47467,15 @@ positional features such as functional sites in nucleotide sequences.Cheminformatics - edam - bioinformatics Chemical informatics BioCatalogue:Chemoinformatics - events - topic Chemoinformatics - Topic for the application of information technology to chemistry in biological research environment. - topics beta12orEarlier + Topic concerning the application of information technology to chemistry in biological research environment. + + + + @@ -51086,21 +47487,20 @@ positional features such as functional sites in nucleotide sequences. Biological modelling Biological system modelling - events beta12orEarlier BioCatalogue:Systems Biology BioCatalogue:Model Analysis - edam - bioinformatics - topic Biological models Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. BioCatalogue:Model Creation - topics BioCatalogue:Model Execution This includes databases of models and methods to construct or analyse a model. + + + + @@ -51110,19 +47510,16 @@ positional features such as functional sites in nucleotide sequences. Statistics - events - Topic for the application of statistical methods to biological problems. + Topic concerning the application of statistical methods to biological problems. beta12orEarlier BioCatalogue:Biostatistics - Biometry - bioinformatics - topics - topic - Biometrics - edam Biostatistics + + + + @@ -51132,16 +47529,13 @@ positional features such as functional sites in nucleotide sequences. 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). - edam - topic - beta12orEarlier true beta12orEarlier - bioinformatics - topics + Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). + beta12orEarlier The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. + @@ -51151,12 +47545,16 @@ positional features such as functional sites in nucleotide sequences. Molecular modelling - edam - Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + Comparative modeling + Molecular modeling + Homology modelling beta12orEarlier - topics - bioinformatics - topic + Comparative modelling + Homology modeling + + + @@ -51166,16 +47564,13 @@ positional features such as functional sites in nucleotide sequences. Protein function prediction - bioinformatics Topic concerning the prediction of functional properties of a protein. - topic + true BioCatalogue:Function Prediction beta12orEarlier 1.2 - topics - true - edam + @@ -51187,11 +47582,10 @@ positional features such as functional sites in nucleotide sequences. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. - edam - bioinformatics beta12orEarlier - topics - topic + + + @@ -51201,16 +47595,13 @@ positional features such as functional sites in nucleotide sequences. Transmembrane protein prediction - topics + true beta12orEarlier beta12orEarlier Predict transmembrane domains and topology in protein sequences. - topic - bioinformatics - true - edam + @@ -51220,17 +47611,14 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure comparison - beta12orEarlier - beta12orEarlier - topic Use this concept for methods that are exclusively for nucleic acid structures. - topics + beta12orEarlier Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. true - edam - bioinformatics + beta12orEarlier + @@ -51240,16 +47628,14 @@ positional features such as functional sites in nucleotide sequences. Oncology - Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer. - beta12orEarlier - topic - bioinformatics Cancer biology - Cancer - topics - edam - events - Cancer resources + Cancer + beta12orEarlier + Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. + + + + @@ -51260,12 +47646,14 @@ positional features such as functional sites in nucleotide sequences.Toxins and targets + Toxins beta12orEarlier - topic + Targets Topic concerning structural and associated data for toxic chemical substances. - topics - bioinformatics - edam + + + + @@ -51275,15 +47663,12 @@ positional features such as functional sites in nucleotide sequences. Tool topic - edam - bioinformatics - A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. - topics beta12orEarlier - topic true + A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. beta12orEarlier + @@ -51293,15 +47678,12 @@ positional features such as functional sites in nucleotide sequences. Study topic - bioinformatics - topic - topics - beta12orEarlier - A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. beta12orEarlier - edam true + beta12orEarlier + A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + @@ -51311,12 +47693,12 @@ positional features such as functional sites in nucleotide sequences. Nomenclature - topics beta12orEarlier 1.3 Topic concerning biological nomenclature (naming), symbols and terminology. true + @@ -51326,15 +47708,12 @@ positional features such as functional sites in nucleotide sequences. Disease genes and proteins + beta12orEarlier Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. - topic true - topics 1.3 - edam - beta12orEarlier - bioinformatics + @@ -51345,14 +47724,13 @@ positional features such as functional sites in nucleotide sequences.Protein structure analysis Topic concerning protein secondary or tertiary structural data and/or associated annotation. - edam - events beta12orEarlier http://edamontology.org/topic_3040 - topics Protein structure - bioinformatics - topic + + + + @@ -51365,9 +47743,9 @@ positional features such as functional sites in nucleotide sequences.1.3 Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. true - topics beta12orEarlier + @@ -51377,17 +47755,14 @@ positional features such as functional sites in nucleotide sequences. Gene resources - Gene database true + Gene database Informatics resource (typically a database) primarily focussed on genes. 