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 a community project and its development can be followed and contributed to at https://github.com/edamontology/edamontology. 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. https://github.com/edamontology/edamontology/graphs/contributors and many more! Federico Bianchini Hervé Ménager Jon Ison Matúš Kalaš 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. application/rdf+xml EDAM - The ontology of data analysis and management unstable(1.26) 1.25-20240924T0027Z-unstable(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 '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 "Supported by the given data format" here means, that the given format enables representation of data that satisfies the 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' 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. Related term 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. data_0005 beta12orEarlier beta12orEarlier A type of computational resource used in bioinformatics. Resource type true data_0006 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). data_0007 beta12orEarlier beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. Tool true data_0581 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 data_0582 beta12orEarlier An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. Ontology data_0583 beta12orEarlier 1.5 A directory on disk from which files are read. Directory metadata true data_0831 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 data_0832 beta12orEarlier beta12orEarlier Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. HGNC vocabulary true data_0835 beta12orEarlier beta12orEarlier Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). UMLS vocabulary true data_0842 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. data_0843 beta12orEarlier beta12orEarlier An entry (retrievable via URL) from a biological database. Database entry true data_0844 beta12orEarlier Mass of a molecule. Molecular mass data_0845 beta12orEarlier PDBML:pdbx_formal_charge Net charge of a molecule. Molecular charge data_0846 beta12orEarlier A specification of a chemical structure. Chemical structure specification Chemical formula data_0847 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 data_0848 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 data_0849 beta12orEarlier SO:2000061 A molecular sequence and associated metadata. Sequence record http://purl.bioontology.org/ontology/MSH/D058977 data_0850 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 data_0851 beta12orEarlier 1.5 A character used to replace (mask) other characters in a molecular sequence. Sequence mask character true data_0852 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 data_0853 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 data_0854 beta12orEarlier 1.5 A specification of sequence length(s). Sequence length specification true data_0855 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 data_0856 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 data_0857 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 data_0858 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 data_0859 beta12orEarlier beta12orEarlier Data files used by motif or profile methods. Sequence signature model true data_0860 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 data_0861 beta12orEarlier 1.5 Alignment of exact matches between subsequences (words) within two or more molecular sequences. Sequence alignment (words) true data_0862 beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. Dotplot data_0863 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 data_0864 beta12orEarlier 1.5 Some simple value controlling a sequence alignment (or similar 'match') operation. Sequence alignment parameter true data_0865 beta12orEarlier A value representing molecular sequence similarity. Sequence similarity score data_0866 beta12orEarlier 1.5 Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. Sequence alignment metadata true data_0867 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 data_0868 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 data_0869 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 data_0870 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 data_0871 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 data_0872 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 data_0874 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 data_0875 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 data_0876 beta12orEarlier 1.8 Secondary structure (predicted or real) of a protein. Protein features report (secondary structure) true data_0877 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 data_0878 beta12orEarlier true Alignment of the (1D representations of) secondary structure of two or more proteins. Secondary structure alignment (protein) Protein secondary structure alignment data_0879 beta12orEarlier beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. Secondary structure alignment metadata (protein) true data_0880 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 data_0881 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 data_0882 beta12orEarlier beta12orEarlier An informative report of RNA secondary structure alignment-derived data or metadata. Secondary structure alignment metadata (RNA) true data_0883 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 data_0884 beta12orEarlier beta12orEarlier An entry from a molecular tertiary (3D) structure database. Tertiary structure record true data_0885 beta12orEarlier 1.8 Results (hits) from searching a database of tertiary structure. Structure database search results true data_0886 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 data_0887 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 data_0888 beta12orEarlier A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. Structure similarity score data_0889 beta12orEarlier Some type of structural (3D) profile or template (representing a structure or structure alignment). 3D profile Structural (3D) profile Structural profile data_0890 beta12orEarlier A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). Structural profile alignment Structural (3D) profile alignment data_0891 beta12orEarlier 1.5 An alignment of a sequence to a 3D profile (representing structures or a structure alignment). Sequence-3D profile alignment true data_0892 beta12orEarlier Matrix of values used for scoring sequence-structure compatibility. Protein sequence-structure scoring matrix data_0893 beta12orEarlier An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). Sequence-structure alignment data_0894 beta12orEarlier 1.4 An informative report about a specific amino acid. Amino acid annotation true data_0895 beta12orEarlier 1.4 An informative report about a specific peptide. Peptide annotation true data_0896 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 data_0897 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 data_0899 beta12orEarlier 1.8 3D structural motifs in a protein. Protein structural motifs and surfaces true data_0900 beta12orEarlier 1.5 Data concerning the classification of the sequences and/or structures of protein structural domain(s). Protein domain classification true data_0901 beta12orEarlier 1.8 structural domains or 3D folds in a protein or polypeptide chain. Protein features report (domains) true data_0902 beta12orEarlier 1.4 An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. Protein architecture report true data_0903 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 data_0904 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 data_0905 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 data_0906 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 data_0907 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 