4048 24.09.2024 00:27 UTC EDAM http://edamontology.org/ "EDAM relations, concept properties, and subsets" EDAM_data http://edamontology.org/data_ "EDAM types of data" EDAM_format http://edamontology.org/format_ "EDAM data formats" EDAM_operation http://edamontology.org/operation_ "EDAM operations" EDAM_topic http://edamontology.org/topic_ "EDAM topics" EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. EDAM is a community project and its development can be followed and contributed to at https://github.com/edamontology/edamontology. https://github.com/edamontology/edamontology/graphs/contributors and many more! Federico Bianchini Hervé Ménager Jon Ison Matúš Kalaš application/rdf+xml EDAM - The ontology of data analysis and management EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. dev(1.26) Matúš Kalaš 1.25-20240924T0027Z-dev(1.26) 1.13 true Publication reference 'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferably including a DOI, pointing to a citeable publication of the given data format. Publication Citation true Version in which a concept was created. Created in true A comment explaining why the comment should be or was deprecated, including name of person commenting (jison, mkalas etc.). deprecation_comment 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 Documentation true 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead. Example true 'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats. N.B.: File extensions that are not correspondigly defined at http://filext.com are recorded in EDAM only if not in conflict with http://filext.com, and/or unique and usual within life-science computing. Separated by bar ('|'), without a dot ('.') prefix, preferably not all capital characters. File extension true "Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard. 'Information standard' trailing modifier (qualifier, 'information_standard') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an information standard supported by the given data format. Minimum information checklist Minimum information standard Information standard true When 'true', the concept has been proposed to be deprecated. deprecation_candidate true When 'true', the concept has been proposed to be refactored. refactor_candidate true When 'true', the concept has been proposed or is supported within Debian as a tag. isdebtag true 'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format. MIME type Media type true Whether terms associated with this concept are recommended for use in annotation. notRecommendedForAnnotation true Version in which a concept was made obsolete. Obsolete since true EDAM concept URI of the erstwhile "parent" of a now deprecated concept. Old parent true EDAM concept URI of an erstwhile related concept (by has_input, has_output, has_topic, is_format_of, etc.) of a now deprecated concept. Old related true 'Ontology used' concept property ('ontology_used' metadata tag) of format concepts links to a domain ontology that is used inside the given data format, or contains a note about ontology use within the format. Ontology used true 'Organisation' trailing modifier (qualifier, 'organisation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an organisation that developed, standardised, and maintains the given data format. Organization Organisation true A comment explaining the proposed refactoring, including name of person commenting (jison, mkalas etc.). refactor_comment true 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. Regular expression Related term 'Related term' concept property ('related_term'; supposedly a synonym modifier in OBO format) states a related term - not necessarily closely semantically related - that users (also non-specialists) may use when searching. true 'Repository' trailing modifier (qualifier, 'repository') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to the public source-code repository where the given data format is developed or maintained. Public repository Source-code repository Repository true Name of thematic editor (http://biotools.readthedocs.io/en/latest/governance.html#registry-editors) responsible for this concept and its children. thematic_editor false false false OBO_REL:is_a 'A has_format B' defines for the subject A, that it has the object B as its data format. 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) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. has format false false false OBO_REL:is_a 'A has_function B' defines for the subject A, that it has the object B as its function. OBO_REL:bearer_of true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. has function 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. true In very unusual cases. false false false OBO_REL:is_a 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. 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'. has identifier false false false OBO_REL:is_a 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. OBO_REL:has_participant true Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. has input 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. true In very unusual cases. false false false OBO_REL:is_a 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. OBO_REL:has_participant true Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. has output 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. true In very unusual cases. false false false OBO_REL:is_a 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. has topic true In very unusual cases. false false false OBO_REL:is_a 'A is_format_of B' defines for the subject A, that it is a data format of the object B. OBO_REL:quality_of false Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. is format of 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. false false false OBO_REL:is_a 'A is_function_of B' defines for the subject A, that it is a function of the object B. OBO_REL:function_of OBO_REL:inheres_in true Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. is function of 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. 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. true In very unusual cases. false false false OBO_REL:is_a 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. false Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. is identifier of false false false OBO_REL:is_a 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. OBO_REL:participates_in true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. is input of 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 inputs or input arguments. true In very unusual cases. false false false OBO_REL:is_a 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. OBO_REL:participates_in true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. is output of 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. true In very unusual cases. false false false OBO_REL:is_a 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). OBO_REL:quality_of true Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. is topic of 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. true In very unusual cases. beta12orEarlier beta12orEarlier A type of computational resource used in bioinformatics. Resource type true beta12orEarlier true Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. Data record Data set Datum Data 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). Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). beta12orEarlier beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. Tool true beta12orEarlier beta12orEarlier A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. Database true beta12orEarlier An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. Ontology beta12orEarlier 1.5 A directory on disk from which files are read. Directory metadata true beta12orEarlier beta12orEarlier Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. MeSH vocabulary true beta12orEarlier beta12orEarlier Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. HGNC vocabulary true beta12orEarlier beta12orEarlier Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). UMLS vocabulary true beta12orEarlier true A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). ID Identifier Almost exact but limited to identifying resources, and being unambiguous. beta12orEarlier beta12orEarlier An entry (retrievable via URL) from a biological database. Database entry true beta12orEarlier Mass of a molecule. Molecular mass beta12orEarlier PDBML:pdbx_formal_charge Net charge of a molecule. Molecular charge beta12orEarlier A specification of a chemical structure. Chemical structure specification Chemical formula beta12orEarlier A QSAR quantitative descriptor (name-value pair) of chemical structure. QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. QSAR descriptor beta12orEarlier Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata). 1.23 A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. Non-sequence characters may be used for example for gaps and translation stop. Raw sequence true beta12orEarlier SO:2000061 A molecular sequence and associated metadata. Sequence record http://purl.bioontology.org/ontology/MSH/D058977 beta12orEarlier A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. Alignment reference SO:0001260 An example is an alignment reference; one or a set of reference molecular sequences, structures, or profiles used for alignment of genomic, transcriptomic, or proteomic experimental data. This concept may be used for arbitrary sequence sets and associated data arising from processing. Sequence set beta12orEarlier 1.5 A character used to replace (mask) other characters in a molecular sequence. Sequence mask character true beta12orEarlier 1.5 A label (text token) describing the type of sequence masking to perform. Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. Sequence mask type true beta12orEarlier 1.20 The strand of a DNA sequence (forward or reverse). The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. DNA sense specification true beta12orEarlier 1.5 A specification of sequence length(s). Sequence length specification true beta12orEarlier 1.5 Basic or general information concerning molecular sequences. This is used for such things as a report including the sequence identifier, type and length. Sequence metadata true beta12orEarlier How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). Sequence feature source beta12orEarlier A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. Database hits (sequence) Sequence database hits Sequence database search results Sequence search 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. Sequence search results beta12orEarlier Report on the location of matches ("hits") between sequences, sequence profiles, motifs (conserved or functional patterns) and other types of sequence signatures. Profile-profile alignment Protein secondary database search results Search results (protein secondary database) Sequence motif hits Sequence motif matches Sequence profile alignment Sequence profile hits Sequence profile matches Sequence-profile alignment A "profile-profile alignment" is an alignment of two sequence profiles, each profile typically representing a sequence alignment. A "sequence-profile alignment" is an alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). This includes reports of hits from a search of a protein secondary or domain database. Data associated with the search or alignment might also be included, e.g. ranked list of best-scoring sequences, a graphical representation of scores etc. Sequence signature matches beta12orEarlier beta12orEarlier Data files used by motif or profile methods. Sequence signature model true beta12orEarlier Sequence signature data concerns specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. Sequence signature data beta12orEarlier 1.5 Alignment of exact matches between subsequences (words) within two or more molecular sequences. Sequence alignment (words) true beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. Dotplot beta12orEarlier Alignment of multiple molecular sequences. Multiple sequence alignment msa Sequence alignment http://purl.bioontology.org/ontology/MSH/D016415 http://semanticscience.org/resource/SIO_010066 beta12orEarlier 1.5 Some simple value controlling a sequence alignment (or similar 'match') operation. Sequence alignment parameter true beta12orEarlier A value representing molecular sequence similarity. Sequence similarity score beta12orEarlier 1.5 Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. Sequence alignment metadata true beta12orEarlier An informative report of molecular sequence alignment-derived data or metadata. Sequence alignment metadata Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. Sequence alignment report beta12orEarlier "Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data. 1.25 or earlier A profile-profile alignment (each profile typically representing a sequence alignment). Profile-profile alignment true beta12orEarlier "Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data. 1.24 Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). Sequence-profile alignment true beta12orEarlier Moby:phylogenetic_distance_matrix A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. Phylogenetic distance matrix Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. Sequence distance matrix beta12orEarlier 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 Phylogenetic character data http://www.evolutionaryontology.org/cdao.owl#Character beta12orEarlier Moby:Tree Moby:myTree Moby:phylogenetic_tree The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. Phylogeny 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'. Phylogenetic tree http://purl.bioontology.org/ontology/MSH/D010802 http://www.evolutionaryontology.org/cdao.owl#Tree beta12orEarlier Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. Substitution matrix 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). Comparison matrix beta12orEarlier beta12orEarlier Predicted or actual protein topology represented as a string of protein secondary structure elements. The location and size of the secondary structure elements and intervening loop regions is usually indicated. Protein topology true beta12orEarlier 1.8 Secondary structure (predicted or real) of a protein. Protein features report (secondary structure) true beta12orEarlier 1.8 Super-secondary structure of protein sequence(s). Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. Protein features report (super-secondary) true beta12orEarlier true Alignment of the (1D representations of) secondary structure of two or more proteins. Secondary structure alignment (protein) Protein secondary structure alignment beta12orEarlier beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. Secondary structure alignment metadata (protein) true beta12orEarlier Moby:RNAStructML An informative report of secondary structure (predicted or real) of an RNA molecule. Secondary structure (RNA) This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. RNA secondary structure beta12orEarlier true Moby:RNAStructAlignmentML Alignment of the (1D representations of) secondary structure of two or more RNA molecules. Secondary structure alignment (RNA) RNA secondary structure alignment beta12orEarlier beta12orEarlier An informative report of RNA secondary structure alignment-derived data or metadata. Secondary structure alignment metadata (RNA) true beta12orEarlier 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. Coordinate model Structure data The coordinate data may be predicted or real. Structure http://purl.bioontology.org/ontology/MSH/D015394 beta12orEarlier beta12orEarlier An entry from a molecular tertiary (3D) structure database. Tertiary structure record true beta12orEarlier 1.8 Results (hits) from searching a database of tertiary structure. Structure database search results true beta12orEarlier Alignment (superimposition) of molecular tertiary (3D) structures. A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. Structure alignment beta12orEarlier 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. Structure alignment report beta12orEarlier A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. Structure similarity score beta12orEarlier Some type of structural (3D) profile or template (representing a structure or structure alignment). 