1.3 - edam - bioinformatics - topic beta12orEarlier - topics Gene resource + @@ -51398,11 +47773,11 @@ positional features such as functional sites in nucleotide sequences.Yeast 1.3 - topics true beta12orEarlier Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. + @@ -51413,13 +47788,12 @@ positional features such as functional sites in nucleotide sequences.Eukaryotes beta12orEarlier - edam The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. - topic Eukaryote - topics - bioinformatics + + + @@ -51430,12 +47804,11 @@ positional features such as functional sites in nucleotide sequences.Invertebrates Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. - topics - bioinformatics beta12orEarlier The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. - edam - topic + + + @@ -51447,12 +47820,10 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - topics - topic - bioinformatics - edam The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. - Vertebrate + + + @@ -51462,14 +47833,12 @@ positional features such as functional sites in nucleotide sequences. Unicellular eukaryotes - bioinformatics Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. - Unicellular eukaryote - topics The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. beta12orEarlier - topic - edam + + + @@ -51480,11 +47849,11 @@ positional features such as functional sites in nucleotide sequences.Protein structure alignment 1.3 - topics true beta12orEarlier Topic concerning protein secondary or tertiary structure alignments. + @@ -51493,16 +47862,14 @@ positional features such as functional sites in nucleotide sequences. X-ray crystallography - - bioinformatics - topics - Topic concerning X-ray crystallography data. - beta13 - edam + + + Crystallography beta12orEarlier - topic - true - + Topic concerning the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials. + + + @@ -51512,16 +47879,13 @@ positional features such as functional sites in nucleotide sequences. Ontologies, nomenclature and classification - topic - beta12orEarlier Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. - topics + beta12orEarlier 1.3 - edam - bioinformatics true + @@ -51532,14 +47896,17 @@ positional features such as functional sites in nucleotide sequences.Immunoproteins, genes and antigens - edam - topics + Immunogenes + Immunoproteins beta12orEarlier - bioinformatics This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." - Immunoproteins and immunopeptides - topic + Antigens + Immunopeptides Topic concerning immunity-related genes, proteins and their ligands. + + + + @@ -51549,16 +47916,13 @@ positional features such as functional sites in nucleotide sequences. Molecules - edam true beta12orEarlier - Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. beta12orEarlier - topics - bioinformatics - topic + Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. CHEBI:23367 + @@ -51568,16 +47932,16 @@ positional features such as functional sites in nucleotide sequences. Toxicology + Computational toxicology beta12orEarlier - topics Toxicology - topic Toxicoinformatics - events - edam - bioinformatics Topic concerning toxins and the adverse effects of these chemical substances on living organisms. + + + + @@ -51588,15 +47952,12 @@ positional features such as functional sites in nucleotide sequences.High-throughput sequencing beta12orEarlier - topics - beta13 - edam - bioinformatics Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. true - topic + beta13 Next-generation sequencing + @@ -51607,12 +47968,11 @@ positional features such as functional sites in nucleotide sequences.Structural clustering beta12orEarlier - topics - topic - bioinformatics Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. Structure classification - edam + + + @@ -51623,12 +47983,11 @@ positional features such as functional sites in nucleotide sequences.Gene regulatory networks - topic beta12orEarlier - topics - edam - bioinformatics Topic concerning gene regulatory networks. + + + @@ -51638,15 +47997,12 @@ positional features such as functional sites in nucleotide sequences. Disease (specific) - topic - edam - bioinformatics beta12orEarlier - topics - beta12orEarlier true Informatics resources dedicated to one or more specific diseases (not diseases in general). + beta12orEarlier + @@ -51656,15 +48012,12 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid design - bioinformatics - edam - beta12orEarlier - topics - topic true + beta12orEarlier 1.3 Topic for the design of nucleic acid sequences with specific conformations. + @@ -51674,15 +48027,12 @@ positional features such as functional sites in nucleotide sequences. Primer or probe design - true - topics - topic - 1.3 beta13 - bioinformatics + true Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. - edam + 1.3 + @@ -51692,16 +48042,13 @@ positional features such as functional sites in nucleotide sequences. Structure databases - edam - topic - Structure data resources Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. - bioinformatics - true + Structure data resources 1.2 - topics + true beta13 + @@ -51712,14 +48059,11 @@ positional features such as functional sites in nucleotide sequences.Nucleic acid structure 1.2 - topics - bioinformatics Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. - topic - edam beta13 true + @@ -51730,17 +48074,14 @@ positional features such as functional sites in nucleotide sequences.Sequence databases 1.3 - edam - bioinformatics Sequence data resources - topics beta13 Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. Sequence data resource Sequence data - topic true + @@ -51750,16 +48091,13 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sequences - topic - topics - bioinformatics Nucleotide sequences true Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. 1.3 - edam beta13 + @@ -51769,15 +48107,12 @@ positional features such as functional sites in nucleotide sequences. Protein sequences - 1.3 - topic - topics - Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. true - edam + 1.3 beta13 - bioinformatics + Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + @@ -51788,9 +48123,9 @@ positional features such as functional sites in nucleotide sequences.Protein interaction networks true - topics 1.3 + @@ -51800,13 +48135,12 @@ positional features such as functional sites in nucleotide sequences. Molecular biology - topic - bioinformatics - topics Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. - edam beta13 - events + + + + @@ -51816,12 +48150,12 @@ positional features such as functional sites in nucleotide sequences. Mammals - topics Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. 1.3 beta13 true + @@ -51831,16 +48165,13 @@ positional features such as functional sites in nucleotide sequences. Biodiversity - topics - Biodiversity data resources - events Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. - Biodiversity data resource - topic - bioinformatics beta13 - edam + + + + @@ -51852,16 +48183,13 @@ positional features such as functional sites in nucleotide sequences. beta13 Sequence clusters - topic 1.3 Sequence families Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. - edam - topics true - bioinformatics This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + @@ -51872,16 +48200,15 @@ positional features such as functional sites in nucleotide sequences.Genetics Gene resource - bioinformatics beta13 - edam Genetics data resources - topic Gene database Topic concerning the study of genes, genetic variation and heredity in living organisms. - events - topics + + + + @@ -51891,12 +48218,11 @@ positional features such as functional sites in nucleotide sequences. Quantitative genetics - topics Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). - edam - bioinformatics - topic beta13 + + + @@ -51906,13 +48232,12 @@ positional features such as functional sites in nucleotide sequences. Population genetics - topics - topic beta13 Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. - edam - events - bioinformatics + + + + @@ -51923,10 +48248,11 @@ positional features such as functional sites in nucleotide sequences.Regulatory RNA beta13 + true 1.3 Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). - topics + @@ -51936,13 +48262,14 @@ positional features such as functional sites in nucleotide sequences. Documentation and help - bioinformatics + Documentation beta13 - events - topics - topic - edam + Help Topic concerning the documentation of resources such as tools, services and databases and how to get help. + + + + @@ -51952,15 +48279,12 @@ positional features such as functional sites in nucleotide sequences. Genetic organisation - topics - edam - beta13 - topic true - bioinformatics + beta13 Topic concerning the structural and functional organisation of genes and other genetic elements. 1.3 + @@ -51974,18 +48298,16 @@ positional features such as functional sites in nucleotide sequences.Molecular medicine Health and disease beta13 - Topic for the application of information technology to health, disease and biomedicine. Healthcare informatics Translational medicine Biomedical informatics - edam Clinical informatics Health informatics - events - bioinformatics - topic - topics - Medicine + Topic concerning the application of information technology to health, disease and biomedicine. + + + + @@ -51996,12 +48318,11 @@ positional features such as functional sites in nucleotide sequences.Developmental biology beta13 - bioinformatics - topic - events - edam Topic concerning how organisms grow and develop. - topics + + + + @@ -52011,13 +48332,12 @@ positional features such as functional sites in nucleotide sequences. Embryology - topic - events Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. - topics beta13 - edam - bioinformatics + + + + @@ -52028,12 +48348,11 @@ positional features such as functional sites in