data_0909 beta12orEarlier The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. Vmax data_0910 beta12orEarlier Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. Km data_0911 beta12orEarlier 1.4 An informative report about a specific nucleotide base. Nucleotide base annotation true data_0912 beta12orEarlier 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 Nucleic acid structural properties stiffness, curvature, twist/roll data or other conformational parameters or properties. This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid property data_0914 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 data_0916 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 data_0917 beta12orEarlier beta12orEarlier A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. Gene classification true data_0918 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 data_0919 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 data_0920 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 data_0923 beta12orEarlier 1.8 PCR experiments, e.g. quantitative real-time PCR. PCR experiment report true data_0924 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 data_0925 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'. data_0926 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 data_0927 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 data_0928 beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. Gene expression pattern Gene expression profile data_0931 beta12orEarlier 1.8 microarray experiments including conditions, protocol, sample:data relationships etc. Microarray experiment report true data_0932 beta12orEarlier beta13 Data on oligonucleotide probes (typically for use with DNA microarrays). Oligonucleotide probe data true data_0933 beta12orEarlier beta12orEarlier Output from a serial analysis of gene expression (SAGE) experiment. SAGE experimental data true data_0934 beta12orEarlier beta12orEarlier Massively parallel signature sequencing (MPSS) data. MPSS experimental data true data_0935 beta12orEarlier beta12orEarlier Sequencing by synthesis (SBS) data. SBS experimental data true data_0936 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 data_0937 beta12orEarlier Protein X-ray crystallographic data X-ray crystallography data. Electron density map data_0938 beta12orEarlier Nuclear magnetic resonance (NMR) raw data, typically for a protein. Protein NMR data Raw NMR data data_0939 beta12orEarlier Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. CD spectrum Protein circular dichroism (CD) spectroscopic data CD spectra data_0940 beta12orEarlier Volume map data from electron microscopy. 3D volume map EM volume map Electron microscopy volume map Volume map data_0941 beta12orEarlier 1.19 Annotation on a structural 3D model (volume map) from electron microscopy. Electron microscopy model true data_0942 beta12orEarlier Two-dimensional gel electrophoresis image. 2D PAGE image data_0943 beta12orEarlier Spectra from mass spectrometry. Mass spectrometry spectra Mass spectrum data_0944 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 data_0945 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 data_0946 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 data_0947 beta12orEarlier beta12orEarlier A map (typically a diagram) of a biological pathway. Biological pathway map true data_0948 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 data_0949 beta12orEarlier Basic information, annotation or documentation concerning a workflow (but not the workflow itself). Workflow metadata data_0950 beta12orEarlier A biological model represented in mathematical terms. Biological model Mathematical model data_0951 beta12orEarlier A value representing estimated statistical significance of some observed data; typically sequence database hits. Statistical estimate score data_0952 beta12orEarlier 1.5 Resource definition for an EMBOSS database. EMBOSS database resource definition true data_0953 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 data_0954 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 data_0955 beta12orEarlier An index of data of biological relevance. Data index data_0956 beta12orEarlier A human-readable collection of information concerning an analysis of an index of biological data. Database index annotation Data index report data_0957 beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. Database metadata data_0958 beta12orEarlier Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. Tool metadata data_0959 beta12orEarlier 1.5 Textual metadata on a submitted or completed job. Job metadata true data_0960 beta12orEarlier Textual metadata on a software author or end-user, for example a person or other software. User metadata data_0962 beta12orEarlier A human-readable collection of information about a specific chemical compound. Chemical compound annotation Chemical structure report Small molecule annotation Small molecule report data_0963 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 data_0964 beta12orEarlier 1.4 An informative report about a specific scent. Scent annotation true data_0966 beta12orEarlier A term (name) from an ontology. Ontology class name Ontology terms Ontology term data_0967 beta12orEarlier Data concerning or derived from a concept from a biological ontology. Ontology class metadata Ontology term metadata Ontology concept data data_0968 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 data_0970 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 data_0971 beta12orEarlier A scientific text, typically a full text article from a scientific journal. Article text Scientific article Article data_0972 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 data_0974 beta12orEarlier beta12orEarlier An identifier of a biological entity or phenomenon. Entity identifier true data_0975 beta12orEarlier beta12orEarlier An identifier of a data resource. Data resource identifier true data_0976 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) data_0977 beta12orEarlier true An identifier of a bioinformatics tool, e.g. an application or web service. Tool identifier data_0978 beta12orEarlier beta12orEarlier Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). Discrete entity identifier true data_0979 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 data_0980 beta12orEarlier beta12orEarlier Name or other identifier of a collection of discrete biological entities. Entity collection identifier true data_0981 beta12orEarlier beta12orEarlier Name or other identifier of a physical, observable biological occurrence or event. Phenomenon identifier true data_0982 beta12orEarlier true Name or other identifier of a molecule. Molecule identifier data_0983 beta12orEarlier true Identifier (e.g. character symbol) of a specific atom. Atom identifier Atom ID data_0984 beta12orEarlier true Name of a specific molecule. Molecule name data_0985 beta12orEarlier 1.5 A label (text token) describing the type a molecule. For example, 'Protein', 'DNA', 'RNA' etc. Molecule type true data_0986 beta12orEarlier beta12orEarlier Unique identifier of a chemical compound. Chemical identifier true data_0987 beta12orEarlier Name of a chromosome. Chromosome name data_0988 beta12orEarlier true Identifier of a peptide chain. Peptide identifier data_0989 beta12orEarlier true Identifier of a protein. Protein identifier data_0990 beta12orEarlier Unique name of a chemical compound. Chemical name Compound name data_0991 beta12orEarlier Unique registry number of a chemical compound. Chemical registry number data_0992 beta12orEarlier beta12orEarlier Code word for a ligand, for example from a PDB file. Ligand identifier true data_0993 beta12orEarlier true Identifier of a drug. Drug identifier data_0994 beta12orEarlier true Identifier of an amino acid. Residue identifier Amino acid