3D profile Structural (3D) profile Structural profile beta12orEarlier A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). Structural profile alignment Structural (3D) profile alignment beta12orEarlier 1.5 An alignment of a sequence to a 3D profile (representing structures or a structure alignment). Sequence-3D profile alignment true beta12orEarlier Matrix of values used for scoring sequence-structure compatibility. Protein sequence-structure scoring matrix beta12orEarlier An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). Sequence-structure alignment beta12orEarlier 1.4 An informative report about a specific amino acid. Amino acid annotation true beta12orEarlier 1.4 An informative report about a specific peptide. Peptide annotation true beta12orEarlier An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. Gene product annotation Protein report beta12orEarlier A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. Protein physicochemical property Protein properties Protein sequence statistics This is a broad data type and is used a placeholder for other, more specific types. Data may be based on analysis of nucleic acid sequence or structural data, 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 property beta12orEarlier 1.8 3D structural motifs in a protein. Protein structural motifs and surfaces true beta12orEarlier 1.5 Data concerning the classification of the sequences and/or structures of protein structural domain(s). Protein domain classification true beta12orEarlier 1.8 structural domains or 3D folds in a protein or polypeptide chain. Protein features report (domains) true beta12orEarlier 1.4 An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. Protein architecture report true beta12orEarlier 1.8 A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc. Protein folding report true beta12orEarlier beta13 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. Protein features (mutation) true beta12orEarlier Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein interaction raw data beta12orEarlier Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc. Protein interaction record Protein interaction report Protein report (interaction) Protein-protein interaction data Atom interaction data Protein non-covalent interactions report Residue interaction data Protein interaction data beta12orEarlier Protein classification data An informative report on a specific protein family or other classification or group of protein sequences or structures. Protein family annotation Protein family report beta12orEarlier The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. Vmax beta12orEarlier Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. Km beta12orEarlier 1.4 An informative report about a specific nucleotide base. Nucleotide base annotation true beta12orEarlier Nucleic acid structural properties stiffness, curvature, twist/roll data or other conformational parameters or properties. A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. Nucleic acid physicochemical property GC-content Nucleic acid property (structural) Nucleic acid structural property This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid property beta12orEarlier Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. Codon usage report This is a broad data type and is used a placeholder for other, more specific types. Codon usage data beta12orEarlier Moby:GeneInfo Moby:gene Moby_namespace:Human_Readable_Description A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. Gene and transcript structure (report) Gene annotation Gene features report Gene function (report) Gene structure (repot) Nucleic acid features (gene and transcript structure) This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). Gene report beta12orEarlier beta12orEarlier A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. Gene classification true beta12orEarlier 1.8 stable, naturally occurring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. DNA variation true beta12orEarlier A human-readable collection of information about a specific chromosome. This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. Chromosome report beta12orEarlier A human-readable collection of information about the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. Genotype/phenotype annotation Genotype/phenotype report beta12orEarlier 1.8 PCR experiments, e.g. quantitative real-time PCR. PCR experiment report true beta12orEarlier Fluorescence trace data generated by an automated DNA sequencer, which can be interpreted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. This is the raw data produced by a DNA sequencing machine. Sequence trace beta12orEarlier An assembly of fragments of a (typically genomic) DNA sequence. Contigs SO:0000353 SO:0001248 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. Sequence assembly SO:0001248 Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. beta12orEarlier Radiation hybrid scores (RH) scores for one or more markers. Radiation Hybrid (RH) scores Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. RH scores beta12orEarlier A human-readable collection of information about the linkage of alleles. Gene annotation (linkage) Linkage disequilibrium (report) This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). Genetic linkage report beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. Gene expression pattern Gene expression profile beta12orEarlier 1.8 microarray experiments including conditions, protocol, sample:data relationships etc. Microarray experiment report true beta12orEarlier beta13 Data on oligonucleotide probes (typically for use with DNA microarrays). Oligonucleotide probe data true beta12orEarlier beta12orEarlier Output from a serial analysis of gene expression (SAGE) experiment. SAGE experimental data true beta12orEarlier beta12orEarlier Massively parallel signature sequencing (MPSS) data. MPSS experimental data true beta12orEarlier beta12orEarlier Sequencing by synthesis (SBS) data. SBS experimental data true beta12orEarlier 1.14 Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. Sequence tag profile (with gene assignment) true beta12orEarlier Protein X-ray crystallographic data X-ray crystallography data. Electron density map beta12orEarlier Nuclear magnetic resonance (NMR) raw data, typically for a protein. Protein NMR data Raw NMR data beta12orEarlier Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. CD spectrum Protein circular dichroism (CD) spectroscopic data CD spectra beta12orEarlier Volume map data from electron microscopy. 3D volume map EM volume map Electron microscopy volume map Volume map beta12orEarlier 1.19 Annotation on a structural 3D model (volume map) from electron microscopy. Electron microscopy model true beta12orEarlier Two-dimensional gel electrophoresis image. 2D PAGE image beta12orEarlier Spectra from mass spectrometry. Mass spectrometry spectra Mass spectrum beta12orEarlier A set of peptide masses (peptide mass fingerprint) from mass spectrometry. Peak list Protein fingerprint Molecular weights standard fingerprint A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides. Peptide mass fingerprint beta12orEarlier Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer. 'Protein identification' Peptide spectrum match Peptide identification beta12orEarlier beta12orEarlier An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. Pathway or network annotation true beta12orEarlier beta12orEarlier A map (typically a diagram) of a biological pathway. Biological pathway map true beta12orEarlier 1.5 A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. Data resource definition true beta12orEarlier Basic information, annotation or documentation concerning a workflow (but not the workflow itself). Workflow metadata beta12orEarlier A biological model represented in mathematical terms. Biological model Mathematical model beta12orEarlier A value representing estimated statistical significance of some observed data; typically sequence database hits. Statistical estimate score beta12orEarlier 1.5 Resource definition for an EMBOSS database. EMBOSS database resource definition true beta12orEarlier 1.5 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. Version information true beta12orEarlier A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. Database cross-mapping beta12orEarlier An index of data of biological relevance. Data index beta12orEarlier A human-readable collection of information concerning an analysis of an index of biological data. Database index annotation Data index report beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. Database metadata beta12orEarlier Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. Tool metadata beta12orEarlier 1.5 Textual metadata on a submitted or completed job. Job metadata true beta12orEarlier Textual metadata on a software author or end-user, for example a person or other software. User metadata beta12orEarlier A human-readable collection of information about a specific chemical compound. Chemical compound annotation Chemical structure report Small molecule annotation Small molecule report beta12orEarlier A human-readable collection of information about a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. Cell line annotation Organism strain data Cell line report beta12orEarlier 1.4 An informative report about a specific scent. Scent annotation true beta12orEarlier A term (name) from an ontology. Ontology class name Ontology terms Ontology term beta12orEarlier Data concerning or derived from a concept from a biological ontology. Ontology class metadata Ontology term metadata Ontology concept data beta12orEarlier Moby:BooleanQueryString Moby:Global_Keyword Moby:QueryString Moby:Wildcard_Query Keyword(s) or phrase(s) used (typically) for text-searching purposes. Phrases Term Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. Keyword beta12orEarlier Moby:GCP_SimpleCitation Moby:Publication Bibliographic data that uniquely identifies a scientific article, book or other published material. Bibliographic reference Reference 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. Citation beta12orEarlier A scientific text, typically a full text article from a scientific journal. Article text Scientific article Article beta12orEarlier A human-readable collection of information resulting from text mining. Text mining output A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. Text mining report beta12orEarlier beta12orEarlier An identifier of a biological entity or phenomenon. Entity identifier true beta12orEarlier beta12orEarlier An identifier of a data resource. Data resource identifier true beta12orEarlier true An identifier that identifies a particular type of data. Identifier (typed) 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 (by type of entity) beta12orEarlier true An identifier of a bioinformatics tool, e.g. an application or web service. Tool identifier beta12orEarlier beta12orEarlier Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). Discrete entity identifier true beta12orEarlier 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). Entity feature identifier true beta12orEarlier beta12orEarlier Name or other identifier of a collection of discrete biological entities. Entity collection identifier true beta12orEarlier beta12orEarlier Name or other identifier of a physical, observable biological occurrence or event. Phenomenon identifier true beta12orEarlier true Name or other identifier of a molecule. Molecule identifier beta12orEarlier true Identifier (e.g. character symbol) of a specific atom. Atom identifier Atom ID beta12orEarlier true Name of a specific molecule. Molecule name beta12orEarlier 1.5 A label (text token) describing the type a molecule. For example, 'Protein', 'DNA', 'RNA' etc. Molecule type true beta12orEarlier beta12orEarlier Unique identifier of a chemical compound. Chemical identifier true beta12orEarlier Name of a chromosome. Chromosome name beta12orEarlier true Identifier of a peptide chain. Peptide identifier beta12orEarlier true Identifier of a protein. Protein identifier beta12orEarlier Unique name of a chemical compound. Chemical name Compound name beta12orEarlier Unique registry number of a chemical compound. Chemical registry number beta12orEarlier beta12orEarlier Code word for a ligand, for example from a PDB file. Ligand identifier true beta12orEarlier true Identifier of a drug. Drug identifier beta12orEarlier true Identifier of an amino acid. Residue identifier Amino acid identifier beta12orEarlier true Name or other identifier of a nucleotide. Nucleotide identifier beta12orEarlier true Identifier of a monosaccharide. Monosaccharide identifier beta12orEarlier Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. ChEBI chemical name This is the recommended chemical name for use for example in database annotation. Chemical name (ChEBI) beta12orEarlier IUPAC recommended name of a chemical compound. IUPAC chemical name Chemical name (IUPAC) beta12orEarlier International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO). INN chemical name Chemical name (INN) beta12orEarlier Brand name of a chemical compound. Brand chemical name Chemical name (brand) beta12orEarlier Synonymous name of a chemical compound. Synonymous chemical name Chemical name (synonymous) beta12orEarlier CAS registry number of a chemical compound; a unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. CAS chemical registry number Chemical registry number (CAS) CAS number beta12orEarlier Beilstein registry number of a chemical compound. Beilstein chemical registry number Chemical registry number (Beilstein) beta12orEarlier Gmelin registry number of a chemical compound. Gmelin chemical registry number Chemical registry number (Gmelin) beta12orEarlier 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. Component identifier code Short ligand name HET group name beta12orEarlier String of one or more ASCII characters representing an amino acid. Amino acid name beta12orEarlier String of one or more ASCII characters representing a nucleotide. Nucleotide code beta12orEarlier PDBML:pdbx_PDB_strand_id WHATIF: chain Identifier of a polypeptide chain from a protein. Chain identifier PDB chain identifier PDB strand id Polypeptide chain identifier Protein chain identifier This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA Polypeptide chain ID beta12orEarlier Name of a protein. Protein name beta12orEarlier Name or other identifier of an enzyme or record from a database of enzymes. Enzyme identifier beta12orEarlier [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ Moby:Annotated_EC_Number Moby:EC_Number An Enzyme Commission (EC) number of an enzyme. EC EC code Enzyme Commission number EC number beta12orEarlier Name of an enzyme. Enzyme name beta12orEarlier Name of a restriction enzyme. Restriction enzyme name beta12orEarlier 1.5 A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. Sequence position specification true beta12orEarlier A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. Sequence feature ID beta12orEarlier PDBML:_atom_site.id WHATIF: PDBx_atom_site WHATIF: number A position of one or more points (base or residue) in a sequence, or part of such a specification. SO:0000735 Sequence position beta12orEarlier Specification of range(s) of sequence positions. Sequence range beta12orEarlier beta12orEarlier Name or other identifier of an nucleic acid feature. Nucleic acid feature identifier true beta12orEarlier beta12orEarlier Name or other identifier of a protein feature. Protein feature identifier true 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 method Sequence feature type A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. Sequence feature key beta12orEarlier Typically one of the EMBL or Swiss-Prot feature qualifiers. Feature qualifiers hold information about a feature beyond that provided by the feature key and location. Sequence feature qualifier beta12orEarlier A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label. Sequence feature name 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. Sequence feature label beta12orEarlier The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. UFO EMBOSS Uniform Feature Object beta12orEarlier beta12orEarlier String of one or more ASCII characters representing a codon. Codon name true beta12orEarlier true Moby:GeneAccessionList An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. Gene identifier beta12orEarlier Moby_namespace:Global_GeneCommonName Moby_namespace:Global_GeneSymbol The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. Gene symbol beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs:LocusID http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene An NCBI unique identifier of a gene. Entrez gene ID Gene identifier (Entrez) Gene identifier (NCBI) NCBI gene ID NCBI geneid Gene ID (NCBI) beta12orEarlier beta12orEarlier An NCBI RefSeq unique identifier of a gene. Gene identifier (NCBI RefSeq) true beta12orEarlier beta12orEarlier An NCBI UniGene unique identifier of a gene. Gene identifier (NCBI UniGene) true beta12orEarlier beta12orEarlier An Entrez unique identifier of a gene. Gene identifier (Entrez) true beta12orEarlier Identifier of a gene or feature from the CGD database. CGD ID Gene ID (CGD) beta12orEarlier Identifier of a gene from DictyBase. Gene ID (DictyBase) beta12orEarlier Unique identifier for a gene (or other feature) from the Ensembl database. Gene ID (Ensembl) Ensembl gene ID beta12orEarlier S[0-9]+ Identifier of an entry from the SGD database. SGD identifier Gene ID (SGD) beta12orEarlier [a-zA-Z_0-9\.-]* Moby_namespace:GeneDB Identifier of a gene from the GeneDB database. GeneDB identifier Gene ID (GeneDB) beta12orEarlier Identifier of an entry from the TIGR database. TIGR identifier beta12orEarlier Gene:[0-9]{7} Identifier of an gene from the TAIR database. TAIR accession (gene) beta12orEarlier true Identifier of a protein structural domain. This is typically a character or string concatenated with a PDB identifier and a chain identifier. Protein domain ID beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. SCOP domain identifier beta12orEarlier 1nr3A00 Identifier of a protein domain from CATH. CATH domain identifier CATH domain ID beta12orEarlier A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. SCOP concise classification string (sccs) beta12orEarlier 33229 Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. SCOP unique identifier sunid 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. SCOP sunid beta12orEarlier 3.30.1190.10.1.1.1.1.1 A code number identifying a node from the CATH database. CATH code CATH node identifier CATH node ID beta12orEarlier The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). Kingdom name beta12orEarlier The name of a species (typically a taxonomic group) of organism. Organism species Species name beta12orEarlier The name of a strain of an organism variant, typically a plant, virus or bacterium. Strain name beta12orEarlier true A string of characters that name or otherwise identify a resource on the Internet. URIs URI beta12orEarlier true An identifier of a biological or bioinformatics database. Database identifier Database ID beta12orEarlier The name of a directory. Directory name beta12orEarlier The name (or part of a name) of a file (of any type). File name beta12orEarlier Name of an ontology of biological or bioinformatics concepts and relations. Ontology name beta12orEarlier Moby:Link Moby:URL A Uniform Resource Locator (URL). URL beta12orEarlier A Uniform Resource Name (URN). URN beta12orEarlier A Life Science Identifier (LSID) - a unique identifier of some 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>] LSID beta12orEarlier The name of a biological or bioinformatics database. Database name beta12orEarlier beta13 The name of a molecular sequence database. Sequence database name true beta12orEarlier The name of a file (of any type) with restricted possible values. Enumerated file name beta12orEarlier The extension of a file name. A file extension is the characters appearing after the final '.' in the file name. File name extension beta12orEarlier The base name of a file. A file base name is the file name stripped of its directory specification and extension. File base name beta12orEarlier Name of a QSAR descriptor. QSAR descriptor name beta12orEarlier beta12orEarlier An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. This concept is required for completeness. It should never have child concepts. Database entry identifier true beta12orEarlier true An identifier of molecular sequence(s) or entries from a molecular sequence database. Sequence identifier beta12orEarlier true An identifier of a set of molecular sequence(s). Sequence set ID beta12orEarlier beta12orEarlier Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. Sequence signature identifier true beta12orEarlier true Identifier of a molecular sequence alignment, for example a record from an alignment database. Sequence alignment ID beta12orEarlier beta12orEarlier Identifier of a phylogenetic distance matrix. Phylogenetic distance matrix identifier true beta12orEarlier true Identifier of a phylogenetic tree for example from a phylogenetic tree database. Phylogenetic