nucleotide sequences.Anatomy Topic concerning the form and function of the structures of living organisms. - topics - topic beta13 - bioinformatics - edam - events + + + + @@ -52043,18 +48362,15 @@ positional features such as functional sites in nucleotide sequences. Literature and reference - events Literature sources Literature search - BioCatalogue: Document Discovery - bioinformatics - edam - topics Topic concerning the scientific literature, reference information and documentation. - BioCatalogue: Literature retrieval - topic beta13 + + + + @@ -52064,14 +48380,13 @@ positional features such as functional sites in nucleotide sequences. Biology - topics - bioinformatics - topic - events - edam Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. beta13 Biological science + + + + @@ -52079,19 +48394,19 @@ positional features such as functional sites in nucleotide sequences. - Biological databases and data management - - bioinformatics - topics - topic - A topic concerning the general handling of bioinformatics data stored in digital archives such as databanks, databases proper, web portals and other data resources. - Biological data management - Biological data handling + Data management + + Knowledge management + Databases + Data handling beta13 - Biological databases - edam - events + Databases + Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. + + + + @@ -52101,16 +48416,13 @@ positional features such as functional sites in nucleotide sequences. Sequence feature detection - true - topics - edam beta13 + true Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. - topic - bioinformatics 1.3 + @@ -52121,14 +48433,11 @@ positional features such as functional sites in nucleotide sequences.Nucleic acid feature detection 1.3 - topic - Topic concerning the detection of positional features such as functional sites in nucleotide sequences. - bioinformatics - topics - edam beta13 + Topic concerning the detection of positional features such as functional sites in nucleotide sequences. true + @@ -52139,14 +48448,11 @@ positional features such as functional sites in nucleotide sequences.Protein feature detection true - beta13 - topic - edam - bioinformatics - topics 1.3 Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. + beta13 + @@ -52156,17 +48462,14 @@ positional features such as functional sites in nucleotide sequences. Biological system modelling + Topic for modelling biological systems in mathematical terms. beta13 true - bioinformatics BioCatalogue:Model Execution - topic - edam - Topic for modelling biological systems in mathematical terms. - topics 1.2 BioCatalogue:Model Analysis + @@ -52177,12 +48480,14 @@ positional features such as functional sites in nucleotide sequences.Data acquisition and deposition Topic concerning the acquisition and deposition of biological data. - edam + Data deposition + Data acquisition Database submission beta13 - bioinformatics - topics - topic + Deposition + + + @@ -52192,17 +48497,14 @@ positional features such as functional sites in nucleotide sequences. Genes and proteins resources - topic - bioinformatics + true + Gene and protein families beta13 Gene family - 1.3 Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. - true - topics - Gene and protein families - edam + 1.3 + @@ -52211,15 +48513,16 @@ positional features such as functional sites in nucleotide sequences. Sequencing - - topics - events - bioinformatics + + Next generation sequencing 1.1 - topic Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. - edam + Next gen sequencing + + + + @@ -52234,13 +48537,10 @@ positional features such as functional sites in nucleotide sequences.Chip seq 1.3 Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. - bioinformatics - topics - edam Chip sequencing true - topic + @@ -52253,18 +48553,15 @@ positional features such as functional sites in nucleotide sequences.true This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. WTSS - topics Small RNA-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. 1.3 - edam - bioinformatics 1.1 - topic Whole transcriptome shotgun sequencing RNA-seq Small RNA-seq + @@ -52274,16 +48571,13 @@ positional features such as functional sites in nucleotide sequences. DNA methylation - bioinformatics - topic - topics - edam + 1.1 1.3 true - 1.1 Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + @@ -52292,15 +48586,14 @@ positional features such as functional sites in nucleotide sequences. Metabolomics - - bioinformatics + 1.1 - topic - edam - events Topic concerning 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. - topics + + + + @@ -52311,16 +48604,14 @@ positional features such as functional sites in nucleotide sequences.Epigenomics - bioinformatics - events + Topic concerning 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. - topic - Epigenetics - A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. - topics - edam 1.1 + + + + @@ -52331,17 +48622,16 @@ positional features such as functional sites in nucleotide sequences.Metagenomics - events 1.1 Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. - edam - bioinformatics - topic - Environmental genomics - Ecogenomics - topics - Community genomics + Environmental genomics + Community genomics + Ecogenomics + + + + @@ -52352,12 +48642,11 @@ positional features such as functional sites in nucleotide sequences.Structural variation Genomic structural variation - edam - bioinformatics Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. 