identifier data_0995 beta12orEarlier true Name or other identifier of a nucleotide. Nucleotide identifier data_0996 beta12orEarlier true Identifier of a monosaccharide. Monosaccharide identifier data_0997 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) data_0998 beta12orEarlier IUPAC recommended name of a chemical compound. IUPAC chemical name Chemical name (IUPAC) data_0999 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) data_1000 beta12orEarlier Brand name of a chemical compound. Brand chemical name Chemical name (brand) data_1001 beta12orEarlier Synonymous name of a chemical compound. Synonymous chemical name Chemical name (synonymous) data_1002 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 data_1003 beta12orEarlier Beilstein registry number of a chemical compound. Beilstein chemical registry number Chemical registry number (Beilstein) data_1004 beta12orEarlier Gmelin registry number of a chemical compound. Gmelin chemical registry number Chemical registry number (Gmelin) data_1005 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 data_1006 beta12orEarlier String of one or more ASCII characters representing an amino acid. Amino acid name data_1007 beta12orEarlier String of one or more ASCII characters representing a nucleotide. Nucleotide code data_1008 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 data_1009 beta12orEarlier Name of a protein. Protein name data_1010 beta12orEarlier Name or other identifier of an enzyme or record from a database of enzymes. Enzyme identifier data_1011 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 data_1012 beta12orEarlier Name of an enzyme. Enzyme name data_1013 beta12orEarlier Name of a restriction enzyme. Restriction enzyme name data_1014 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 data_1015 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 data_1016 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 data_1017 beta12orEarlier Specification of range(s) of sequence positions. Sequence range data_1018 beta12orEarlier beta12orEarlier Name or other identifier of an nucleic acid feature. Nucleic acid feature identifier true data_1019 beta12orEarlier beta12orEarlier Name or other identifier of a protein feature. Protein feature identifier true data_1020 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 data_1021 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 data_1022 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 data_1023 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 data_1024 beta12orEarlier beta12orEarlier String of one or more ASCII characters representing a codon. Codon name true data_1025 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 data_1026 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 data_1027 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) data_1028 beta12orEarlier beta12orEarlier An NCBI RefSeq unique identifier of a gene. Gene identifier (NCBI RefSeq) true data_1029 beta12orEarlier beta12orEarlier An NCBI UniGene unique identifier of a gene. Gene identifier (NCBI UniGene) true data_1030 beta12orEarlier beta12orEarlier An Entrez unique identifier of a gene. Gene identifier (Entrez) true data_1031 beta12orEarlier Identifier of a gene or feature from the CGD database. CGD ID Gene ID (CGD) data_1032 beta12orEarlier Identifier of a gene from DictyBase. Gene ID (DictyBase) data_1033 beta12orEarlier Unique identifier for a gene (or other feature) from the Ensembl database. Gene ID (Ensembl) Ensembl gene ID data_1034 beta12orEarlier S[0-9]+ Identifier of an entry from the SGD database. SGD identifier Gene ID (SGD) data_1035 beta12orEarlier [a-zA-Z_0-9\.-]* Moby_namespace:GeneDB Identifier of a gene from the GeneDB database. GeneDB identifier Gene ID (GeneDB) data_1036 beta12orEarlier Identifier of an entry from the TIGR database. TIGR identifier data_1037 beta12orEarlier Gene:[0-9]{7} Identifier of an gene from the TAIR database. TAIR accession (gene) data_1038 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 data_1039 beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. SCOP domain identifier data_1040 beta12orEarlier 1nr3A00 Identifier of a protein domain from CATH. CATH domain identifier CATH domain ID data_1041 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) data_1042 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 data_1043 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 data_1044 beta12orEarlier The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). Kingdom name data_1045 beta12orEarlier The name of a species (typically a taxonomic group) of organism. Organism species Species name data_1046 beta12orEarlier The name of a strain of an organism variant, typically a plant, virus or bacterium. Strain name data_1047 beta12orEarlier true A string of characters that name or otherwise identify a resource on the Internet. URIs URI data_1048 beta12orEarlier true An identifier of a biological or bioinformatics database. Database identifier Database ID data_1049 beta12orEarlier The name of a directory. Directory name data_1050 beta12orEarlier The name (or part of a name) of a file (of any type). File name data_1051 beta12orEarlier Name of an ontology of biological or bioinformatics concepts and relations. Ontology name data_1052 beta12orEarlier Moby:Link Moby:URL A Uniform Resource Locator (URL). URL data_1053 beta12orEarlier A Uniform Resource Name (URN). URN data_1055 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 data_1056 beta12orEarlier The name of a biological or bioinformatics database. Database name data_1057 beta12orEarlier beta13 The name of a molecular sequence database. Sequence database name true data_1058 beta12orEarlier The name of a file (of any type) with restricted possible values. Enumerated file name data_1059 beta12orEarlier The extension of a file name. A file extension is the characters appearing after the final '.' in the file name. File name extension data_1060 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 data_1061 beta12orEarlier Name of a QSAR descriptor. QSAR descriptor name data_1062 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 data_1063 beta12orEarlier true An identifier of molecular sequence(s) or entries from a molecular sequence database. Sequence identifier data_1064 beta12orEarlier true An identifier of a set of molecular sequence(s). Sequence set ID data_1065 beta12orEarlier beta12orEarlier Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. Sequence signature identifier true data_1066 beta12orEarlier true Identifier of a molecular sequence alignment, for example a record from an alignment database. Sequence alignment ID data_1067 beta12orEarlier beta12orEarlier Identifier of a phylogenetic distance matrix. Phylogenetic distance matrix identifier true data_1068 beta12orEarlier true Identifier of a phylogenetic tree for example from a phylogenetic tree database. Phylogenetic tree ID data_1069 beta12orEarlier true An identifier of a comparison matrix. Substitution matrix identifier Comparison matrix identifier data_1070 beta12orEarlier true A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. Structure ID data_1071 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 data_1072 beta12orEarlier true Identifier of an entry from a database of tertiary structure alignments. Structure alignment ID data_1073 beta12orEarlier true Identifier of an index of amino acid physicochemical and biochemical property data. Amino acid index ID data_1074 beta12orEarlier true Molecular interaction ID Identifier of a report of protein interactions from a protein interaction database (typically). Protein interaction ID data_1075 beta12orEarlier true Identifier of a protein family. Protein secondary database record identifier Protein family identifier data_1076 beta12orEarlier Unique name of a codon usage