tree ID beta12orEarlier true An identifier of a comparison matrix. Substitution matrix identifier Comparison matrix identifier beta12orEarlier true A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. Structure ID beta12orEarlier true Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). Structural profile identifier Structural (3D) profile ID beta12orEarlier true Identifier of an entry from a database of tertiary structure alignments. Structure alignment ID beta12orEarlier true Identifier of an index of amino acid physicochemical and biochemical property data. Amino acid index ID beta12orEarlier true Molecular interaction ID Identifier of a report of protein interactions from a protein interaction database (typically). Protein interaction ID beta12orEarlier true Identifier of a protein family. Protein secondary database record identifier Protein family identifier beta12orEarlier Unique name of a codon usage table. Codon usage table name beta12orEarlier true Identifier of a transcription factor (or a TF binding site). Transcription factor identifier beta12orEarlier true Identifier of an entry from a database of microarray data. Experiment annotation ID beta12orEarlier true Identifier of an entry from a database of electron microscopy data. Electron microscopy model ID beta12orEarlier true Accession of a report of gene expression (e.g. a gene expression profile) from a database. Gene expression profile identifier Gene expression report ID beta12orEarlier true Identifier of an entry from a database of genotypes and phenotypes. Genotype and phenotype annotation ID beta12orEarlier true Identifier of an entry from a database of biological pathways or networks. Pathway or network identifier beta12orEarlier true Identifier of a biological or biomedical workflow, typically from a database of workflows. Workflow ID beta12orEarlier true Identifier of a data type definition from some provider. Data resource definition identifier Data resource definition ID beta12orEarlier true Identifier of a mathematical model, typically an entry from a database. Biological model identifier Biological model ID beta12orEarlier true Identifier of an entry from a database of chemicals. Chemical compound identifier Compound ID Small molecule identifier Compound identifier beta12orEarlier A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. Ontology concept ID beta12orEarlier true Unique identifier of a scientific article. Article identifier Article ID beta12orEarlier FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. FlyBase ID beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. WormBase name beta12orEarlier Class of an object from the WormBase database. A WormBase class describes the type of object such as 'sequence' or 'protein'. WormBase class beta12orEarlier true A persistent, unique identifier of a molecular sequence database entry. Sequence accession number Sequence accession beta12orEarlier 1.5 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). Sequence type true beta12orEarlier The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. EMBOSS USA EMBOSS Uniform Sequence Address beta12orEarlier true Accession number of a protein sequence database entry. Protein sequence accession number Sequence accession (protein) beta12orEarlier true Accession number of a nucleotide sequence database entry. Nucleotide sequence accession number Sequence accession (nucleic acid) beta12orEarlier (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ Accession number of a RefSeq database entry. RefSeq ID RefSeq accession beta12orEarlier 1.0 Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. UniProt accession (extended) true beta12orEarlier An identifier of PIR sequence database entry. PIR ID PIR accession number PIR identifier beta12orEarlier 1.2 Identifier of a TREMBL sequence database entry. TREMBL accession true beta12orEarlier Primary identifier of a Gramene database entry. Gramene primary ID Gramene primary identifier beta12orEarlier Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. EMBL/GenBank/DDBJ ID beta12orEarlier A unique identifier of an entry (gene cluster) from the NCBI UniGene database. UniGene ID UniGene cluster ID UniGene identifier Sequence cluster ID (UniGene) beta12orEarlier Identifier of a dbEST database entry. dbEST ID dbEST accession beta12orEarlier Identifier of a dbSNP database entry. dbSNP identifier dbSNP ID beta12orEarlier beta12orEarlier The EMBOSS type of a molecular sequence. See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. EMBOSS sequence type true beta12orEarlier 1.5 List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). EMBOSS listfile true beta12orEarlier true An identifier of a cluster of molecular sequence(s). Sequence cluster ID beta12orEarlier Unique identifier of an entry from the COG database. COG ID Sequence cluster ID (COG) beta12orEarlier true Identifier of a sequence motif, for example an entry from a motif database. Sequence motif identifier beta12orEarlier true Identifier of a sequence profile. A sequence profile typically represents a sequence alignment. Sequence profile ID beta12orEarlier Identifier of an entry from the ELMdb database of protein functional sites. ELM ID beta12orEarlier PS[0-9]{5} Accession number of an entry from the Prosite database. Prosite ID Prosite accession number beta12orEarlier Unique identifier or name of a HMMER hidden Markov model. HMMER hidden Markov model ID beta12orEarlier Unique identifier or name of a profile from the JASPAR database. JASPAR profile ID beta12orEarlier 1.5 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. Sequence alignment type true beta12orEarlier beta12orEarlier The type of a BLAST sequence alignment. BLAST sequence alignment type true beta12orEarlier 1.5 A label (text token) describing the type of a phylogenetic tree. For example 'nj', 'upgmp' etc. Phylogenetic tree type true beta12orEarlier Accession number of an entry from the TreeBASE database. TreeBASE study accession number beta12orEarlier Accession number of an entry from the TreeFam database. TreeFam accession number beta12orEarlier 1.5 A label (text token) describing the type of a comparison matrix. For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. Comparison matrix type true beta12orEarlier Unique name or identifier of a comparison matrix. Substitution matrix name See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. Comparison matrix name beta12orEarlier [0-9][a-zA-Z_0-9]{3} An identifier of an entry from the PDB database. PDB identifier PDBID A PDB identification code which consists of 4 characters, the first of which is a digit in the range 0 - 9; the remaining 3 are alphanumeric, and letters are upper case only. (source: https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1996.pdf) PDB ID beta12orEarlier Identifier of an entry from the AAindex database. AAindex ID beta12orEarlier Accession number of an entry from the BIND database. BIND accession number beta12orEarlier EBI\-[0-9]+ Accession number of an entry from the IntAct database. IntAct accession number beta12orEarlier Name of a protein family. Protein family name beta12orEarlier Name of an InterPro entry, usually indicating the type of protein matches for that entry. InterPro entry name beta12orEarlier IPR015590 IPR[0-9]{6} Primary accession number of an InterPro entry. InterPro primary accession InterPro primary accession number Every InterPro entry has a unique accession number to provide a persistent citation of database records. InterPro accession beta12orEarlier Secondary accession number of an InterPro entry. InterPro secondary accession number InterPro secondary accession beta12orEarlier Unique identifier of an entry from the Gene3D database. Gene3D ID beta12orEarlier PIRSF[0-9]{6} Unique identifier of an entry from the PIRSF database. PIRSF ID beta12orEarlier PR[0-9]{5} The unique identifier of an entry in the PRINTS database. PRINTS code beta12orEarlier PF[0-9]{5} Accession number of a Pfam entry. Pfam accession number beta12orEarlier SM[0-9]{5} Accession number of an entry from the SMART database. SMART accession number beta12orEarlier Unique identifier (number) of a hidden Markov model from the Superfamily database. Superfamily hidden Markov model number beta12orEarlier Accession number of an entry (family) from the TIGRFam database. TIGRFam accession number TIGRFam ID beta12orEarlier PD[0-9]+ A ProDom domain family accession number. ProDom is a protein domain family database. ProDom accession number beta12orEarlier Identifier of an entry from the TRANSFAC database. TRANSFAC accession number beta12orEarlier [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ Accession number of an entry from the ArrayExpress database. ArrayExpress experiment ID ArrayExpress accession number beta12orEarlier [0-9]+ PRIDE experiment accession number. PRIDE experiment accession number beta12orEarlier Identifier of an entry from the EMDB electron microscopy database. EMDB ID beta12orEarlier [GDS|GPL|GSE|GSM][0-9]+ Accession number of an entry from the GEO database. GEO accession number beta12orEarlier Identifier of an entry from the GermOnline database. GermOnline ID beta12orEarlier Identifier of an entry from the EMAGE database. EMAGE ID beta12orEarlier true Accession number of an entry from a database of disease. Disease ID beta12orEarlier Identifier of an entry from the HGVbase database. HGVbase ID beta12orEarlier beta12orEarlier Identifier of an entry from the HIVDB database. HIVDB identifier true beta12orEarlier [*#+%^]?[0-9]{6} Identifier of an entry from the OMIM database. OMIM ID beta12orEarlier Unique identifier of an object from one of the KEGG databases (excluding the GENES division). KEGG object identifier beta12orEarlier REACT_[0-9]+(\.[0-9]+)? Identifier of an entry from the Reactome database. Reactome ID Pathway ID (reactome) beta12orEarlier beta12orEarlier Identifier of an entry from the aMAZE database. Pathway ID (aMAZE) true beta12orEarlier Identifier of an pathway from the BioCyc biological pathways database. BioCyc pathway ID Pathway ID (BioCyc) beta12orEarlier Identifier of an entry from the INOH database. INOH identifier Pathway ID (INOH) beta12orEarlier Identifier of an entry from the PATIKA database. PATIKA ID Pathway ID (PATIKA) beta12orEarlier 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. Pathway ID (CPDB) beta12orEarlier PTHR[0-9]{5} Identifier of a biological pathway from the Panther Pathways database. Panther Pathways ID Pathway ID (Panther) beta12orEarlier MIR:00100005 MIR:[0-9]{8} Unique identifier of a MIRIAM data resource. This is the identifier used internally by MIRIAM for a data type. MIRIAM identifier beta12orEarlier The name of a data type from the MIRIAM database. MIRIAM data type name beta12orEarlier urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 The URI (URL or URN) of a data entity from the MIRIAM database. identifiers.org synonym 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. MIRIAM URI beta12orEarlier UniProt|Enzyme Nomenclature 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. MIRIAM data type primary name UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. beta12orEarlier A synonymous name of a data type from the MIRIAM database. A synonymous name for a MIRIAM data type taken from a controlled vocabulary. MIRIAM data type synonymous name beta12orEarlier Unique identifier of a Taverna workflow. Taverna workflow ID beta12orEarlier Name of a biological (mathematical) model. Biological model name beta12orEarlier (BIOMD|MODEL)[0-9]{10} Unique identifier of an entry from the BioModel database. BioModel ID beta12orEarlier [0-9]+ Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. PubChem compound accession identifier PubChem CID beta12orEarlier [0-9]+ Identifier of an entry from the ChemSpider database. ChemSpider ID beta12orEarlier CHEBI:[0-9]+ Identifier of an entry from the ChEBI database. ChEBI IDs ChEBI identifier ChEBI ID beta12orEarlier An identifier of a concept from the BioPax ontology. BioPax concept ID beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a concept from The Gene Ontology. GO concept identifier GO concept ID beta12orEarlier An identifier of a concept from the MeSH vocabulary. MeSH concept ID beta12orEarlier An identifier of a concept from the HGNC controlled vocabulary. HGNC concept ID beta12orEarlier 9662|3483|182682 [1-9][0-9]{0,8} 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 NCBI taxonomy identifier NCBI taxonomy ID beta12orEarlier An identifier of a concept from the Plant Ontology (PO). Plant Ontology concept ID beta12orEarlier An identifier of a concept from the UMLS vocabulary. UMLS concept ID beta12orEarlier FMA:[0-9]+ An identifier of a concept from Foundational Model of Anatomy. Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. FMA concept ID beta12orEarlier An identifier of a concept from the EMAP mouse ontology. EMAP concept ID beta12orEarlier An identifier of a concept from the ChEBI ontology. ChEBI concept ID beta12orEarlier An identifier of a concept from the MGED ontology. MGED concept ID beta12orEarlier 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. myGrid concept ID beta12orEarlier 4963447 [1-9][0-9]{0,8} PubMed unique identifier of an article. PMID PubMed ID beta12orEarlier (doi\:)?[0-9]{2}\.[0-9]{4}/.* Digital Object Identifier (DOI) of a published article. Digital Object Identifier DOI beta12orEarlier Medline UI (unique identifier) of an article. Medline unique identifier The use of Medline UI has been replaced by the PubMed unique identifier. Medline UI beta12orEarlier The name of a computer package, application, method or function. Tool name beta12orEarlier The unique name of a signature (sequence classifier) method. Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. Tool name (signature) beta12orEarlier The name of a BLAST tool. BLAST name This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. Tool name (BLAST) beta12orEarlier The name of a FASTA tool. This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. Tool name (FASTA) beta12orEarlier The name of an EMBOSS application. Tool name (EMBOSS) beta12orEarlier The name of an EMBASSY package. Tool name (EMBASSY package) beta12orEarlier A QSAR constitutional descriptor. QSAR constitutional descriptor QSAR descriptor (constitutional) beta12orEarlier A QSAR electronic descriptor. QSAR electronic descriptor QSAR descriptor (electronic) beta12orEarlier A QSAR geometrical descriptor. QSAR geometrical descriptor QSAR descriptor (geometrical) beta12orEarlier A QSAR topological descriptor. QSAR topological descriptor QSAR descriptor (topological) beta12orEarlier A QSAR molecular descriptor. QSAR molecular descriptor QSAR descriptor (molecular) beta12orEarlier Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. Sequence set (protein) beta12orEarlier Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. Sequence set (nucleic acid) beta12orEarlier A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. The cluster might include sequences identifiers, short descriptions, alignment and summary information. Sequence cluster beta12orEarlier beta12orEarlier A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. Psiblast checkpoint file true beta12orEarlier beta12orEarlier Sequences generated by HMMER package in FASTA-style format. HMMER synthetic sequences set true beta12orEarlier A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. Proteolytic digest beta12orEarlier SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. Restriction digest beta12orEarlier Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. PCR primers beta12orEarlier beta12orEarlier File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. vectorstrip cloning vector definition file true beta12orEarlier beta12orEarlier A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. Primer3 internal oligo mishybridizing library true beta12orEarlier beta12orEarlier 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. Primer3 mispriming library file true beta12orEarlier beta12orEarlier File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. primersearch primer pairs sequence record true beta12orEarlier A cluster of protein sequences. Protein sequence cluster The sequences are typically related, for example a family of sequences. Sequence cluster (protein) beta12orEarlier A cluster of nucleotide sequences. Nucleotide sequence cluster The sequences are typically related, for example a family of sequences. Sequence cluster (nucleic acid) beta12orEarlier The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. Sequence length beta12orEarlier 1.5 Size of a sequence word. Word size is used for example in word-based sequence database search methods. Word size true beta12orEarlier 1.5 Size of a sequence window. A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. Window size true beta12orEarlier 1.5 Specification of range(s) of length of sequences. Sequence length range true beta12orEarlier beta12orEarlier Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. Sequence information report true beta12orEarlier An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. Sequence properties report Sequence property beta12orEarlier Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. Feature record Features General sequence features Sequence features report SO:0000110 This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. Sequence features http://purl.bioontology.org/ontology/MSH/D058977 beta12orEarlier beta13 Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Sequence features (comparative) true beta12orEarlier beta12orEarlier A report of general sequence properties derived from protein sequence data. Sequence property (protein) true beta12orEarlier beta12orEarlier A report of general sequence properties derived from nucleotide sequence data. Sequence property (nucleic acid) true beta12orEarlier A report on sequence complexity, for example low-complexity or repeat regions in sequences. Sequence property (complexity) Sequence complexity report beta12orEarlier A report on ambiguity in molecular sequence(s). Sequence property (ambiguity) Sequence ambiguity report beta12orEarlier A report (typically a table) on character or word composition / frequency of a molecular sequence(s). Sequence composition Sequence property (composition) Sequence composition report beta12orEarlier A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. Peptide molecular weight hits beta12orEarlier A plot of third base position variability in a nucleotide sequence. Base position variability plot beta12orEarlier beta12orEarlier A table of character or word composition / frequency of a molecular sequence. Sequence composition table true beta12orEarlier A table of base frequencies of a nucleotide sequence. Base frequencies table beta12orEarlier A table of word composition of a