1.1 - topic - topics + + + @@ -52367,13 +48656,12 @@ positional features such as functional sites in nucleotide sequences. DNA packaging - topic Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. - topics - edam beta12orEarlier - bioinformatics + + + @@ -52383,16 +48671,13 @@ positional features such as functional sites in nucleotide sequences. DNA-Seq - edam - 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. - bioinformatics true - topics - 1.3 DNA-seq + 1.3 + 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. 1.1 - topic + @@ -52402,16 +48687,13 @@ positional features such as functional sites in nucleotide sequences. RNA-Seq alignment - topics - topic beta12orEarlier - bioinformatics RNA-seq alignment - Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. 1.3 + Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. true - edam + @@ -52422,15 +48704,12 @@ positional features such as functional sites in nucleotide sequences.ChIP-on-chip ChIP-chip - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. - topic - topics - bioinformatics - true 1.1 - edam + Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. 1.3 + true + @@ -52440,15 +48719,14 @@ positional features such as functional sites in nucleotide sequences. Data security - topics Security - bioinformatics - 1.3 - Topic concerning the protection of data, for example, patient health data. Security - topic - edam + 1.3 Privacy + Topic concerning the protection of data, for example, patient health data. + + + @@ -52459,16 +48737,15 @@ positional features such as functional sites in nucleotide sequences.Sample collections Specimen collections - edam biosamples 1.3 - bioinformatics Topic concerning biological samples and specimens. - events biobanking - topics - topic samples + + + + @@ -52479,15 +48756,14 @@ positional features such as functional sites in nucleotide sequences.Biochemistry - events - topic - edam + Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry - bioinformatics - topics - A topic concerning chemical substances and physico-chemical processes and that occur within living organisms. 1.3 Chemical biology + + + + @@ -52498,13 +48774,12 @@ positional features such as functional sites in nucleotide sequences.Phylogenetics - bioinformatics - edam 1.3 Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). - topics - topic + + + @@ -52515,16 +48790,15 @@ positional features such as functional sites in nucleotide sequences.Epigenetics 1.3 - A topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. Histone modification - bioinformatics DNA methylation - topics - edam This includes sub-topics such as histone modification and DNA methylation. - events - topic + Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. + + + + @@ -52534,13 +48808,12 @@ positional features such as functional sites in nucleotide sequences. Biotechnology - topics 1.3 - edam - topic - events - Topic concerning the exploitation of biological processes for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. - bioinformatics + Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. + + + + @@ -52551,13 +48824,12 @@ positional features such as functional sites in nucleotide sequences.Phenomics - edam - events 1.3 - topic - topics Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. - bioinformatics + + + + @@ -52567,13 +48839,12 @@ positional features such as functional sites in nucleotide sequences. Evolutionary biology - topics - events 1.3 - edam - bioinformatics - topic Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. + + + + @@ -52583,13 +48854,12 @@ positional features such as functional sites in nucleotide sequences. Physiology - edam - bioinformatics Topic concerning the functions of living organisms and their constituent parts. 1.3 - topics - topic - events + + + + @@ -52599,13 +48869,12 @@ positional features such as functional sites in nucleotide sequences. Microbiology - topics - events 1.3 - topic Topic concerning the biology of microorganisms. - bioinformatics - edam + + + + @@ -52615,14 +48884,13 @@ positional features such as functional sites in nucleotide sequences. Parasitology - topic 1.3 - events - bioinformatics Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - topics - edam Topic concerning the biology of parasites. + + + + @@ -52633,15 +48901,13 @@ positional features such as functional sites in nucleotide sequences.Medicine Biomedical research + 1.3 Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. Experimental medicine - edam - 1.3 - bioinformatics - topics - events - Molecular medicine - topic + + + + @@ -52651,14 +48917,13 @@ positional features such as functional sites in nucleotide sequences. Neurobiology - topics - bioinformatics Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. 