table. Codon usage table name data_1077 beta12orEarlier true Identifier of a transcription factor (or a TF binding site). Transcription factor identifier data_1078 beta12orEarlier true Identifier of an entry from a database of microarray data. Experiment annotation ID data_1079 beta12orEarlier true Identifier of an entry from a database of electron microscopy data. Electron microscopy model ID data_1080 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 data_1081 beta12orEarlier true Identifier of an entry from a database of genotypes and phenotypes. Genotype and phenotype annotation ID data_1082 beta12orEarlier true Identifier of an entry from a database of biological pathways or networks. Pathway or network identifier data_1083 beta12orEarlier true Identifier of a biological or biomedical workflow, typically from a database of workflows. Workflow ID data_1084 beta12orEarlier true Identifier of a data type definition from some provider. Data resource definition identifier Data resource definition ID data_1085 beta12orEarlier true Identifier of a mathematical model, typically an entry from a database. Biological model identifier Biological model ID data_1086 beta12orEarlier true Identifier of an entry from a database of chemicals. Chemical compound identifier Compound ID Small molecule identifier Compound identifier data_1087 beta12orEarlier A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. Ontology concept ID data_1088 beta12orEarlier true Unique identifier of a scientific article. Article identifier Article ID data_1089 beta12orEarlier FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. FlyBase ID data_1091 beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. WormBase name data_1092 beta12orEarlier Class of an object from the WormBase database. A WormBase class describes the type of object such as 'sequence' or 'protein'. WormBase class data_1093 beta12orEarlier true A persistent, unique identifier of a molecular sequence database entry. Sequence accession number Sequence accession data_1094 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 data_1095 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 data_1096 beta12orEarlier true Accession number of a protein sequence database entry. Protein sequence accession number Sequence accession (protein) data_1097 beta12orEarlier true Accession number of a nucleotide sequence database entry. Nucleotide sequence accession number Sequence accession (nucleic acid) data_1098 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 data_1099 beta12orEarlier 1.0 Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. UniProt accession (extended) true data_1100 beta12orEarlier An identifier of PIR sequence database entry. PIR ID PIR accession number PIR identifier data_1101 beta12orEarlier 1.2 Identifier of a TREMBL sequence database entry. TREMBL accession true data_1102 beta12orEarlier Primary identifier of a Gramene database entry. Gramene primary ID Gramene primary identifier data_1103 beta12orEarlier Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. EMBL/GenBank/DDBJ ID data_1104 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) data_1105 beta12orEarlier Identifier of a dbEST database entry. dbEST ID dbEST accession data_1106 beta12orEarlier Identifier of a dbSNP database entry. dbSNP identifier dbSNP ID data_1110 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 data_1111 beta12orEarlier 1.5 List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). EMBOSS listfile true data_1112 beta12orEarlier true An identifier of a cluster of molecular sequence(s). Sequence cluster ID data_1113 beta12orEarlier Unique identifier of an entry from the COG database. COG ID Sequence cluster ID (COG) data_1114 beta12orEarlier true Identifier of a sequence motif, for example an entry from a motif database. Sequence motif identifier data_1115 beta12orEarlier true Identifier of a sequence profile. A sequence profile typically represents a sequence alignment. Sequence profile ID data_1116 beta12orEarlier Identifier of an entry from the ELMdb database of protein functional sites. ELM ID data_1117 beta12orEarlier PS[0-9]{5} Accession number of an entry from the Prosite database. Prosite ID Prosite accession number data_1118 beta12orEarlier Unique identifier or name of a HMMER hidden Markov model. HMMER hidden Markov model ID data_1119 beta12orEarlier Unique identifier or name of a profile from the JASPAR database. JASPAR profile ID data_1120 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 data_1121 beta12orEarlier beta12orEarlier The type of a BLAST sequence alignment. BLAST sequence alignment type true data_1122 beta12orEarlier 1.5 A label (text token) describing the type of a phylogenetic tree. For example 'nj', 'upgmp' etc. Phylogenetic tree type true data_1123 beta12orEarlier Accession number of an entry from the TreeBASE database. TreeBASE study accession number data_1124 beta12orEarlier Accession number of an entry from the TreeFam database. TreeFam accession number data_1125 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 data_1126 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 data_1127 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 data_1128 beta12orEarlier Identifier of an entry from the AAindex database. AAindex ID data_1129 beta12orEarlier Accession number of an entry from the BIND database. BIND accession number data_1130 beta12orEarlier EBI\-[0-9]+ Accession number of an entry from the IntAct database. IntAct accession number data_1131 beta12orEarlier Name of a protein family. Protein family name data_1132 beta12orEarlier Name of an InterPro entry, usually indicating the type of protein matches for that entry. InterPro entry name data_1133 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 data_1134 beta12orEarlier Secondary accession number of an InterPro entry. InterPro secondary accession number InterPro secondary accession data_1135 beta12orEarlier Unique identifier of an entry from the Gene3D database. Gene3D ID data_1136 beta12orEarlier PIRSF[0-9]{6} Unique identifier of an entry from the PIRSF database. PIRSF ID data_1137 beta12orEarlier PR[0-9]{5} The unique identifier of an entry in the PRINTS database. PRINTS code data_1138 beta12orEarlier PF[0-9]{5} Accession number of a Pfam entry. Pfam accession number data_1139 beta12orEarlier SM[0-9]{5} Accession number of an entry from the SMART database. SMART accession number data_1140 beta12orEarlier Unique identifier (number) of a hidden Markov model from the Superfamily database. Superfamily hidden Markov model number data_1141 beta12orEarlier Accession number of an entry (family) from the TIGRFam database. TIGRFam accession number TIGRFam ID data_1142 beta12orEarlier PD[0-9]+ A ProDom domain family accession number. ProDom is a protein domain family database. ProDom accession number data_1143 beta12orEarlier Identifier of an entry from the TRANSFAC database. TRANSFAC accession number data_1144 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 data_1145 beta12orEarlier [0-9]+ PRIDE experiment accession number. PRIDE experiment accession number data_1146 beta12orEarlier Identifier of an entry from the EMDB electron microscopy database. EMDB ID data_1147 beta12orEarlier [GDS|GPL|GSE|GSM][0-9]+ Accession number of an entry from the GEO database. GEO accession number data_1148 beta12orEarlier Identifier of an entry from the GermOnline database. GermOnline ID data_1149 beta12orEarlier Identifier of an entry from the EMAGE database. EMAGE ID data_1150 beta12orEarlier true Accession number of an entry from a database of disease. Disease ID data_1151 beta12orEarlier Identifier of an entry from the HGVbase database. HGVbase ID data_1152 beta12orEarlier beta12orEarlier Identifier of an entry from the HIVDB database. HIVDB identifier true data_1153 beta12orEarlier [*#+%^]?