nucleotide sequence. Base word frequencies table beta12orEarlier A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) Amino acid frequencies table beta12orEarlier A table of amino acid word composition of a protein sequence. Sequence composition (amino acid words) Amino acid word frequencies table beta12orEarlier beta12orEarlier Annotation of a molecular sequence in DAS format. DAS sequence feature annotation true beta12orEarlier Annotation of positional sequence features, organised into a standard feature table. Sequence feature table Feature table beta12orEarlier A map of (typically one) DNA sequence annotated with positional or non-positional features. DNA map Map beta12orEarlier An informative report on intrinsic positional features of a nucleotide sequence, formatted to be machine-readable. Feature table (nucleic acid) Nucleic acid feature table Genome features Genomic features This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. Nucleic acid features beta12orEarlier An informative report on intrinsic positional features of a protein sequence. Feature table (protein) Protein feature table This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. Protein features beta12orEarlier Moby:GeneticMap A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. Linkage map 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. Genetic map beta12orEarlier A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. Sequence map beta12orEarlier A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. Physical map beta12orEarlier beta12orEarlier Image of a sequence with matches to signatures, motifs or profiles. Sequence signature map true beta12orEarlier A map showing banding patterns derived from direct observation of a stained chromosome. Chromosome map Cytogenic map Cytologic map 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. Cytogenetic map beta12orEarlier A gene map showing distances between loci based on relative cotransduction frequencies. DNA transduction map beta12orEarlier 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. Gene map beta12orEarlier Sequence map of a plasmid (circular DNA). Plasmid map beta12orEarlier Sequence map of a whole genome. Genome map beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. Restriction map beta12orEarlier beta12orEarlier Image showing matches between protein sequence(s) and InterPro Entries. The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. InterPro compact match image true beta12orEarlier beta12orEarlier Image showing detailed information on matches between protein sequence(s) and InterPro Entries. The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. InterPro detailed match image true beta12orEarlier beta12orEarlier 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. InterPro architecture image true beta12orEarlier beta12orEarlier SMART protein schematic in PNG format. SMART protein schematic true beta12orEarlier beta12orEarlier Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. GlobPlot domain image true beta12orEarlier 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. Sequence motif matches true beta12orEarlier 1.5 Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. The report might include derived data map such as classification, annotation, organisation, periodicity etc. Sequence features (repeats) true beta12orEarlier 1.5 A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. Gene and transcript structure (report) true beta12orEarlier 1.8 regions of a nucleic acid sequence containing mobile genetic elements. Mobile genetic elements true beta12orEarlier 1.5 A report on quadruplex-forming motifs in a nucleotide sequence. Nucleic acid features (quadruplexes) true beta12orEarlier 1.8 Report on nucleosome formation potential or exclusion sequence(s). Nucleosome exclusion sequences true beta12orEarlier beta13 A report on exonic splicing enhancers (ESE) in an exon. Gene features (exonic splicing enhancer) true beta12orEarlier 1.5 A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. Nucleic acid features (microRNA) true beta12orEarlier 1.8 protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Coding region true beta12orEarlier beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. Gene features (SECIS element) true beta12orEarlier 1.8 transcription factor binding sites (TFBS) in a DNA sequence. Transcription factor binding sites true beta12orEarlier beta12orEarlier A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. Protein features (sites) true beta12orEarlier 1.8 signal peptides or signal peptide cleavage sites in protein sequences. Protein features report (signal peptides) true beta12orEarlier 1.8 cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. Protein features report (cleavage sites) true beta12orEarlier 1.8 post-translation modifications in a protein sequence, typically describing the specific sites involved. Protein features (post-translation modifications) true beta12orEarlier 1.8 catalytic residues (active site) of an enzyme. Protein features report (active sites) true beta12orEarlier 1.8 ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. Protein features report (binding sites) true beta12orEarlier beta13 A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. Epitope mapping is commonly done during vaccine design. Protein features (epitopes) true beta12orEarlier 1.8 RNA and DNA-binding proteins and binding sites in protein sequences. Protein features report (nucleic acid binding sites) true beta12orEarlier beta12orEarlier A report on epitopes that bind to MHC class I molecules. MHC Class I epitopes report true beta12orEarlier beta12orEarlier A report on predicted epitopes that bind to MHC class II molecules. MHC Class II epitopes report true beta12orEarlier beta13 A report or plot of PEST sites in a protein sequence. 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. Protein features (PEST sites) true beta12orEarlier beta12orEarlier Scores from a sequence database search (for example a BLAST search). Sequence database hits scores list true beta12orEarlier beta12orEarlier Alignments from a sequence database search (for example a BLAST search). Sequence database hits alignments list true beta12orEarlier beta12orEarlier A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). Sequence database hits evaluation data true beta12orEarlier beta12orEarlier Alphabet for the motifs (patterns) that MEME will search for. MEME motif alphabet true beta12orEarlier beta12orEarlier MEME background frequencies file. MEME background frequencies file true beta12orEarlier beta12orEarlier File of directives for ordering and spacing of MEME motifs. MEME motifs directive file true beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. Dirichlet distribution beta12orEarlier 1.4 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. HMM emission and transition counts true beta12orEarlier Regular expression pattern. Regular expression beta12orEarlier Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. Sequence motif beta12orEarlier Some type of statistical model representing a (typically multiple) sequence alignment. Sequence profile http://semanticscience.org/resource/SIO_010531 beta12orEarlier An informative report about a specific or conserved protein sequence pattern. InterPro entry Protein domain signature Protein family signature Protein region signature Protein repeat signature Protein site signature Protein signature beta12orEarlier beta12orEarlier A nucleotide regular expression pattern from the Prosite database. Prosite nucleotide pattern true beta12orEarlier beta12orEarlier A protein regular expression pattern from the Prosite database. Prosite protein pattern true beta12orEarlier A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. PFM Position frequency matrix beta12orEarlier A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. PWM Contributions of individual sequences to the matrix might be uneven (weighted). Position weight matrix beta12orEarlier A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. ICM Information content matrix beta12orEarlier A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences. HMM Hidden Markov model beta12orEarlier One or more fingerprints (sequence classifiers) as used in the PRINTS database. Fingerprint beta12orEarlier beta12orEarlier A protein signature of the type used in the EMBASSY Signature package. Domainatrix signature true beta12orEarlier beta12orEarlier NULL hidden Markov model representation used by the HMMER package. HMMER NULL hidden Markov model true beta12orEarlier 1.5 A protein family signature (sequence classifier) from the InterPro database. Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. Protein family signature true beta12orEarlier 1.5 A protein domain signature (sequence classifier) from the InterPro database. Protein domain signatures identify structural or functional domains or other units with defined boundaries. Protein domain signature true beta12orEarlier 1.5 A protein region signature (sequence classifier) from the InterPro database. A protein region signature defines a region which cannot be described as a protein family or domain signature. Protein region signature true beta12orEarlier 1.5 A protein repeat signature (sequence classifier) from the InterPro database. A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. Protein repeat signature true beta12orEarlier 1.5 A protein site signature (sequence classifier) from the InterPro database. A protein site signature is a classifier for a specific site in a protein. Protein site signature true beta12orEarlier 1.4 A protein conserved site signature (sequence classifier) from the InterPro database. A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. Protein conserved site signature true beta12orEarlier 1.4 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. Protein active site signature true beta12orEarlier 1.4 A protein binding site signature (sequence classifier) from the InterPro database. A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. Protein binding site signature true beta12orEarlier 1.4 A protein post-translational modification signature (sequence classifier) from the InterPro database. A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. Protein post-translational modification signature true beta12orEarlier true Alignment of exactly two molecular sequences. Sequence alignment (pair) Pair sequence alignment http://semanticscience.org/resource/SIO_010068 beta12orEarlier beta12orEarlier Alignment of more than two molecular sequences. Sequence alignment (multiple) true beta12orEarlier Alignment of multiple nucleotide sequences. Sequence alignment (nucleic acid) DNA sequence alignment RNA sequence alignment Nucleic acid sequence alignment beta12orEarlier Alignment of multiple protein sequences. Sequence alignment (protein) Protein sequence alignment beta12orEarlier Alignment of multiple molecular sequences of different types. Sequence alignment (hybrid) Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. Hybrid sequence alignment beta12orEarlier 1.12 Alignment of exactly two nucleotide sequences. Sequence alignment (nucleic acid pair) true beta12orEarlier 1.12 Alignment of exactly two protein sequences. Sequence alignment (protein pair) true beta12orEarlier beta12orEarlier Alignment of exactly two molecular sequences of different types. Hybrid sequence alignment (pair) true beta12orEarlier beta12orEarlier Alignment of more than two nucleotide sequences. Multiple nucleotide sequence alignment true beta12orEarlier beta12orEarlier Alignment of more than two protein sequences. Multiple protein sequence alignment true beta12orEarlier A simple floating point number defining the penalty for opening or extending a gap in an alignment. Alignment score or penalty beta12orEarlier beta12orEarlier Whether end gaps are scored or not. Score end gaps control true beta12orEarlier beta12orEarlier Controls the order of sequences in an output sequence alignment. Aligned sequence order true beta12orEarlier A penalty for opening a gap in an alignment. Gap opening penalty beta12orEarlier A penalty for extending a gap in an alignment. Gap extension penalty beta12orEarlier A penalty for gaps that are close together in an alignment. Gap separation penalty beta12orEarlier beta12orEarlier 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. Terminal gap penalty true beta12orEarlier The score for a 'match' used in various sequence database search applications with simple scoring schemes. Match reward score beta12orEarlier The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. Mismatch penalty score beta12orEarlier This is the threshold drop in score at which extension of word alignment is halted. Drop off score beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. Gap opening penalty (integer) true beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. Gap opening penalty (float) true beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for extending a gap in an alignment. Gap extension penalty (integer) true beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for extending a gap in an alignment. Gap extension penalty (float) true beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for gaps that are close together in an alignment. Gap separation penalty (integer) true beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for gaps that are close together in an alignment. Gap separation penalty (float) true beta12orEarlier 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. Terminal gap opening penalty 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. Terminal gap extension penalty beta12orEarlier Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. Sequence identity beta12orEarlier Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. Data Type is float probably. Sequence similarity beta12orEarlier beta12orEarlier Data on molecular sequence alignment quality (estimated accuracy). Sequence alignment metadata (quality report) true beta12orEarlier 1.4 Data on character conservation in a molecular sequence alignment. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. Sequence alignment report (site conservation) true beta12orEarlier 1.4 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. Sequence alignment report (site correlation) true beta12orEarlier beta12orEarlier Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). Sequence-profile alignment (Domainatrix signature) true beta12orEarlier 1.5 Alignment of molecular sequence(s) to a hidden Markov model(s). Sequence-profile alignment (HMM) true beta12orEarlier 1.5 Alignment of molecular sequences to a protein fingerprint from the PRINTS database. Sequence-profile alignment (fingerprint) true beta12orEarlier Continuous quantitative data that may be read during phylogenetic tree calculation. Phylogenetic continuous quantitative characters Quantitative traits Phylogenetic continuous quantitative data beta12orEarlier Character data with discrete states that may be read during phylogenetic tree calculation. Discrete characters Discretely coded characters Phylogenetic discrete states Phylogenetic discrete data beta12orEarlier One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. Phylogenetic report (cliques) Phylogenetic character cliques beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. Phylogenetic report (invariants) Phylogenetic invariants beta12orEarlier 1.5 A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. Phylogenetic report true beta12orEarlier A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. Phylogenetic tree report (DNA substitution model) Sequence alignment report (DNA substitution model) Substitution model DNA substitution model beta12orEarlier 1.4 Data about the shape of a phylogenetic tree. Phylogenetic tree report (tree shape) true beta12orEarlier 1.4 Data on the confidence of a phylogenetic tree. Phylogenetic tree report (tree evaluation) true beta12orEarlier Distances, such as Branch Score distance, between two or more phylogenetic trees. Phylogenetic tree report (tree distances) Phylogenetic tree distances beta12orEarlier 1.4 Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. Phylogenetic tree report (tree stratigraphic) true beta12orEarlier Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. Phylogenetic report (character contrasts) Phylogenetic character contrasts beta12orEarlier beta12orEarlier Matrix of integer numbers for sequence comparison. Comparison matrix (integers) true beta12orEarlier beta12orEarlier Matrix of floating point numbers for sequence comparison. Comparison matrix (floats) true beta12orEarlier Matrix of integer or floating point numbers for nucleotide comparison. Nucleotide comparison matrix Nucleotide substitution matrix Comparison matrix (nucleotide) beta12orEarlier Matrix of integer or floating point numbers for amino acid comparison. Amino acid comparison matrix Amino acid substitution matrix Comparison matrix (amino acid) beta12orEarlier beta12orEarlier Matrix of integer numbers for nucleotide comparison. Nucleotide comparison matrix (integers) true beta12orEarlier beta12orEarlier Matrix of floating point numbers for nucleotide comparison. Nucleotide comparison matrix (floats) true beta12orEarlier beta12orEarlier Matrix of integer numbers for amino acid comparison. Amino acid comparison matrix (integers) true beta12orEarlier beta12orEarlier Matrix of floating point numbers for amino acid comparison. Amino acid comparison matrix (floats) true beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. Nucleic acid structure beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules. Protein structures Protein structure 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. 