1.3 - events Neuroscience - topic - edam + + + + @@ -52666,15 +48931,16 @@ positional features such as functional sites in nucleotide sequences. - Epidemiology + Public health and epidemiology - events - bioinformatics + Epidemiology + Public health 1.3 - edam - topics Topic concerning the the patterns, cause, and effect of disease within populations. - topic + + + + @@ -52685,13 +48951,12 @@ positional features such as functional sites in nucleotide sequences.Biophysics - edam - events - topics Topic concerning the use of physics to study biological system. - topic - bioinformatics 1.3 + + + + @@ -52703,17 +48968,16 @@ positional features such as functional sites in nucleotide sequences. Biomathematics - topic - events - topics - Theoretical biology 1.3 + Theoretical biology Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. Mathematical biology This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). BioCatalogue:Model Execution - edam - bioinformatics + + + + @@ -52724,14 +48988,13 @@ positional features such as functional sites in nucleotide sequences.Transcriptomics - topics - Transcriptome Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. - bioinformatics - topic - edam - events 1.3 + Transcriptome + + + + @@ -52741,13 +49004,12 @@ positional features such as functional sites in nucleotide sequences. Chemistry - bioinformatics - events - edam - topic Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. 1.3 - topics + + + + @@ -52758,13 +49020,12 @@ positional features such as functional sites in nucleotide sequences.Mathematics 1.3 - topic - edam - events - bioinformatics - topics Maths Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. + + + + @@ -52774,13 +49035,12 @@ positional features such as functional sites in nucleotide sequences. Computer science - topics - bioinformatics - edam - events 1.3 - topic Topic concerning the theory and practical use of computer systems. + + + + @@ -52791,12 +49051,11 @@ positional features such as functional sites in nucleotide sequences.Physics 1.3 - events - topics Topic concerning the study of matter, space and time, and related concepts such as energy and force. - edam - bioinformatics - topic + + + + @@ -52807,13 +49066,12 @@ positional features such as functional sites in nucleotide sequences.RNA splicing - topics 1.3 This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. - edam - bioinformatics - topic + + + @@ -52823,13 +49081,12 @@ positional features such as functional sites in nucleotide sequences. Molecular genetics - bioinformatics 1.3 - edam - topic Topic concerning the structure and function of genes at a molecular level. - topics - events + + + + @@ -52839,14 +49096,16 @@ positional features such as functional sites in nucleotide sequences. Respiratory medicine + Pulmonary disorders + 1.3 + Pulmonary medicine + Respiratory disease Topic concerning the study of respiratory system. - events Pulmonology - topics - 1.3 - bioinformatics - topic - edam + + + + @@ -52855,13 +49114,13 @@ positional features such as functional sites in nucleotide sequences. Metabolic disease - + Topic concerning the study of metabolic diseases. 1.3 - edam - topic - bioinformatics - topics + 1.4 + true + + @@ -52871,12 +49130,14 @@ positional features such as functional sites in nucleotide sequences. Infectious disease - topic 1.3 - Topic concerning to the study of infectious diseases. - bioinformatics - topics - edam + Communicable disease + Topic concerning 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). + Transmissable disease + + + + @@ -52886,12 +49147,12 @@ positional features such as functional sites in nucleotide sequences. Rare diseases - topics - edam Topic concerning the study of rare diseases. - bioinformatics - topic 1.3 + + + + @@ -52903,12 +49164,11 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. - edam - bioinformatics 1.3 - events - topics - topic + + + + @@ -52919,12 +49179,12 @@ positional features such as functional sites in nucleotide sequences.Neurology 1.3 - bioinformatics - topic - topics - events + Neurological disorders Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - edam + + + + @@ -52934,13 +49194,15 @@ positional features such as functional sites in nucleotide sequences. Cardiology - topics - bioinformatics - events + Heart disease Topic concerning the diseases and abnormalities of the heart and circulatory system. 1.3 - edam - topic + Cardiovascular medicine + Cardiovascular disease + + + + @@ -52950,16 +49212,14 @@ positional features such as functional sites in nucleotide sequences. Drug discovery - - edam - topics - Medicinal chemistry - topic - Topic concerning 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. - bioinformatics + 1.3 - events + This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Topic concerning the discovery and design of drugs or potential drug compounds. + + + + @@ -52971,13 +49231,12 @@ positional features such as functional sites in nucleotide sequences. Tissue collection Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. - bioinformatics - biobanking - events - edam - topic 1.3 - topics + biobanking + + + + @@ -52987,13 +49246,12 @@ positional features such as functional sites in nucleotide sequences. Mouse clinic - topic Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. - topics - edam - bioinformatics 1.3 - events + + + + @@ -53003,13 +49261,12 @@ positional features such as functional sites in nucleotide sequences. Microbial collection - topic Topic concerning collections of microbial cells including bacteria, yeasts and moulds. 