[0-9]{6} Identifier of an entry from the OMIM database. OMIM ID data_1154 beta12orEarlier Unique identifier of an object from one of the KEGG databases (excluding the GENES division). KEGG object identifier data_1155 beta12orEarlier REACT_[0-9]+(\.[0-9]+)? Identifier of an entry from the Reactome database. Reactome ID Pathway ID (reactome) data_1156 beta12orEarlier beta12orEarlier Identifier of an entry from the aMAZE database. Pathway ID (aMAZE) true data_1157 beta12orEarlier Identifier of an pathway from the BioCyc biological pathways database. BioCyc pathway ID Pathway ID (BioCyc) data_1158 beta12orEarlier Identifier of an entry from the INOH database. INOH identifier Pathway ID (INOH) data_1159 beta12orEarlier Identifier of an entry from the PATIKA database. PATIKA ID Pathway ID (PATIKA) data_1160 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) data_1161 beta12orEarlier PTHR[0-9]{5} Identifier of a biological pathway from the Panther Pathways database. Panther Pathways ID Pathway ID (Panther) data_1162 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 data_1163 beta12orEarlier The name of a data type from the MIRIAM database. MIRIAM data type name data_1164 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 data_1165 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'. data_1166 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 data_1167 beta12orEarlier Unique identifier of a Taverna workflow. Taverna workflow ID data_1170 beta12orEarlier Name of a biological (mathematical) model. Biological model name data_1171 beta12orEarlier (BIOMD|MODEL)[0-9]{10} Unique identifier of an entry from the BioModel database. BioModel ID data_1172 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 data_1173 beta12orEarlier [0-9]+ Identifier of an entry from the ChemSpider database. ChemSpider ID data_1174 beta12orEarlier CHEBI:[0-9]+ Identifier of an entry from the ChEBI database. ChEBI IDs ChEBI identifier ChEBI ID data_1175 beta12orEarlier An identifier of a concept from the BioPax ontology. BioPax concept ID data_1176 beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a concept from The Gene Ontology. GO concept identifier GO concept ID data_1177 beta12orEarlier An identifier of a concept from the MeSH vocabulary. MeSH concept ID data_1178 beta12orEarlier An identifier of a concept from the HGNC controlled vocabulary. HGNC concept ID data_1179 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 data_1180 beta12orEarlier An identifier of a concept from the Plant Ontology (PO). Plant Ontology concept ID data_1181 beta12orEarlier An identifier of a concept from the UMLS vocabulary. UMLS concept ID data_1182 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 data_1183 beta12orEarlier An identifier of a concept from the EMAP mouse ontology. EMAP concept ID data_1184 beta12orEarlier An identifier of a concept from the ChEBI ontology. ChEBI concept ID data_1185 beta12orEarlier An identifier of a concept from the MGED ontology. MGED concept ID data_1186 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 data_1187 beta12orEarlier 4963447 [1-9][0-9]{0,8} PubMed unique identifier of an article. PMID PubMed ID data_1188 beta12orEarlier (doi\:)?[0-9]{2}\.[0-9]{4}/.* Digital Object Identifier (DOI) of a published article. Digital Object Identifier DOI data_1189 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 data_1190 beta12orEarlier The name of a computer package, application, method or function. Tool name data_1191 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) data_1192 beta12orEarlier The name of a BLAST tool. BLAST name This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. Tool name (BLAST) data_1193 beta12orEarlier The name of a FASTA tool. This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. Tool name (FASTA) data_1194 beta12orEarlier The name of an EMBOSS application. Tool name (EMBOSS) data_1195 beta12orEarlier The name of an EMBASSY package. Tool name (EMBASSY package) data_1201 beta12orEarlier A QSAR constitutional descriptor. QSAR constitutional descriptor QSAR descriptor (constitutional) data_1202 beta12orEarlier A QSAR electronic descriptor. QSAR electronic descriptor QSAR descriptor (electronic) data_1203 beta12orEarlier A QSAR geometrical descriptor. QSAR geometrical descriptor QSAR descriptor (geometrical) data_1204 beta12orEarlier A QSAR topological descriptor. QSAR topological descriptor QSAR descriptor (topological) data_1205 beta12orEarlier A QSAR molecular descriptor. QSAR molecular descriptor QSAR descriptor (molecular) data_1233 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) data_1234 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) data_1235 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 data_1236 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 data_1237 beta12orEarlier beta12orEarlier Sequences generated by HMMER package in FASTA-style format. HMMER synthetic sequences set true data_1238 beta12orEarlier A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. Proteolytic digest data_1239 beta12orEarlier SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. Restriction digest data_1240 beta12orEarlier Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. PCR primers data_1241 beta12orEarlier beta12orEarlier File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. vectorstrip cloning vector definition file true data_1242 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 data_1243 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 data_1244 beta12orEarlier beta12orEarlier File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. primersearch primer pairs sequence record true data_1245 beta12orEarlier A cluster of protein sequences. Protein sequence cluster The sequences are typically related, for example a family of sequences. Sequence cluster (protein) data_1246 beta12orEarlier A cluster of nucleotide sequences. Nucleotide sequence cluster The sequences are typically related, for example a family of sequences. Sequence cluster (nucleic acid) data_1249 beta12orEarlier The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. Sequence length data_1250 beta12orEarlier 1.5 Size of a sequence word. Word size is used for example in word-based sequence database search methods. Word size true data_1251 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 data_1252 beta12orEarlier 1.5 Specification of range(s) of length of sequences. Sequence length range true data_1253 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 data_1254 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 data_1255 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 data_1256 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 data_1257 beta12orEarlier beta12orEarlier A report of general sequence properties derived from protein sequence data. Sequence property (protein) true data_1258 beta12orEarlier beta12orEarlier A report of general sequence properties derived from nucleotide sequence data. Sequence property (nucleic acid) true data_1259 beta12orEarlier A report on sequence complexity, for example low-complexity or repeat regions in sequences. Sequence property (complexity) Sequence complexity report data_1260 beta12orEarlier A report on ambiguity in molecular sequence(s). Sequence property (ambiguity) Sequence ambiguity report data_1261 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 data_1262 beta12orEarlier A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. Peptide molecular weight hits data_1263 beta12orEarlier A plot of third base position variability in a nucleotide sequence. Base position variability plot data_1264 beta12orEarlier beta12orEarlier A table of character or word composition / frequency of a molecular sequence. Sequence composition table true data_1265 beta12orEarlier A table of base frequencies of a nucleotide sequence. Base