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. Protein-ligand complex beta12orEarlier 3D coordinate and associated data for a carbohydrate (3D) structure. Carbohydrate structure beta12orEarlier 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. CHEBI:23367 Small molecule structure beta12orEarlier 3D coordinate and associated data for a DNA tertiary (3D) structure. DNA structure beta12orEarlier 3D coordinate and associated data for an RNA tertiary (3D) structure. RNA structure beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. tRNA structure beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. Protein chain beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. Protein domain beta12orEarlier 1.5 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). Protein structure (all atoms) true beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). Protein structure (C-alpha atoms) C-beta atoms from amino acid side-chains may be included. C-alpha trace beta12orEarlier beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). Protein chain (all atoms) true beta12orEarlier beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). C-beta atoms from amino acid side-chains may be included. Protein chain (C-alpha atoms) true beta12orEarlier beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). Protein domain (all atoms) true beta12orEarlier beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). C-beta atoms from amino acid side-chains may be included. Protein domain (C-alpha atoms) true beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. Pair structure alignment Structure alignment (pair) beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two molecular tertiary (3D) structures. Structure alignment (multiple) true beta12orEarlier Alignment (superimposition) of protein tertiary (3D) structures. Structure alignment (protein) Protein structure alignment beta12orEarlier Alignment (superimposition) of nucleic acid tertiary (3D) structures. Structure alignment (nucleic acid) Nucleic acid structure alignment beta12orEarlier 1.12 Alignment (superimposition) of exactly two protein tertiary (3D) structures. Structure alignment (protein pair) true beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two protein tertiary (3D) structures. Multiple protein tertiary structure alignment true beta12orEarlier 1.5 Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). Structure alignment (protein all atoms) true beta12orEarlier 1.5 Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). C-beta atoms from amino acid side-chains may be considered. Structure alignment (protein C-alpha atoms) true beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). Pairwise protein tertiary structure alignment (all atoms) true beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). C-beta atoms from amino acid side-chains may be included. Pairwise protein tertiary structure alignment (C-alpha atoms) true beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). Multiple protein tertiary structure alignment (all atoms) true beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). C-beta atoms from amino acid side-chains may be included. Multiple protein tertiary structure alignment (C-alpha atoms) true beta12orEarlier 1.12 Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. Structure alignment (nucleic acid pair) true beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. Multiple nucleic acid tertiary structure alignment true beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. Structure alignment (RNA) RNA structure alignment beta12orEarlier Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. Structural transformation matrix beta12orEarlier beta12orEarlier DaliLite hit table of protein chain tertiary structure alignment data. The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. DaliLite hit table true beta12orEarlier beta12orEarlier A score reflecting structural similarities of two molecules. Molecular similarity score true beta12orEarlier Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. RMSD Root-mean-square deviation beta12orEarlier A measure of the similarity between two ligand fingerprints. A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. Tanimoto similarity score beta12orEarlier A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. 3D-1D scoring matrix beta12orEarlier A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. Amino acid index beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. Chemical classes (amino acids) Amino acid index (chemical classes) beta12orEarlier Statistical protein contact potentials. Contact potentials (amino acid pair-wise) Amino acid pair-wise contact potentials beta12orEarlier Molecular weights of amino acids. Molecular weight (amino acids) Amino acid index (molecular weight) beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. Hydropathy (amino acids) Amino acid index (hydropathy) beta12orEarlier Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. White-Wimley data (amino acids) Amino acid index (White-Wimley data) beta12orEarlier Van der Waals radii of atoms for different amino acid residues. van der Waals radii (amino acids) Amino acid index (van der Waals radii) beta12orEarlier 1.5 An informative report on a specific enzyme. Enzyme report true beta12orEarlier 1.5 An informative report on a specific restriction enzyme such as enzyme reference data. This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. Restriction enzyme report true beta12orEarlier List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. The report might include associated data such as frequency of peptide fragment molecular weights. Peptide molecular weights beta12orEarlier Report on the hydrophobic moment of a polypeptide sequence. Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. Peptide hydrophobic moment beta12orEarlier The aliphatic index of a protein. The aliphatic index is the relative protein volume occupied by aliphatic side chains. Protein aliphatic index 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. Protein sequence hydropathy plot beta12orEarlier 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. Protein charge plot beta12orEarlier The solubility or atomic solvation energy of a protein sequence or structure. Protein solubility data Protein solubility beta12orEarlier Data on the crystallizability of a protein sequence. Protein crystallizability data Protein crystallizability beta12orEarlier Data on the stability, intrinsic disorder or globularity of a protein sequence. Protein globularity data Protein globularity beta12orEarlier The titration curve of a protein. Protein titration curve beta12orEarlier The isoelectric point of one proteins. Protein isoelectric point beta12orEarlier The pKa value of a protein. Protein pKa value beta12orEarlier The hydrogen exchange rate of a protein. Protein hydrogen exchange rate beta12orEarlier The extinction coefficient of a protein. Protein extinction coefficient beta12orEarlier The optical density of a protein. Protein optical density beta12orEarlier beta13 An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). Protein subcellular localisation true beta12orEarlier An report on allergenicity / immunogenicity of peptides and proteins. Peptide immunogenicity Peptide immunogenicity report 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 data beta12orEarlier beta13 A report on the immunogenicity of MHC class I or class II binding peptides. MHC peptide immunogenicity report true beta12orEarlier A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains. Protein property (structural) Protein report (structure) Protein structural property Protein structure report (domain) Protein structure-derived report Protein structure report beta12orEarlier Report on the quality of a protein three-dimensional model. Protein property (structural quality) Protein report (structural quality) Protein structure report (quality evaluation) Protein structure validation report Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. Protein structural quality report beta12orEarlier 1.12 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. Protein non-covalent interactions report true beta12orEarlier 1.4 Informative report on flexibility or motion of a protein structure. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein flexibility or motion report true beta12orEarlier Data on the solvent accessible or buried surface area of a protein structure. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. Protein solvent accessibility beta12orEarlier 1.4 Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein surface report true beta12orEarlier Phi/psi angle data or a Ramachandran plot of a protein structure. Ramachandran plot beta12orEarlier Data on the net charge distribution (dipole moment) of a protein structure. Protein dipole moment beta12orEarlier A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. Protein distance matrix beta12orEarlier An amino acid residue contact map for a protein structure. Protein contact map beta12orEarlier Report on clusters of contacting residues in protein structures such as a key structural residue network. Protein residue 3D cluster beta12orEarlier Patterns of hydrogen bonding in protein structures. Protein hydrogen bonds beta12orEarlier 1.4 Non-canonical atomic interactions in protein structures. Protein non-canonical interactions true beta12orEarlier 1.5 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. CATH node true beta12orEarlier 1.5 Information on a node from the SCOP database. SCOP node true beta12orEarlier beta12orEarlier An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. EMBASSY domain classification true beta12orEarlier 1.5 Information on a protein 'class' node from the CATH database. CATH class true beta12orEarlier 1.5 Information on a protein 'architecture' node from the CATH database. CATH architecture true beta12orEarlier 1.5 Information on a protein 'topology' node from the CATH database. CATH topology true beta12orEarlier 1.5 Information on a protein 'homologous superfamily' node from the CATH database. CATH homologous superfamily true beta12orEarlier 1.5 Information on a protein 'structurally similar group' node from the CATH database. CATH structurally similar group true beta12orEarlier 1.5 Information on a protein 'functional category' node from the CATH database. CATH functional category true beta12orEarlier beta12orEarlier A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s). Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. Protein fold recognition report true beta12orEarlier 1.8 protein-protein interaction(s), including interactions between protein domains. Protein-protein interaction report true beta12orEarlier An informative report on protein-ligand (small molecule) interaction(s). Protein-drug interaction report Protein-ligand interaction report beta12orEarlier 1.8 protein-DNA/RNA interaction(s). Protein-nucleic acid interactions report true beta12orEarlier Nucleic acid melting curve: a melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the proportion of nucleic acid which are double-stranded versus temperature. Nucleic acid probability profile: a probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature Nucleic acid stitch profile: stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. Nucleic acid temperature profile: a temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Plots melting temperature versus base position. Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. Nucleic acid stability profile Melting map Nucleic acid melting curve 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 melting profile beta12orEarlier Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid enthalpy beta12orEarlier Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid entropy beta12orEarlier beta12orEarlier Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid melting temperature true beta12orEarlier 1.21 Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid stitch profile true beta12orEarlier DNA base pair stacking energies data. DNA base pair stacking energies data beta12orEarlier DNA base pair twist angle data. DNA base pair twist angle data beta12orEarlier DNA base trimer roll angles data. DNA base trimer roll angles data beta12orEarlier beta12orEarlier RNA parameters used by the Vienna package. Vienna RNA parameters true beta12orEarlier beta12orEarlier Structure constraints used by the Vienna package. Vienna RNA structure constraints true beta12orEarlier beta12orEarlier RNA concentration data used by the Vienna package. Vienna RNA concentration data true beta12orEarlier beta12orEarlier RNA calculated energy data generated by the Vienna package. Vienna RNA calculated energy true beta12orEarlier Dotplot of RNA base pairing probability matrix. Such as generated by the Vienna package. Base pairing probability matrix dotplot beta12orEarlier A human-readable collection of information about RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. Nucleic acid report (folding model) Nucleic acid report (folding) RNA secondary structure folding classification RNA secondary structure folding probabilities Nucleic acid folding report beta12orEarlier Table of codon usage data calculated from one or more nucleic acid sequences. A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. Codon usage table beta12orEarlier A genetic code for an organism. A genetic code need not include detailed codon usage information. Genetic code beta12orEarlier beta12orEarlier A simple measure of synonymous codon usage bias often used to predict gene expression levels. Codon adaptation index true beta12orEarlier A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. Synonymous codon usage statistic plot Codon usage bias plot beta12orEarlier 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. Nc statistic true beta12orEarlier The differences in codon usage fractions between two codon usage tables. Codon usage fraction difference beta12orEarlier A human-readable collection of information about the influence of genotype on drug response. The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. Pharmacogenomic test report beta12orEarlier A human-readable collection of information about a specific disease. For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. Disease report beta12orEarlier 1.8 A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). Linkage disequilibrium (report) true beta12orEarlier A graphical 2D tabular representation of expression data, typically derived from an omics experiment. A heat map is a table where rows and columns correspond to different features and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that context. Heat map beta12orEarlier beta12orEarlier Affymetrix library file of information about which probes belong to which probe set. Affymetrix probe sets library file true beta12orEarlier beta12orEarlier Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. GIN file Affymetrix probe sets information library file true beta12orEarlier 1.12 Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. Molecular weights standard fingerprint true beta12orEarlier 1.8 A report typically including a map (diagram) of a metabolic pathway. This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. Metabolic pathway report true beta12orEarlier 1.8 genetic information processing pathways. Genetic information processing pathway report true beta12orEarlier 1.8 environmental information processing pathways. Environmental information processing pathway report true beta12orEarlier 1.8 A report typically including a map (diagram) of a signal transduction pathway. Signal transduction pathway report true beta12orEarlier 1.8 Topic concernning cellular process pathways. Cellular process pathways report true beta12orEarlier 1.8 disease pathways, typically of human disease. Disease pathway or network report true beta12orEarlier 1.21 A report typically including a map (diagram) of drug structure relationships. Drug structure relationship map true beta12orEarlier 1.8 networks of protein interactions. Protein interaction networks true beta12orEarlier 1.5 An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. MIRIAM datatype true beta12orEarlier A simple floating point number defining the lower or upper limit of an expectation value (E-value). Expectation value An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. E-value beta12orEarlier The z-value is the number of standard deviations a data value is above or below a mean value. A z-value might be specified as a threshold for reporting hits from database searches. Z-value beta12orEarlier 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. P-value beta12orEarlier 1.5 Information on a database (or ontology) version, for example name, version number and release date. Database version information true beta12orEarlier 1.5 Information on an application version, for example name, version number and release date. Tool version information true beta12orEarlier beta12orEarlier Information on a version of the CATH database. CATH version information true beta12orEarlier beta12orEarlier Cross-mapping of Swiss-Prot codes to PDB identifiers. Swiss-Prot to PDB mapping true beta12orEarlier beta12orEarlier Cross-references from a sequence record to other databases. Sequence database cross-references true beta12orEarlier 1.5 Metadata on the status of a submitted job. Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). Job status true beta12orEarlier 1.0 The (typically numeric) unique identifier of a submitted job. Job ID true beta12orEarlier 1.5 A label (text token) describing the type of job, for example interactive or non-interactive. Job type true beta12orEarlier 1.5 A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. Tool log true beta12orEarlier beta12orEarlier DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. DaliLite log file true beta12orEarlier beta12orEarlier STRIDE log file. STRIDE log file true beta12orEarlier beta12orEarlier NACCESS log file. NACCESS log file true beta12orEarlier beta12orEarlier EMBOSS wordfinder log file. EMBOSS wordfinder log file true beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) domainatrix application log file. EMBOSS domainatrix log file true beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) sites application log file. EMBOSS sites log file true beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. EMBOSS supermatcher error file true beta12orEarlier beta12orEarlier EMBOSS megamerger log file. EMBOSS megamerger log file true beta12orEarlier beta12orEarlier EMBOSS megamerger log file. EMBOSS whichdb log file true beta12orEarlier beta12orEarlier EMBOSS vectorstrip log file. EMBOSS vectorstrip log file true beta12orEarlier A username on a computer system or a website. Username beta12orEarlier A password on a computer system, or a website. Password beta12orEarlier Moby:Email Moby:EmailAddress A valid email address of an end-user. Email address beta12orEarlier The name of a person. Person name beta12orEarlier 1.5 Number of iterations of an algorithm. Number of iterations true beta12orEarlier 1.5 Number of entities (for example database hits, sequences, alignments etc) to write to an output file. Number of output entities true beta12orEarlier beta12orEarlier Controls the order of hits (reported matches) in an output file from a database search. Hit sort order true beta12orEarlier A drug structure relationship map is report (typically a map diagram) of drug structure relationships. A human-readable collection of information about a specific drug. Drug annotation Drug structure relationship map Drug report 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. See also 'Phylogenetic tree' Phylogenetic tree image beta12orEarlier Image of RNA secondary structure, knots, pseudoknots etc. RNA secondary structure image beta12orEarlier Image of protein secondary structure. Protein secondary structure image beta12orEarlier Image of one or more molecular tertiary (3D) structures. Structure image beta12orEarlier Image of two or more aligned molecular sequences possibly annotated with alignment features. Sequence alignment image beta12orEarlier An image of the structure of a small chemical compound. Small molecule structure image Chemical structure sketch Small molecule sketch The molecular identifier and formula are typically included. Chemical structure image beta12orEarlier A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. Fate map beta12orEarlier An image of spots from a microarray experiment. Microarray spots image beta12orEarlier beta12orEarlier A term from the BioPax ontology. BioPax term true beta12orEarlier beta12orEarlier A term definition from The Gene Ontology (GO). GO true beta12orEarlier beta12orEarlier A term from the MeSH vocabulary. MeSH true beta12orEarlier beta12orEarlier A term from the HGNC controlled vocabulary. HGNC true beta12orEarlier beta12orEarlier A term from the NCBI taxonomy vocabulary. NCBI taxonomy vocabulary true beta12orEarlier beta12orEarlier A term from the Plant Ontology (PO). Plant ontology term true beta12orEarlier beta12orEarlier A term from the UMLS vocabulary. UMLS true beta12orEarlier beta12orEarlier A term from Foundational Model of Anatomy. Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. FMA true beta12orEarlier beta12orEarlier A term from the EMAP mouse ontology. EMAP true beta12orEarlier beta12orEarlier A term from the ChEBI ontology. ChEBI true beta12orEarlier beta12orEarlier A term from the MGED ontology. MGED true beta12orEarlier beta12orEarlier A term from the myGrid ontology. The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. myGrid true beta12orEarlier beta12orEarlier A term definition for a biological process from the Gene Ontology (GO). Data Type is an enumerated string. GO (biological process) true beta12orEarlier beta12orEarlier A term definition for a molecular function from the Gene Ontology (GO). Data Type is an enumerated string. GO (molecular function) true beta12orEarlier beta12orEarlier A term definition for a cellular component from the Gene Ontology (GO). Data Type is an enumerated string. GO (cellular component) true beta12orEarlier 1.5 A relation type defined in an ontology. Ontology relation type true beta12orEarlier The definition of a concept from an ontology. Ontology class definition Ontology concept definition beta12orEarlier 1.4 A comment on a concept from an ontology. Ontology concept comment true beta12orEarlier beta12orEarlier Reference for a concept from an ontology. Ontology concept reference true beta12orEarlier beta12orEarlier Information on a published article provided by the doc2loc program. The doc2loc output includes the url, format, type and availability code of a document for every service provider. doc2loc document information true beta12orEarlier PDBML:PDB_residue_no WHATIF: pdb_number A residue identifier (a string) from a PDB file. PDB residue number beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). Cartesian coordinate Atomic coordinate beta12orEarlier 1.21 Cartesian x coordinate of an atom (in a molecular structure). Atomic x coordinate true beta12orEarlier 1.21 Cartesian y coordinate of an atom (in a molecular structure). Atomic y coordinate true beta12orEarlier 1.21 Cartesian z coordinate of an atom (in a molecular structure). Atomic z coordinate true beta12orEarlier PDBML:pdbx_PDB_atom_name WHATIF: PDBx_auth_atom_id WHATIF: PDBx_type_symbol WHATIF: alternate_atom WHATIF: atom_type Identifier (a string) of a specific atom from a PDB file for a molecular structure. PDB atom name beta12orEarlier Data on a single atom from a protein structure. Atom data CHEBI:33250 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 atom beta12orEarlier Data on a single amino acid residue position in a protein structure. 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. Protein residue beta12orEarlier Name of an atom. Atom name beta12orEarlier WHATIF: type Three-letter amino acid residue names as used in PDB files. PDB residue name beta12orEarlier PDBML:pdbx_PDB_model_num WHATIF: model_number Identifier of a model structure from a PDB file. Model number PDB model number beta12orEarlier beta13 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. CATH domain report true beta12orEarlier beta12orEarlier FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). CATH representative domain sequences (ATOM) true beta12orEarlier beta12orEarlier FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). CATH representative domain sequences (COMBS) true beta12orEarlier beta12orEarlier FASTA sequence database for all CATH domains (based on PDB ATOM records). CATH domain sequences (ATOM) true beta12orEarlier beta12orEarlier FASTA sequence database for all CATH domains (based on COMBS sequence data). CATH domain sequences (COMBS) true beta12orEarlier Information on an molecular sequence version. Sequence version information Sequence version beta12orEarlier A numerical value, that is some type of scored value arising for example from a prediction method. Score beta12orEarlier beta13 Report on general functional properties of specific protein(s). For properties that can be mapped to a sequence, use 'Sequence report' instead. Protein report (function) true beta12orEarlier 1.3 Name of a gene from Aspergillus Genome Database. Gene name (ASPGD) true beta12orEarlier 1.3 Name of a gene from Candida Genome Database. Gene name (CGD) true beta12orEarlier 1.3 Name of a gene from dictyBase database. Gene name (dictyBase) true beta12orEarlier 1.3 Primary name of a gene from EcoGene Database. Gene name (EcoGene primary) true beta12orEarlier 1.3 Name of a gene from MaizeGDB (maize genes) database. Gene name (MaizeGDB) true beta12orEarlier 1.3 Name of a gene from Saccharomyces Genome Database. Gene name (SGD) true beta12orEarlier 1.3 Name of a gene from Tetrahymena Genome Database. Gene name (TGD) true beta12orEarlier 1.3 Symbol of a gene from E.coli Genetic Stock Center. Gene name (CGSC) true beta12orEarlier 1.3 Symbol of a gene approved by the HUGO Gene Nomenclature Committee. Gene name (HGNC) true beta12orEarlier 1.3 Symbol of a gene from the Mouse Genome Database. Gene name (MGD) true beta12orEarlier 1.3 Symbol of a gene from Bacillus subtilis Genome Sequence Project. Gene name (Bacillus subtilis) true beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB Identifier of a gene from PlasmoDB Plasmodium Genome Resource. Gene ID (PlasmoDB) beta12orEarlier Identifier of a gene from EcoGene Database. EcoGene Accession EcoGene ID Gene ID (EcoGene) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: FB http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase Gene identifier from FlyBase database. Gene ID (FlyBase) beta12orEarlier beta13 Gene identifier from Glossina morsitans GeneDB database. Gene ID (GeneDB Glossina morsitans) true beta12orEarlier beta13 Gene identifier from Leishmania major GeneDB database. Gene ID (GeneDB Leishmania major) true beta12orEarlier beta13 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum Gene identifier from Plasmodium falciparum GeneDB database. Gene ID (GeneDB Plasmodium falciparum) true beta12orEarlier beta13 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe Gene identifier from Schizosaccharomyces pombe GeneDB database. Gene ID (GeneDB Schizosaccharomyces pombe) true beta12orEarlier beta13 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei Gene identifier from Trypanosoma brucei GeneDB database. Gene ID (GeneDB Trypanosoma brucei) true beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene Gene identifier from Gramene database. Gene ID (Gramene) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD http://www.geneontology.org/doc/GO.xrf_abbs: VMD Gene identifier from Virginia Bioinformatics Institute microbial database. Gene ID (Virginia microbial) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: SGN Gene identifier from Sol Genomics Network. Gene ID (SGN) beta12orEarlier WBGene[0-9]{8} http://www.geneontology.org/doc/GO.xrf_abbs: WB http://www.geneontology.org/doc/GO.xrf_abbs: WormBase Gene identifier used by WormBase database. Gene ID (WormBase) beta12orEarlier beta12orEarlier Any name (other than the recommended one) for a gene. Gene synonym true beta12orEarlier The name of an open reading frame attributed by a sequencing project. ORF name beta12orEarlier beta12orEarlier A component of a larger sequence assembly. Sequence assembly component true beta12orEarlier beta12orEarlier A report on a chromosome aberration such as abnormalities in chromosome structure. Chromosome annotation (aberration) true beta12orEarlier true An identifier of a clone (cloned molecular sequence) from a database. Clone ID beta12orEarlier PDBML:pdbx_PDB_ins_code WHATIF: insertion_code An insertion code (part of the residue number) for an amino acid residue from a PDB file. PDB insertion code beta12orEarlier WHATIF: PDBx_occupancy The fraction of an atom type present at a site in a molecular structure. The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. Atomic occupancy beta12orEarlier WHATIF: PDBx_B_iso_or_equiv Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. Isotropic B factor beta12orEarlier A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. Deletion-based cytogenetic map 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. Deletion map beta12orEarlier A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. Quantitative trait locus map QTL map beta12orEarlier Moby:Haplotyping_Study_obj A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. Haplotype map beta12orEarlier 1.21 Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. Map set data true beta12orEarlier beta12orEarlier A feature which may mapped (positioned) on a genetic or other type of map. Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. Map feature true beta12orEarlier 1.5 A designation of the type of map (genetic map, physical map, sequence map etc) or map set. Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. Map type true beta12orEarlier The name of a protein fold. Protein fold name beta12orEarlier Moby:BriefTaxonConcept Moby:PotentialTaxon The name of a group of organisms belonging to the same taxonomic rank. Taxonomic rank Taxonomy rank For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. Taxon beta12orEarlier true A unique identifier of a (group of) organisms. Organism identifier beta12orEarlier The name of a genus of organism. Genus name beta12orEarlier Moby:GCP_Taxon Moby:TaxonName Moby:TaxonScientificName Moby:TaxonTCS Moby:iANT_organism-xml The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. Taxonomic information Taxonomic name 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 classification beta12orEarlier Moby_namespace:iHOPorganism A unique identifier for an organism used in the iHOP database. iHOP organism ID beta12orEarlier Common name for an organism as used in the GenBank database. Genbank common name beta12orEarlier The name of a taxon from the NCBI taxonomy database. NCBI taxon beta12orEarlier beta12orEarlier An alternative for a word. Synonym true beta12orEarlier beta12orEarlier A common misspelling of a word. Misspelling true beta12orEarlier beta12orEarlier An abbreviation of a phrase or word. Acronym true beta12orEarlier beta12orEarlier A term which is likely to be misleading of its meaning. Misnomer true beta12orEarlier Moby:Author Information on the authors of a published work. Author ID beta12orEarlier An identifier representing an author in the DragonDB database. DragonDB author identifier beta12orEarlier Moby:DescribedLink A URI along with annotation describing the data found at the address. Annotated URI beta12orEarlier beta12orEarlier A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. UniProt keywords true beta12orEarlier Moby_namespace:GENEFARM_GeneID Identifier of a gene from the GeneFarm database. Gene ID (GeneFarm) beta12orEarlier Moby_namespace:Blattner_number The blattner identifier for a gene. Blattner number beta12orEarlier beta13 Moby_namespace:MIPS_GE_Maize Identifier for genetic elements in MIPS Maize database. Gene ID (MIPS Maize) true beta12orEarlier beta13 Moby_namespace:MIPS_GE_Medicago Identifier for genetic elements in MIPS Medicago database. Gene ID (MIPS Medicago) true beta12orEarlier 1.3 The name of an Antirrhinum Gene from the DragonDB database. Gene name (DragonDB) true beta12orEarlier 1.3 A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. Gene name (Arabidopsis) true beta12orEarlier Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. iHOP symbol beta12orEarlier 1.3 Name of a gene from the GeneFarm database. Gene name (GeneFarm) true beta12orEarlier true A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. Locus identifier Locus name Locus ID beta12orEarlier AT[1-5]G[0-9]{5} http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases). AGI ID AGI identifier AGI locus code Arabidopsis gene loci number Locus ID (AGI) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID Identifier for loci from ASPGD (Aspergillus Genome Database). Locus ID (ASPGD) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG Identifier for loci from Magnaporthe grisea Database at the Broad Institute. Locus ID (MGG) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: CGD http://www.geneontology.org/doc/GO.xrf_abbs: CGDID Identifier for loci from CGD (Candida Genome Database). CGD locus identifier CGDID Locus ID (CGD) beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. Locus ID (CMR) beta12orEarlier Moby_namespace:LocusID http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag Identifier for loci from NCBI database. Locus ID (NCBI) NCBI locus tag beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: SGD http://www.geneontology.org/doc/GO.xrf_abbs: SGDID Identifier for loci from SGD (Saccharomyces Genome Database). SGDID Locus ID (SGD) beta12orEarlier Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. Locus ID (MMP) beta12orEarlier Moby_namespace:DDB_gene Identifier of locus from DictyBase (Dictyostelium discoideum). Locus ID (DictyBase) beta12orEarlier Moby_namespace:EntrezGene_EntrezGeneID Moby_namespace:EntrezGene_ID Identifier of a locus from EntrezGene database. Locus ID (EntrezGene) beta12orEarlier Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). Locus ID (MaizeGDB) beta12orEarlier beta12orEarlier Moby:SO_QTL A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). A QTL sometimes but does not necessarily correspond to a gene. Quantitative trait locus true beta12orEarlier Moby_namespace:GeneId Identifier of a gene from the KOME database. Gene ID (KOME) beta12orEarlier Moby:Tropgene_locus Identifier of a locus from the Tropgene database. Locus ID (Tropgene) beta12orEarlier true An alignment of molecular sequences, structures or profiles derived from them. Alignment beta12orEarlier Data for an atom (in a molecular structure). General atomic property Atomic property beta12orEarlier Moby_namespace:SP_KW http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. UniProt keyword beta12orEarlier 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. Ordered locus name true beta12orEarlier Moby:GCP_MapInterval Moby:GCP_MapPoint Moby:GCP_MapPosition Moby:GenePosition Moby:HitPosition Moby:Locus Moby:MapPosition Moby:Position PDBML:_atom_site.id A position in a map (for example a genetic map), either a single position (point) or a region / interval. Locus Map position 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. Sequence coordinates beta12orEarlier Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. Amino acid data Amino acid property beta12orEarlier beta13 A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. This is a broad data type and is used a placeholder for other, more specific types. Annotation true beta12orEarlier Data describing a molecular map (genetic or physical) or a set of such maps, including various attributes of, data extracted from or derived from the analysis of them, but excluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped. Map attribute Map set data Map data beta12orEarlier beta12orEarlier Data used by the Vienna RNA analysis package. Vienna RNA structural data true beta12orEarlier 1.5 Data used to replace (mask) characters in a molecular sequence. Sequence mask parameter true beta12orEarlier Data concerning chemical reaction(s) catalysed by enzyme(s). This is a broad data type and is used a placeholder for other, more specific types. Enzyme kinetics data beta12orEarlier 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. Michaelis Menten plot beta12orEarlier 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). Hanes Woolf plot beta12orEarlier beta13 Raw data from or annotation on laboratory experiments. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Experimental data true beta12orEarlier 1.5 Information on a genome version. Genome version information true beta12orEarlier Typically a human-readable summary of body of facts or information indicating why a statement is true or valid. This may include a computational prediction, laboratory experiment, literature reference etc. Evidence beta12orEarlier 1.8 A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Sequence record lite true beta12orEarlier One or more molecular sequences, possibly with associated annotation. Sequences 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. Sequence http://purl.bioontology.org/ontology/MSH/D008969 http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation beta12orEarlier 1.8 A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Nucleic acid sequence record (lite) true beta12orEarlier 1.8 A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Protein sequence record (lite) true beta12orEarlier A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. Document Record You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. Report http://semanticscience.org/resource/SIO_000148 beta12orEarlier General data for a molecule. General molecular property Molecular property (general) beta12orEarlier beta13 Data concerning molecular structural data. This is a broad data type and is used a placeholder for other, more specific types. Structural data true beta12orEarlier A nucleotide sequence motif. Nucleic acid sequence motif DNA sequence motif RNA sequence motif Sequence motif (nucleic acid) beta12orEarlier An amino acid sequence motif. Protein sequence motif Sequence motif (protein) beta12orEarlier 1.5 Some simple value controlling a search operation, typically a search of a database. Search parameter true beta12orEarlier A report of hits from searching a database of some type. Database hits Search results Database search results beta12orEarlier 1.5 The secondary structure assignment (predicted or real) of a nucleic acid or protein. Secondary structure true beta12orEarlier An array of numerical values. Array This is a broad data type and is used a placeholder for other, more specific types. Matrix beta12orEarlier 1.8 Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. This is a broad data type and is used a placeholder for other, more specific types. Alignment data true beta12orEarlier A human-readable collection of information about one or more specific nucleic acid molecules. Nucleic acid report beta12orEarlier A human-readable collection of information about one or more molecular tertiary (3D) structures. It might include annotation on the structure, a computer-generated report of analysis of structural data, and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. Structure-derived report Structure report beta12orEarlier 1.21 A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). Nucleic acid structure data true beta12orEarlier A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. Physicochemical property SO:0000400 Molecular property beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. DNA base structural data beta12orEarlier 1.5 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. Database entry version information true beta12orEarlier true A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. Accession http://semanticscience.org/resource/SIO_000675 http://semanticscience.org/resource/SIO_000731 beta12orEarlier 1.8 single nucleotide polymorphism (SNP) in a DNA sequence. SNP true beta12orEarlier Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. A list of database accessions or identifiers are usually included. Data reference beta12orEarlier true An identifier of a submitted job. Job identifier http://wsio.org/data_009 beta12orEarlier true A name of a thing, which need not necessarily uniquely identify it. Symbolic name Name http://semanticscience.org/resource/SIO_000116 http://usefulinc.com/ns/doap#name Closely related, but focusing on labeling and human readability but not on identification. beta12orEarlier 1.5 A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). Type http://purl.org/dc/elements/1.1/type true beta12orEarlier Authentication data usually used to log in into an account on an information system such as a web application or a database. Account authentication beta12orEarlier A three-letter code used in the KEGG databases to uniquely identify organisms. KEGG organism code beta12orEarlier 1.3 Name of an entry (gene) from the KEGG GENES database. Gene name (KEGG GENES) true beta12orEarlier Identifier of an object from one of the BioCyc databases. BioCyc ID beta12orEarlier Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound ID BioCyc compound identifier Compound ID (BioCyc) beta12orEarlier Identifier of a biological reaction from the BioCyc reactions database. Reaction ID (BioCyc) beta12orEarlier Identifier of an enzyme from the BioCyc enzymes database. BioCyc enzyme ID Enzyme ID (BioCyc) beta12orEarlier true Identifier of a biological reaction from a database. Reaction ID beta12orEarlier true An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. Identifier (hybrid) beta12orEarlier true Identifier of a molecular property. Molecular property identifier beta12orEarlier true Identifier of a codon usage table, for example a genetic code. Codon usage table identifier Codon usage table ID beta12orEarlier Primary identifier of an object from the FlyBase database. FlyBase primary identifier beta12orEarlier Identifier of an object from the WormBase database. WormBase identifier beta12orEarlier CE[0-9]{5} Protein identifier used by WormBase database. WormBase wormpep ID beta12orEarlier beta12orEarlier 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. Nucleic acid features (codon) true beta12orEarlier true An identifier of a map of a molecular sequence. Map identifier beta12orEarlier true An identifier of a software end-user on a website or a database (typically a person or an entity). Person identifier beta12orEarlier true Name or other identifier of a nucleic acid molecule. Nucleic acid identifier beta12orEarlier 1.20 Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). Translation frame specification true beta12orEarlier true An identifier of a genetic code. Genetic code identifier beta12orEarlier Informal name for a genetic code, typically an organism name. Genetic code name beta12orEarlier Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. File format name beta12orEarlier 1.5 A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. Sequence profile type true beta12orEarlier Name of a computer operating system such as Linux, PC or Mac. Operating system name beta12orEarlier beta12orEarlier A type of point or block mutation, including insertion, deletion, change, duplication and moves. Mutation type true beta12orEarlier A logical operator such as OR, AND, XOR, and NOT. Logical operator beta12orEarlier 1.5 A control of the order of data that is output, for example the order of sequences in an alignment. Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. Results sort order true beta12orEarlier beta12orEarlier A simple parameter that is a toggle (boolean value), typically a control for a modal tool. Toggle true beta12orEarlier beta12orEarlier The width of an output sequence or alignment. Sequence width true beta12orEarlier A penalty for introducing or extending a gap in an alignment. Gap penalty beta12orEarlier A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. Melting temperature Nucleic acid melting temperature beta12orEarlier The concentration of a chemical compound. Concentration beta12orEarlier 1.5 Size of the incremental 'step' a sequence window is moved over a sequence. Window step size true beta12orEarlier beta12orEarlier An image of a graph generated by the EMBOSS suite. EMBOSS graph true beta12orEarlier beta12orEarlier An application report generated by the EMBOSS suite. EMBOSS report true beta12orEarlier 1.5 An offset for a single-point sequence position. Sequence offset true beta12orEarlier 1.5 A value that serves as a threshold for a tool (usually to control scoring or output). Threshold true beta12orEarlier beta13 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. Protein report (transcription factor) true beta12orEarlier beta12orEarlier The name of a category of biological or bioinformatics database. Database category name true beta12orEarlier beta12orEarlier Name of a sequence profile. Sequence profile name true beta12orEarlier beta12orEarlier Specification of one or more colors. Color true beta12orEarlier 1.5 A parameter that is used to control rendering (drawing) to a device or image. Rendering parameter true beta12orEarlier Any arbitrary name of a molecular sequence. Sequence name beta12orEarlier 1.5 A temporal date. Date true beta12orEarlier beta12orEarlier Word composition data for a molecular sequence. Word composition true beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. Fickett testcode plot beta12orEarlier A plot of sequence similarities identified from word-matching or character comparison. 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. Sequence similarity plot beta12orEarlier An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. Helical wheel beta12orEarlier An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. Useful for highlighting amphipathicity and other properties. Helical net beta12orEarlier beta12orEarlier A plot of general physicochemical properties of a protein sequence. Protein sequence properties plot true beta12orEarlier A plot of pK versus pH for a protein. Protein ionisation curve beta12orEarlier A plot of character or word composition / frequency of a molecular sequence. Sequence composition plot beta12orEarlier Density plot (of base composition) for a nucleotide sequence. Nucleic acid density plot beta12orEarlier Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). Sequence trace image beta12orEarlier 1.5 A report on siRNA duplexes in mRNA. Nucleic acid features (siRNA) true beta12orEarlier 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. Sequence set (stream) true beta12orEarlier Secondary identifier of an object from the FlyBase database. Secondary identifier are used to handle entries that were merged with or split from other entries in the database. FlyBase secondary identifier beta12orEarlier beta12orEarlier The number of a certain thing. Cardinality true beta12orEarlier beta12orEarlier A single thing. Exactly 1 true beta12orEarlier beta12orEarlier One or more things. 1 or more true beta12orEarlier beta12orEarlier Exactly two things. Exactly 2 true beta12orEarlier beta12orEarlier Two or more things. 2 or more true beta12orEarlier A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. Hash Hash code Hash sum Hash value Sequence checksum beta12orEarlier 1.8 chemical modification of a protein. Protein features report (chemical modifications) true beta12orEarlier 1.5 Data on an error generated by computer system or tool. Error true beta12orEarlier Basic information on any arbitrary database entry. Database entry metadata beta12orEarlier beta13 A cluster of similar genes. Gene cluster true beta12orEarlier 1.8 A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. Sequence record full true beta12orEarlier true An identifier of a plasmid in a database. Plasmid identifier beta12orEarlier true A unique identifier of a specific mutation catalogued in a database. Mutation ID beta12orEarlier 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. Mutation annotation (basic) true beta12orEarlier beta12orEarlier An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. Mutation annotation (prevalence) true beta12orEarlier beta12orEarlier An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. Mutation annotation (prognostic) true beta12orEarlier beta12orEarlier 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. Mutation annotation (functional) true beta12orEarlier The number of a codon, for instance, at which a mutation is located. Codon number beta12orEarlier 1.4 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. Tumor annotation true beta12orEarlier 1.5 Basic information about a server on the web, such as an SRS server. Server metadata true beta12orEarlier The name of a field in a database. Database field name beta12orEarlier Unique identifier of a sequence cluster from the SYSTERS database. SYSTERS cluster ID Sequence cluster ID (SYSTERS) beta12orEarlier Data concerning a biological ontology. Ontology metadata beta12orEarlier beta13 Raw SCOP domain classification data files. These are the parsable data files provided by SCOP. Raw SCOP domain classification true beta12orEarlier beta13 Raw CATH domain classification data files. These are the parsable data files provided by CATH. Raw CATH domain classification true beta12orEarlier 1.4 An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. Heterogen annotation true beta12orEarlier beta12orEarlier Phylogenetic property values data. Phylogenetic property values true beta12orEarlier 1.5 A collection of sequences output from a bootstrapping (resampling) procedure. Bootstrapping is often performed in phylogenetic analysis. Sequence set (bootstrapped) true beta12orEarlier beta12orEarlier A consensus phylogenetic tree derived from comparison of multiple trees. Phylogenetic consensus tree true beta12orEarlier 1.5 A data schema for organising or transforming data of some type. Schema true beta12orEarlier 1.5 A DTD (document type definition). DTD true beta12orEarlier 1.5 An XML Schema. XML Schema true beta12orEarlier 1.5 A relax-NG schema. Relax-NG schema true beta12orEarlier 1.5 An XSLT stylesheet. XSLT stylesheet true beta12orEarlier The name of a data type. Data resource definition name beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. OBO file format name beta12orEarlier Identifier for genetic elements in MIPS database. MIPS genetic element identifier Gene ID (MIPS) beta12orEarlier beta12orEarlier An identifier of protein sequence(s) or protein sequence database entries. Sequence identifier (protein) true beta12orEarlier beta12orEarlier An identifier of nucleotide sequence(s) or nucleotide sequence database entries. Sequence identifier (nucleic acid) true beta12orEarlier An accession number of an entry from the EMBL sequence database. EMBL ID EMBL accession number EMBL identifier EMBL accession beta12orEarlier An identifier of a polypeptide in the UniProt database. UniProt entry name UniProt identifier UniProtKB entry name UniProtKB identifier UniProt ID beta12orEarlier Accession number of an entry from the GenBank sequence database. GenBank ID GenBank accession number GenBank identifier GenBank accession beta12orEarlier Secondary (internal) identifier of a Gramene database entry. Gramene internal ID Gramene internal identifier Gramene secondary ID Gramene secondary identifier beta12orEarlier true An identifier of an entry from a database of molecular sequence variation. Sequence variation ID beta12orEarlier true A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. Gene accession Gene code Gene ID beta12orEarlier 1.3 Name of an entry (gene) from the AceView genes database. Gene name (AceView) true beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ECK Identifier of an E. coli K-12 gene from EcoGene Database. E. coli K-12 gene identifier ECK accession Gene ID (ECK) beta12orEarlier Identifier for a gene approved by the HUGO Gene Nomenclature Committee. HGNC ID Gene ID (HGNC) beta12orEarlier The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. Allele name Gene name beta12orEarlier 1.3 Name of an entry (gene) from the NCBI genes database. Gene name (NCBI) true beta12orEarlier A specification of a chemical structure in SMILES format. SMILES string beta12orEarlier Unique identifier of an entry from the STRING database of protein-protein interactions. STRING ID beta12orEarlier 1.4 An informative report on a specific virus. Virus annotation true beta12orEarlier 1.4 An informative report on the taxonomy of a specific virus. Virus annotation (taxonomy) true beta12orEarlier [0-9]+ Identifier of a biological reaction from the SABIO-RK reactions database. Reaction ID (SABIO-RK) beta12orEarlier A human-readable collection of information about one or more specific carbohydrate 3D structure(s). Carbohydrate report beta12orEarlier 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. NCBI GI number 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. GI number 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. NCBI accession.version 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. NCBI version beta12orEarlier The name of a cell line. Cell line name beta12orEarlier The exact name of a cell line. Cell line name (exact) beta12orEarlier The truncated name of a cell line. Cell line name (truncated) beta12orEarlier The name of a cell line without any punctuation. Cell line name (no punctuation) beta12orEarlier The assonant name of a cell line. Cell line name (assonant) beta12orEarlier true A unique, persistent identifier of an enzyme. Enzyme accession Enzyme ID beta12orEarlier Identifier of an enzyme from the REBASE enzymes database. REBASE enzyme number beta12orEarlier DB[0-9]{5} Unique identifier of a drug from the DrugBank database. DrugBank ID beta12orEarlier A unique identifier assigned to NCBI protein sequence records. protein gi protein gi number 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. GI number (protein) beta12orEarlier A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system. Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches. Bit score beta12orEarlier 1.20 Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. Translation phase specification true beta12orEarlier Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. Provenance metadata This is a broad data type and is used a placeholder for other, more specific types. Resource metadata beta12orEarlier Any arbitrary identifier of an ontology. Ontology identifier beta12orEarlier The name of a concept in an ontology. Ontology concept name beta12orEarlier An identifier of a build of a particular genome. Genome build identifier beta12orEarlier The name of a biological pathway or network. Pathway or network name beta12orEarlier [a-zA-Z_0-9]{2,3}[0-9]{5} Identifier of a pathway from the KEGG pathway database. KEGG pathway ID Pathway ID (KEGG) beta12orEarlier [a-zA-Z_0-9]+ Identifier of a pathway from the NCI-Nature pathway database. Pathway ID (NCI-Nature) beta12orEarlier Identifier of a pathway from the ConsensusPathDB pathway database. Pathway ID (ConsensusPathDB) beta12orEarlier Unique identifier of an entry from the UniRef database. UniRef cluster id UniRef entry accession Sequence cluster ID (UniRef) beta12orEarlier Unique identifier of an entry from the UniRef100 database. UniRef100 cluster id UniRef100 entry accession Sequence cluster ID (UniRef100) beta12orEarlier Unique identifier of an entry from the UniRef90 database. UniRef90 cluster id UniRef90 entry accession Sequence cluster ID (UniRef90) beta12orEarlier Unique identifier of an entry from the UniRef50 database. UniRef50 cluster id UniRef50 entry accession Sequence cluster ID (UniRef50) beta12orEarlier Data concerning or derived from an ontology. Ontological data This is a broad data type and is used a placeholder for other, more specific types. Ontology data beta12orEarlier A human-readable collection of information about a specific RNA family or other group of classified RNA sequences. RNA family annotation RNA family report beta12orEarlier true Identifier of an RNA family, typically an entry from a RNA sequence classification database. RNA family identifier beta12orEarlier Stable accession number of an entry (RNA family) from the RFAM database. RFAM accession beta12orEarlier 1.5 A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. Protein signature type true beta12orEarlier 1.5 An informative report on protein domain-DNA/RNA interaction(s). Domain-nucleic acid interaction report true beta12orEarlier 1.8 An informative report on protein domain-protein domain interaction(s). Domain-domain interactions true beta12orEarlier beta12orEarlier Data on indirect protein domain-protein domain interaction(s). Domain-domain interaction (indirect) true beta12orEarlier true Accession number of a nucleotide or protein sequence database entry. Sequence accession (hybrid) beta12orEarlier beta13 Data concerning two-dimensional polygel electrophoresis. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. 