1.3 - topics - edam - events - bioinformatics + + + + @@ -53019,13 +49276,12 @@ positional features such as functional sites in nucleotide sequences. Cell culture collection - topic - events - edam 1.3 - bioinformatics - topics Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. + + + + @@ -53035,13 +49291,12 @@ positional features such as functional sites in nucleotide sequences. Clone library - events Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. - edam - topic 1.3 - bioinformatics - topics + + + + @@ -53051,14 +49306,12 @@ positional features such as functional sites in nucleotide sequences. Translational medicine - bioinformatics - events - Translational medicine - topic - topics - edam - Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. 1.3 + Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + + + + @@ -53068,17 +49321,16 @@ positional features such as functional sites in nucleotide sequences. Compound libraries and screening - events + 1.3 Chemical screening Compound library Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. - 1.3 Chemical library Translational medicine - edam - topics - bioinformatics - topic + + + + @@ -53089,13 +49341,12 @@ positional features such as functional sites in nucleotide sequences.Biomedical science - bioinformatics - topic - topics - edam 1.3 Topic concerning biological science that is (typically) performed in the context of medicine. - events + + + + @@ -53105,13 +49356,12 @@ positional features such as functional sites in nucleotide sequences. Data identity and mapping - 1.3 - topic Topic concerning the identity of biological data and the mapping of entities in different databases. - events - edam - topics - bioinformatics + 1.3 + + + + @@ -53120,15 +49370,877 @@ positional features such as functional sites in nucleotide sequences. Sequence search - + - bioinformatics Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. - Sequence clusters - topics - edam - topic + Sequence database search 1.3 + + + + + + + + + + + Biomarkers + + Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. + 1.4 + Diagnostic markers + + + + + + + + + + Laboratory techniques + + 1.4 + Lab techniques + Topic concerning the procedures used to conduct an experiment. + + + + + + + + + + + Data analysis + + 1.4 + Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data. + + + + + + + + + + + Data integration + + 1.4 + Topic concerning the combination of data from different sources to provide users with a unified view of these data. + + + + + + + + + + + Biomaterials + + Topic concerning any matter, surface or construct that interacts with a biological system. + 1.4 + Diagnostic markers + + + + + + + + + + + Chemical biology + + + Topic concerning the use of synthetic chemistry to study and manipulate biological systems. + 1.4 + + + + + + + + + + + Analytical chemistry + + Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. + 1.4 + + + + + + + + + + + Synthetic chemistry + + Topic concerning the use of chemistry to create new compounds. + 1.4 + Synthetic organic chemistry + + + + + + + + + + + Computer programming + + Software development + 1.4 + Topic concerning the process that leads from an original formulation of a computing problem to executable programs. + + + + + + + + + + + Drug development + + Medicines development + Drug development science + Medicine development + Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. + 1.4 + + + + + + + + + + + Drug formulation and delivery + + 1.4 + Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. + Drug formulation + Drug delivery + + + + + + + + + + + Pharmacokinetics and pharmacodynamics + + Drug metabolism + Drug metabolism + ADME + Drug absorption + Drug excretion + 1.4 + Drug distribution + Topic concerning the study of how a drug interacts with the body. + Pharmacokinetics + Pharmacodynamics + + + + + + + + + + + Medicine research and development + Medicines research and development + + Topic concerning the discovery, development and approval of medicines. + 1.4 + Drug discovery and development + Health care research + + + + + + + + + + + Safety sciences + + Topic concerning the safety (or lack) of drugs and other medical interventions. + Drug safety + 1.4 + + + + + + + + + + + Pharmacovigilence + + Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. + Pharmacovigilence concerns safety once a drug has gone to market. + 1.4 + + + + + + + + + + + Preclinical and clinical studies + + Clinical studies + 1.4 + Preclinical studies + Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. + + + + + + + + + + + Imaging + + Topic concerning the visual representation of an object. + Microscopy + 1.4 + + + + + + + + + + + Biological imaging + + Topic concerning the use of imaging techniques to understand biology. + 1.4 + + + + + + + + + + + Medical imaging + + Topic concerning the use of imaging techniques for clinical purposes for medical research. + 1.4 + + + + + + + + + + + Light