frequencies table data_1266 beta12orEarlier A table of word composition of a nucleotide sequence. Base word frequencies table data_1267 beta12orEarlier A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) Amino acid frequencies table data_1268 beta12orEarlier A table of amino acid word composition of a protein sequence. Sequence composition (amino acid words) Amino acid word frequencies table data_1269 beta12orEarlier beta12orEarlier Annotation of a molecular sequence in DAS format. DAS sequence feature annotation true data_1270 beta12orEarlier Annotation of positional sequence features, organised into a standard feature table. Sequence feature table Feature table data_1274 beta12orEarlier A map of (typically one) DNA sequence annotated with positional or non-positional features. DNA map Map data_1276 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 data_1277 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 data_1278 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 data_1279 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 data_1280 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 data_1281 beta12orEarlier beta12orEarlier Image of a sequence with matches to signatures, motifs or profiles. Sequence signature map true data_1283 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 data_1284 beta12orEarlier A gene map showing distances between loci based on relative cotransduction frequencies. DNA transduction map data_1285 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 data_1286 beta12orEarlier Sequence map of a plasmid (circular DNA). Plasmid map data_1288 beta12orEarlier Sequence map of a whole genome. Genome map data_1289 beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. Restriction map data_1290 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 data_1291 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 data_1292 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 data_1293 beta12orEarlier beta12orEarlier SMART protein schematic in PNG format. SMART protein schematic true data_1294 beta12orEarlier beta12orEarlier Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. GlobPlot domain image true data_1298 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 data_1299 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 data_1300 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 data_1301 beta12orEarlier 1.8 regions of a nucleic acid sequence containing mobile genetic elements. Mobile genetic elements true data_1303 beta12orEarlier 1.5 A report on quadruplex-forming motifs in a nucleotide sequence. Nucleic acid features (quadruplexes) true data_1306 beta12orEarlier 1.8 Report on nucleosome formation potential or exclusion sequence(s). Nucleosome exclusion sequences true data_1309 beta12orEarlier beta13 A report on exonic splicing enhancers (ESE) in an exon. Gene features (exonic splicing enhancer) true data_1310 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 data_1313 beta12orEarlier 1.8 protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Coding region true data_1314 beta12orEarlier beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. Gene features (SECIS element) true data_1315 beta12orEarlier 1.8 transcription factor binding sites (TFBS) in a DNA sequence. Transcription factor binding sites true data_1321 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 data_1322 beta12orEarlier 1.8 signal peptides or signal peptide cleavage sites in protein sequences. Protein features report (signal peptides) true data_1323 beta12orEarlier 1.8 cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. Protein features report (cleavage sites) true data_1324 beta12orEarlier 1.8 post-translation modifications in a protein sequence, typically describing the specific sites involved. Protein features (post-translation modifications) true data_1325 beta12orEarlier 1.8 catalytic residues (active site) of an enzyme. Protein features report (active sites) true data_1326 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 data_1327 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 data_1328 beta12orEarlier 1.8 RNA and DNA-binding proteins and binding sites in protein sequences. Protein features report (nucleic acid binding sites) true data_1329 beta12orEarlier beta12orEarlier A report on epitopes that bind to MHC class I molecules. MHC Class I epitopes report true data_1330 beta12orEarlier beta12orEarlier A report on predicted epitopes that bind to MHC class II molecules. MHC Class II epitopes report true data_1331 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 data_1338 beta12orEarlier beta12orEarlier Scores from a sequence database search (for example a BLAST search). Sequence database hits scores list true data_1339 beta12orEarlier beta12orEarlier Alignments from a sequence database search (for example a BLAST search). Sequence database hits alignments list true data_1340 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 data_1344 beta12orEarlier beta12orEarlier Alphabet for the motifs (patterns) that MEME will search for. MEME motif alphabet true data_1345 beta12orEarlier beta12orEarlier MEME background frequencies file. MEME background frequencies file true data_1346 beta12orEarlier beta12orEarlier File of directives for ordering and spacing of MEME motifs. MEME motifs directive file true data_1347 beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. Dirichlet distribution data_1348 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 data_1352 beta12orEarlier Regular expression pattern. Regular expression data_1353 beta12orEarlier Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. Sequence motif data_1354 beta12orEarlier Some type of statistical model representing a (typically multiple) sequence alignment. Sequence profile http://semanticscience.org/resource/SIO_010531 data_1355 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 data_1358 beta12orEarlier beta12orEarlier A nucleotide regular expression pattern from the Prosite database. Prosite nucleotide pattern true data_1359 beta12orEarlier beta12orEarlier A protein regular expression pattern from the Prosite database. Prosite protein pattern true data_1361 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 data_1362 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 data_1363 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 data_1364 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 data_1365 beta12orEarlier One or more fingerprints (sequence classifiers) as used in the PRINTS database. Fingerprint data_1368 beta12orEarlier beta12orEarlier A protein signature of the type used in the EMBASSY Signature package. Domainatrix signature true data_1371 beta12orEarlier beta12orEarlier NULL hidden Markov model representation used by the HMMER package. HMMER NULL hidden Markov model true data_1372 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 data_1373 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 data_1374 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 data_1375 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 data_1376 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 data_1377 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 data_1378 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 data_1379 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 data_1380 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 data_1381 beta12orEarlier true Alignment of exactly two molecular sequences. Sequence alignment (pair) Pair sequence alignment http://semanticscience.org/resource/SIO_010068 data_1382 beta12orEarlier beta12orEarlier Alignment of more than two molecular sequences. Sequence alignment (multiple) true data_1383 beta12orEarlier Alignment of multiple nucleotide sequences. Sequence alignment (nucleic acid) DNA sequence alignment