2D PAGE data true beta12orEarlier 1.8 two-dimensional gel electrophoresis experiments, gels or spots in a gel. 2D PAGE report true beta12orEarlier true A persistent, unique identifier of a biological pathway or network (typically a database entry). Pathway or network accession beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more molecules. Secondary structure alignment beta12orEarlier Identifier of an object from the ASTD database. ASTD ID beta12orEarlier Identifier of an exon from the ASTD database. ASTD ID (exon) beta12orEarlier Identifier of an intron from the ASTD database. ASTD ID (intron) beta12orEarlier Identifier of a polyA signal from the ASTD database. ASTD ID (polya) beta12orEarlier Identifier of a transcription start site from the ASTD database. ASTD ID (tss) beta12orEarlier 1.8 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. 2D PAGE spot report true beta12orEarlier true Unique identifier of a spot from a two-dimensional (protein) gel. Spot ID beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. Spot serial number beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. Spot ID (HSC-2DPAGE) beta12orEarlier beta13 Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. Protein-motif interaction true beta12orEarlier true Identifier of a strain of an organism variant, typically a plant, virus or bacterium. Strain identifier beta12orEarlier A unique identifier of an item from the CABRI database. CABRI accession beta12orEarlier 1.8 Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. Experiment report (genotyping) true beta12orEarlier true Identifier of an entry from a database of genotype experiment metadata. Genotype experiment ID beta12orEarlier Identifier of an entry from the EGA database. EGA accession beta12orEarlier IPI[0-9]{8} Identifier of a protein entry catalogued in the International Protein Index (IPI) database. IPI protein ID beta12orEarlier Accession number of a protein from the RefSeq database. RefSeq protein ID RefSeq accession (protein) beta12orEarlier Identifier of an entry (promoter) from the EPD database. EPD identifier EPD ID beta12orEarlier Identifier of an entry from the TAIR database. TAIR accession beta12orEarlier Identifier of an Arabidopsis thaliana gene from the TAIR database. TAIR accession (At gene) beta12orEarlier Identifier of an entry from the UniSTS database. UniSTS accession beta12orEarlier Identifier of an entry from the UNITE database. UNITE accession beta12orEarlier Identifier of an entry from the UTR database. UTR accession beta12orEarlier UPI[A-F0-9]{10} Accession number of a UniParc (protein sequence) database entry. UPI UniParc ID UniParc accession beta12orEarlier Identifier of an entry from the Rouge or HUGE databases. mFLJ/mKIAA number beta12orEarlier 1.4 An informative report on a specific fungus. Fungi annotation true beta12orEarlier 1.4 An informative report on a specific fungus anamorph. Fungi annotation (anamorph) true beta12orEarlier Unique identifier for a protein from the Ensembl database. Ensembl ID (protein) Protein ID (Ensembl) Ensembl protein ID beta12orEarlier 1.4 An informative report on a specific toxin. Toxin annotation true beta12orEarlier beta12orEarlier An informative report on a membrane protein. Protein report (membrane protein) true beta12orEarlier 1.12 An informative report on tentative or known protein-drug interaction(s). Protein-drug interaction report true beta12orEarlier beta13 Data concerning a map of molecular sequence(s). This is a broad data type and is used a placeholder for other, more specific types. Map data true beta12orEarlier Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. This is a broad data type and is used a placeholder for other, more specific types. Phylogenetic data beta12orEarlier beta13 Data concerning one or more protein molecules. This is a broad data type and is used a placeholder for other, more specific types. Protein data true beta12orEarlier beta13 Data concerning one or more nucleic acid molecules. This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid data true beta12orEarlier Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. Article data Scientific text 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. It includes concepts that are best described as scientific text or closely concerned with or derived from text. Text data beta12orEarlier 1.16 Typically a simple numerical or string value that controls the operation of a tool. Parameter true beta12orEarlier beta13 Data concerning a specific type of molecule. This is a broad data type and is used a placeholder for other, more specific types. Molecular data true beta12orEarlier 1.5 An informative report on a specific molecule. Molecule report true beta12orEarlier A human-readable collection of information about a specific organism. Organism annotation Organism report beta12orEarlier A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis. Experiment annotation Experiment metadata Experiment report Protocol beta12orEarlier An attribute of a molecular sequence, possibly in reference to some other sequence. Sequence parameter Sequence attribute beta12orEarlier Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. Sequencing-based expression profile Sequence tag profile (with gene assignment) 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. This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. Sequence tag profile beta12orEarlier Data concerning a mass spectrometry measurement. Mass spectrometry data beta12orEarlier Raw data from experimental methods for determining protein structure. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein structure raw data beta12orEarlier true An identifier of a mutation. Mutation identifier beta12orEarlier beta13 Data concerning an alignment of two or more molecular sequences, structures or derived data. This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. Alignment data true beta12orEarlier beta13 Data concerning an index of data. This is a broad data type and is used a placeholder for other, more specific types. Data index data true beta12orEarlier Single letter amino acid identifier, e.g. G. Amino acid name (single letter) beta12orEarlier Three letter amino acid identifier, e.g. GLY. Amino acid name (three letter) beta12orEarlier Full name of an amino acid, e.g. Glycine. Amino acid name (full name) beta12orEarlier true Identifier of a toxin. Toxin identifier beta12orEarlier Unique identifier of a toxin from the ArachnoServer database. ArachnoServer ID beta12orEarlier 1.5 A simple summary of expressed genes. Expressed gene list true beta12orEarlier Unique identifier of a monomer from the BindingDB database. BindingDB Monomer ID beta12orEarlier beta12orEarlier The name of a concept from the GO ontology. GO concept name true beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a 'biological process' concept from the the Gene Ontology. GO concept ID (biological process) beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a 'molecular function' concept from the the Gene Ontology. GO concept ID (molecular function) beta12orEarlier beta12orEarlier The name of a concept for a cellular component from the GO ontology. GO concept name (cellular component) true beta12orEarlier An image arising from a Northern Blot experiment. Northern blot image beta12orEarlier true Unique identifier of a blot from a Northern Blot. Blot ID beta12orEarlier Unique identifier of a blot from a Northern Blot from the BlotBase database. BlotBase blot ID beta12orEarlier Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. Hierarchy annotation Hierarchy beta12orEarlier beta12orEarlier Identifier of an entry from a database of biological hierarchies. Hierarchy identifier true beta12orEarlier Identifier of an entry from the Brite database of biological hierarchies. Brite hierarchy ID beta12orEarlier beta12orEarlier A type (represented as a string) of cancer. Cancer type true beta12orEarlier A unique identifier for an organism used in the BRENDA database. BRENDA organism ID beta12orEarlier The name of a taxon using the controlled vocabulary of the UniGene database. UniGene organism abbreviation UniGene taxon beta12orEarlier The name of a taxon using the controlled vocabulary of the UTRdb database. UTRdb taxon beta12orEarlier true An identifier of a catalogue of biological resources. Catalogue identifier Catalogue ID beta12orEarlier The name of a catalogue of biological resources from the CABRI database. CABRI catalogue name beta12orEarlier beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. Secondary structure alignment metadata true beta12orEarlier Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19. 1.5 An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). Molecule interaction report true beta12orEarlier Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). Network Pathway Pathway or network beta12orEarlier beta13 Data concerning one or more small molecules. This is a broad data type and is used a placeholder for other, more specific types. Small molecule data true beta12orEarlier beta13 Data concerning a particular genotype, phenotype or a genotype / phenotype relation. Genotype and phenotype data true beta12orEarlier Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification. Gene expression data Gene product profile Gene product quantification data Gene transcription profile Gene transcription quantification data Metabolite expression data Microarray data Non-coding RNA profile Non-coding RNA quantification data Protein expression data RNA profile RNA quantification data RNA-seq data Transcriptome profile Transcriptome quantification data mRNA profile mRNA quantification data Protein profile Protein quantification data Proteome profile Proteome quantification data Expression data beta12orEarlier C[0-9]+ Unique identifier of a chemical compound from the KEGG database. KEGG compound ID KEGG compound identifier Compound ID (KEGG) beta12orEarlier Name (not necessarily stable) an entry (RNA family) from the RFAM database. RFAM name beta12orEarlier R[0-9]+ Identifier of a biological reaction from the KEGG reactions database. Reaction ID (KEGG) beta12orEarlier D[0-9]+ Unique identifier of a drug from the KEGG Drug database. Drug ID (KEGG) beta12orEarlier ENS[A-Z]*[FPTG][0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. Ensembl IDs Ensembl ID beta12orEarlier [A-Z][0-9]+(\.[-[0-9]+])? An identifier of a disease from the International Classification of Diseases (ICD) database. ICD identifier beta12orEarlier [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? Unique identifier of a sequence cluster from the CluSTr database. CluSTr ID CluSTr cluster ID Sequence cluster ID (CluSTr) beta12orEarlier G[0-9]+ Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). KEGG Glycan ID beta12orEarlier [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. TC number OBO file for regular expression. TCDB ID beta12orEarlier MINT\-[0-9]{1,5} Unique identifier of an entry from the MINT database of protein-protein interactions. MINT ID beta12orEarlier DIP[\:\-][0-9]{3}[EN] Unique identifier of an entry from the DIP database of protein-protein interactions. DIP ID beta12orEarlier A[0-9]{6} Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. Signaling Gateway protein ID beta12orEarlier true Identifier of a protein modification catalogued in a database. Protein modification ID beta12orEarlier AA[0-9]{4} Identifier of a protein modification catalogued in the RESID database. RESID ID beta12orEarlier [0-9]{4,7} Identifier of an entry from the RGD database. RGD ID beta12orEarlier AASequence:[0-9]{10} Identifier of a protein sequence from the TAIR database. TAIR accession (protein) beta12orEarlier HMDB[0-9]{5} Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). HMDB ID Compound ID (HMDB) beta12orEarlier LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? Identifier of an entry from the LIPID MAPS database. LM ID LIPID MAPS ID beta12orEarlier PAp[0-9]{8} PDBML:pdbx_PDB_strand_id Identifier of a peptide from the PeptideAtlas peptide databases. PeptideAtlas ID beta12orEarlier 1.7 Identifier of a report of molecular interactions from a database (typically). Molecular interaction ID true beta12orEarlier [0-9]+ A unique identifier of an interaction from the BioGRID database. BioGRID interaction ID beta12orEarlier S[0-9]{2}\.[0-9]{3} Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID Enzyme ID (MEROPS) beta12orEarlier true An identifier of a mobile genetic element. Mobile genetic element ID beta12orEarlier mge:[0-9]+ An identifier of a mobile genetic element from the Aclame database. ACLAME ID beta12orEarlier PWY[a-zA-Z_0-9]{2}\-[0-9]{3} Identifier of an entry from the Saccharomyces genome database (SGD). SGD ID beta12orEarlier true Unique identifier of a book. Book ID beta12orEarlier (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) The International Standard Book Number (ISBN) is for identifying printed books. ISBN beta12orEarlier B[0-9]{5} Identifier of a metabolite from the 3DMET database. 3DMET ID Compound ID (3DMET) 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]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) A unique identifier of an interaction from the MatrixDB database. MatrixDB interaction ID beta12orEarlier [0-9]+ A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. These identifiers are unique within the cPath database, however, they are not stable between releases. cPath ID beta12orEarlier true [0-9]+ Identifier of an assay from the PubChem database. PubChem bioassay ID beta12orEarlier Identifier of an entry from the PubChem database. PubChem identifier PubChem ID beta12orEarlier M[0-9]{4} Identifier of an enzyme reaction mechanism from the MACie database. MACie entry number Reaction ID (MACie) beta12orEarlier MI[0-9]{7} Identifier for a gene from the miRBase database. miRNA ID miRNA identifier miRNA name Gene ID (miRBase) beta12orEarlier ZDB\-GENE\-[0-9]+\-[0-9]+ Identifier for a gene from the Zebrafish information network genome (ZFIN) database. Gene ID (ZFIN) beta12orEarlier [0-9]{5} Identifier of an enzyme-catalysed reaction from the Rhea database. Reaction ID (Rhea) beta12orEarlier UPA[0-9]{5} Identifier of a biological pathway from the Unipathway database. upaid Pathway ID (Unipathway) beta12orEarlier [0-9]+ Identifier of a small molecular from the ChEMBL database. ChEMBL ID Compound ID (ChEMBL) beta12orEarlier [a-zA-Z_0-9]+ Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. LGICdb identifier beta12orEarlier [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. Reaction kinetics ID (SABIO-RK) beta12orEarlier PA[0-9]+ Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). PharmGKB ID beta12orEarlier PA[0-9]+ Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Pathway ID (PharmGKB) beta12orEarlier PA[0-9]+ Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Disease ID (PharmGKB) beta12orEarlier PA[0-9]+ Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Drug ID (PharmGKB) beta12orEarlier DAP[0-9]+ Identifier of a drug from the Therapeutic Target Database (TTD). Drug ID (TTD) beta12orEarlier TTDS[0-9]+ Identifier of a target protein from the Therapeutic Target Database (TTD). Target ID (TTD) beta12orEarlier true A unique identifier of a type or group of cells. Cell type identifier beta12orEarlier [0-9]+ A unique identifier of a neuron from the NeuronDB database. NeuronDB ID beta12orEarlier [a-zA-Z_0-9]+ A unique identifier of a neuron from the NeuroMorpho database. NeuroMorpho ID beta12orEarlier [0-9]+ Identifier of a chemical from the ChemIDplus database. ChemIDplus ID Compound ID (ChemIDplus) beta12orEarlier SMP[0-9]{5} Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). Pathway ID (SMPDB) beta12orEarlier [0-9]+ Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. BioNumbers ID beta12orEarlier T3D[0-9]+ Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. T3DB ID beta12orEarlier true Identifier of a carbohydrate. Carbohydrate identifier beta12orEarlier [0-9]+ Identifier of an entry from the GlycomeDB database. GlycomeDB ID beta12orEarlier [a-zA-Z_0-9]+[0-9]+ Identifier of an entry from the LipidBank database. LipidBank ID beta12orEarlier cd[0-9]{5} Identifier of a conserved domain from the Conserved Domain Database. CDD ID beta12orEarlier [0-9]{1,5} An identifier of an entry from the MMDB database. MMDB accession MMDB ID beta12orEarlier [0-9]+ Unique identifier of an entry from the iRefIndex database of protein-protein interactions. iRefIndex ID beta12orEarlier [0-9]+ Unique identifier of an entry from the ModelDB database. ModelDB ID beta12orEarlier [0-9]+ Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). Pathway ID (DQCS) beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). Ensembl ID (Homo sapiens) true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). Ensembl ID ('Bos taurus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). Ensembl ID ('Canis familiaris') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). Ensembl ID ('Cavia porcellus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). Ensembl ID ('Ciona intestinalis') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). Ensembl ID ('Ciona savignyi') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). Ensembl ID ('Danio rerio') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). Ensembl ID ('Dasypus novemcinctus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). Ensembl ID ('Echinops telfairi') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). Ensembl ID ('Erinaceus europaeus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). Ensembl ID ('Felis catus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). Ensembl ID ('Gallus gallus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). Ensembl ID ('Gasterosteus aculeatus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). Ensembl ID ('Homo sapiens') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). Ensembl ID ('Loxodonta africana') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). Ensembl ID ('Macaca mulatta') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). Ensembl ID ('Monodelphis domestica') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). Ensembl ID ('Mus musculus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). Ensembl ID ('Myotis lucifugus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). Ensembl ID ("Ornithorhynchus anatinus") true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). Ensembl ID ('Oryctolagus cuniculus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). Ensembl ID ('Oryzias latipes') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). Ensembl ID ('Otolemur garnettii') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). Ensembl ID ('Pan troglodytes') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). Ensembl ID ('Rattus norvegicus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). Ensembl ID ('Spermophilus tridecemlineatus') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). Ensembl ID ('Takifugu rubripes') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). Ensembl ID ('Tupaia belangeri') true beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xen