microscopy + + 1.4 + Topic concerning the use of optical instruments to magnify the image of an object. + + + + + + + + + + + Laboratory animal science + + Topic concerning the use of animals and alternatives in experimental research. + 1.4 + + + + + + + + + + + Marine biology + + Topic concerning the study of organisms in the ocean or brackish waters. + 1.4 + + + + + + + + + + + Molecular medicine + + Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. + 1.4 + + + + + + + + + + + Nutritional science + + Nutrition science + 1.4 + Topic concerning 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. + + + + + + + + + + + Omics + + Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. + 1.4 + + + + + + + + + + + Quality affairs + + 1.4 + Good laboratory practice + Quality assurance + Good clinical practice + Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. + Good manufacturing practice + + + + + + + + + + + Regulatory affairs + + 1.4 + Topic concerning 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. + + + + + + + + + + + Regnerative medicine + + Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. + 1.4 + Stem cell research + + + + + + + + + + + Systems medicine + + Topic concerning 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. + 1.4 + + + + + + + + + + + Veterinary medicine + + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. + 1.4 + + + + + + + + + + + Bioengineering + + Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. + Diagnostic markers + 1.4 + + + + + + + + + + + Geriatric medicine + + Geriatrics + 1.4 + Aging + Ageing + Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. + + + + + + + + + + + Allergy, clinical immunology and immunotherapeutics. + + Immunotherapeutics + Allergy + Immunomodulators + Clinical immunology + Immune disorders + 1.4 + Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement. + + + + + + + + + + + Pain medicine + + Algiatry + 1.4 + Ageing + Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. + + + + + + + + + + + Anaesthesiology + + Topic concerning anaesthesia and anaesthetics. + 1.4 + Anaesthetics + + + + + + + + + + + Critical care medicine + + Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. + 1.4 + Emergency medicine + Acute medicine + Geriatrics + + + + + + + + + + + Dermatology + + 1.4 + Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. + Dermatological disorders + + + + + + + + + + + Dentistry + + Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. + 1.4 + + + + + + + + + + + Ear, nose and throat medicine + + Audiovestibular medicine + Head and neck disorders + 1.4 + Otolaryngology + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. + + + + + + + + + + + Endocrinology and metabolism + + Endocrine disorders + Endocrinology + Topic concerning 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. + Metabolism + Metabolic disorders + 1.4 + + + + + + + + + + + Haematology + + Blood disorders + 1.4 + Haematological disorders + Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases. + + + + + + + + + + + Gastroenterology + + Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. + 1.4 + Gastrointestinal disorders + + + + + + + + + + + Gender medicine + + 1.4 + Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. + + + + + + + + + + + Gynaecology and obstetrics + + Obstetrics + Gynaecological disorders + Gynaecology + Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. + 1.4 + + + + + + + + + + + Hepatic and biliary medicine + + Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. + 1.4 + Liver disorders + Hepatobiliary medicine + + + + + + + + + + + Infectious tropical disease + + Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. + 1.4 + + + + + + + + + + + Trauma medicine + + Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. + 1.4 + + + + + + + + + + + Medical toxicology + + 1.4 + Topic concerning 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. + + + + + + + + + + + Musculoskeletal medicine + + 1.4 + Musculoskeletal disorders + Topic concerning 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. + + + + + + + + + + + Opthalmology + + Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. + Audiovestibular medicine + Eye disoders + 1.4 + + + + + + + + + + + Paediatrics + + Child health + Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. + 1.4 + + + + + + + + + + + Psychiatry + + Mental health + Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. + Psychiatric disorders + 1.4 + + + + + + + + + + + Reproductive health + + Fertility medicine + Family planning + Topic concerning the health of the reproductive processes, functions and systems at all stages of life. + 1.4 + Audiovestibular medicine + Reproductive disorders + + + + + + + + + + + Surgery + + 1.4 + Topic concerning 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. + + + + + + + + + + + Urology and nephrology + + Nephrology + Urological disorders + Topic concerning 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. + Kidney disease + Urology + 1.4 + + + + + + + + + + + Complementary medicine + + Alternative medicine + 1.4 + Holistic medicine + Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. + + +