RNA sequence alignment Nucleic acid sequence alignment data_1384 beta12orEarlier Alignment of multiple protein sequences. Sequence alignment (protein) Protein sequence alignment data_1385 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 data_1386 beta12orEarlier 1.12 Alignment of exactly two nucleotide sequences. Sequence alignment (nucleic acid pair) true data_1387 beta12orEarlier 1.12 Alignment of exactly two protein sequences. Sequence alignment (protein pair) true data_1388 beta12orEarlier beta12orEarlier Alignment of exactly two molecular sequences of different types. Hybrid sequence alignment (pair) true data_1389 beta12orEarlier beta12orEarlier Alignment of more than two nucleotide sequences. Multiple nucleotide sequence alignment true data_1390 beta12orEarlier beta12orEarlier Alignment of more than two protein sequences. Multiple protein sequence alignment true data_1394 beta12orEarlier A simple floating point number defining the penalty for opening or extending a gap in an alignment. Alignment score or penalty data_1395 beta12orEarlier beta12orEarlier Whether end gaps are scored or not. Score end gaps control true data_1396 beta12orEarlier beta12orEarlier Controls the order of sequences in an output sequence alignment. Aligned sequence order true data_1397 beta12orEarlier A penalty for opening a gap in an alignment. Gap opening penalty data_1398 beta12orEarlier A penalty for extending a gap in an alignment. Gap extension penalty data_1399 beta12orEarlier A penalty for gaps that are close together in an alignment. Gap separation penalty data_1400 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 data_1401 beta12orEarlier The score for a 'match' used in various sequence database search applications with simple scoring schemes. Match reward score data_1402 beta12orEarlier The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. Mismatch penalty score data_1403 beta12orEarlier This is the threshold drop in score at which extension of word alignment is halted. Drop off score data_1404 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. Gap opening penalty (integer) true data_1405 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. Gap opening penalty (float) true data_1406 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for extending a gap in an alignment. Gap extension penalty (integer) true data_1407 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for extending a gap in an alignment. Gap extension penalty (float) true data_1408 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for gaps that are close together in an alignment. Gap separation penalty (integer) true data_1409 beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for gaps that are close together in an alignment. Gap separation penalty (float) true data_1410 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 data_1411 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 data_1412 beta12orEarlier Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. Sequence identity data_1413 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 data_1414 beta12orEarlier beta12orEarlier Data on molecular sequence alignment quality (estimated accuracy). Sequence alignment metadata (quality report) true data_1415 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 data_1416 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 data_1417 beta12orEarlier beta12orEarlier Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). Sequence-profile alignment (Domainatrix signature) true data_1418 beta12orEarlier 1.5 Alignment of molecular sequence(s) to a hidden Markov model(s). Sequence-profile alignment (HMM) true data_1420 beta12orEarlier 1.5 Alignment of molecular sequences to a protein fingerprint from the PRINTS database. Sequence-profile alignment (fingerprint) true data_1426 beta12orEarlier Continuous quantitative data that may be read during phylogenetic tree calculation. Phylogenetic continuous quantitative characters Quantitative traits Phylogenetic continuous quantitative data data_1427 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 data_1428 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 data_1429 beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. Phylogenetic report (invariants) Phylogenetic invariants data_1438 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 data_1439 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 data_1440 beta12orEarlier 1.4 Data about the shape of a phylogenetic tree. Phylogenetic tree report (tree shape) true data_1441 beta12orEarlier 1.4 Data on the confidence of a phylogenetic tree. Phylogenetic tree report (tree evaluation) true data_1442 beta12orEarlier Distances, such as Branch Score distance, between two or more phylogenetic trees. Phylogenetic tree report (tree distances) Phylogenetic tree distances data_1443 beta12orEarlier 1.4 Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. Phylogenetic tree report (tree stratigraphic) true data_1444 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 data_1446 beta12orEarlier beta12orEarlier Matrix of integer numbers for sequence comparison. Comparison matrix (integers) true data_1447 beta12orEarlier beta12orEarlier Matrix of floating point numbers for sequence comparison. Comparison matrix (floats) true data_1448 beta12orEarlier Matrix of integer or floating point numbers for nucleotide comparison. Nucleotide comparison matrix Nucleotide substitution matrix Comparison matrix (nucleotide) data_1449 beta12orEarlier Matrix of integer or floating point numbers for amino acid comparison. Amino acid comparison matrix Amino acid substitution matrix Comparison matrix (amino acid) data_1450 beta12orEarlier beta12orEarlier Matrix of integer numbers for nucleotide comparison. Nucleotide comparison matrix (integers) true data_1451 beta12orEarlier beta12orEarlier Matrix of floating point numbers for nucleotide comparison. Nucleotide comparison matrix (floats) true data_1452 beta12orEarlier beta12orEarlier Matrix of integer numbers for amino acid comparison. Amino acid comparison matrix (integers) true data_1453 beta12orEarlier beta12orEarlier Matrix of floating point numbers for amino acid comparison. Amino acid comparison matrix (floats) true data_1459 beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. Nucleic acid structure data_1460 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 data_1461 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 data_1462 beta12orEarlier 3D coordinate and associated data for a carbohydrate (3D) structure. Carbohydrate structure data_1463 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 data_1464 beta12orEarlier 3D coordinate and associated data for a DNA tertiary (3D) structure. DNA structure data_1465 beta12orEarlier 3D coordinate and associated data for an RNA tertiary (3D) structure. RNA structure data_1466 beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. tRNA structure data_1467 beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. Protein chain data_1468 beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. Protein domain data_1469 beta12orEarlier 1.5 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). Protein structure (all atoms) true data_1470 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 data_1471 beta12orEarlier beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). Protein chain (all atoms) true data_1472 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 data_1473 beta12orEarlier beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). Protein domain (all atoms) true data_1474 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 data_1479 beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. Pair structure alignment Structure alignment (pair) data_1480 beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two molecular tertiary (3D) structures. Structure alignment (multiple) true data_1481 beta12orEarlier Alignment (superimposition) of protein tertiary (3D) structures. Structure alignment (protein) Protein structure alignment data_1482 beta12orEarlier Alignment (superimposition) of nucleic acid tertiary (3D) structures. Structure alignment (nucleic acid) Nucleic acid structure alignment data_1483 beta12orEarlier 1.12 Alignment (superimposition) of exactly two protein tertiary (3D) structures. Structure alignment (protein pair) true data_1484 beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two protein tertiary (3D) structures. Multiple protein tertiary structure alignment true data_1485 beta12orEarlier 1.5 Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). Structure alignment (protein all atoms) true data_1486 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 data_1487 beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). Pairwise protein tertiary structure alignment (all atoms) true data_1488 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 data_1489 beta12orEarlier beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). Multiple protein tertiary structure alignment (all atoms) true data_1490 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 data_1491 beta12orEarlier 1.12 Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. Structure alignment (nucleic acid pair) true data_1492 beta12orEarlier beta12orEarlier Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. Multiple nucleic acid tertiary structure alignment true data_1493 beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. Structure alignment (RNA) RNA structure alignment data_1494 beta12orEarlier Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. Structural transformation matrix data_1495 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 data_1496 beta12orEarlier beta12orEarlier A score reflecting structural similarities of two molecules. Molecular similarity score true data_1497 beta12orEarlier Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. RMSD Root-mean-square deviation data_1498 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 data_1499 beta12orEarlier A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. 3D-1D scoring matrix data_1501 beta12orEarlier A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. Amino acid index data_1502 beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. Chemical classes (amino acids) Amino acid index (chemical classes) data_1503 beta12orEarlier Statistical protein contact potentials. Contact potentials (amino acid pair-wise) Amino acid pair-wise contact potentials data_1505 beta12orEarlier Molecular weights of amino acids. Molecular weight (amino acids) Amino acid index (molecular weight) data_1506 beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. Hydropathy (amino acids) Amino acid index (hydropathy) data_1507 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) data_1508 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) data_1509 beta12orEarlier 1.5 An informative report on a specific enzyme. Enzyme report true data_1517 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 data_1519 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 data_1520 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 data_1521 beta12orEarlier The aliphatic index of a protein. The aliphatic index is the relative protein volume occupied by aliphatic side chains. Protein aliphatic index data_1522 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 data_1523 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 data_1524 beta12orEarlier The solubility or atomic solvation energy of a protein sequence or structure. Protein solubility data Protein solubility data_1525 beta12orEarlier Data on the crystallizability of a protein sequence. Protein crystallizability data Protein crystallizability data_1526 beta12orEarlier Data on the stability, intrinsic disorder or globularity of a protein sequence. Protein globularity data Protein globularity data_1527 beta12orEarlier The titration curve of a protein. Protein titration curve data_1528 beta12orEarlier The isoelectric point of one proteins. Protein isoelectric point data_1529 beta12orEarlier The pKa value of a protein. Protein pKa value data_1530 beta12orEarlier The hydrogen exchange rate of a protein. Protein hydrogen exchange rate data_1531 beta12orEarlier The extinction coefficient of a protein. Protein extinction coefficient data_1532 beta12orEarlier The optical density of a protein. Protein optical density data_1533 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 data_1534 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 data_1536 beta12orEarlier beta13 A report on the immunogenicity of MHC class I or class II binding peptides. MHC peptide immunogenicity report true data_1537 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 data_1539 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 data_1540 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 data_1541 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 data_1542 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 data_1543 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 data_1544 beta12orEarlier Phi/psi angle data or a Ramachandran plot of a protein structure. Ramachandran plot data_1545 beta12orEarlier Data on the net charge distribution (dipole moment) of a protein structure. Protein dipole moment data_1546 beta12orEarlier A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. Protein distance matrix data_1547 beta12orEarlier An amino acid residue contact map for a protein structure. Protein contact map data_1548 beta12orEarlier Report on clusters of contacting residues in protein structures such as a key structural residue network. Protein residue 3D cluster data_1549 beta12orEarlier Patterns of hydrogen bonding in protein structures. Protein hydrogen bonds data_1550 beta12orEarlier 1.4 Non-canonical atomic interactions in protein structures. Protein non-canonical interactions true data_1553 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 data_1554 beta12orEarlier 1.5 Information on a node from the SCOP database. SCOP node true data_1555 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 data_1556 beta12orEarlier 1.5 Information on a protein 'class' node from the CATH database. CATH class true data_1557 beta12orEarlier 1.5 Information on a protein 'architecture' node from the CATH database. CATH architecture true data_1558 beta12orEarlier 1.5 Information on a protein 'topology' node from the CATH database. CATH topology true data_1559 beta12orEarlier 1.5 Information on a protein 'homologous superfamily' node from the CATH database. CATH homologous superfamily true data_1560 beta12orEarlier 1.5 Information on a protein 'structurally similar group' node from the CATH database. CATH structurally similar group true data_1561 beta12orEarlier 1.5 Information on a protein 'functional category' node from the CATH database. CATH functional category true data_1564 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 data_1565 beta12orEarlier 1.8 protein-protein interaction(s), including interactions between protein domains. Protein-protein interaction report true data_1566 beta12orEarlier An informative report on protein-ligand (small molecule) interaction(s). Protein-drug interaction report Protein-ligand interaction report data_1567 beta12orEarlier 1.8 protein-DNA/RNA interaction(s). Protein-nucleic acid interactions report true data_1583 beta12orEarlier 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 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. Nucleic acid melting profile data_1584 beta12orEarlier Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid enthalpy data_1585 beta12orEarlier Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid entropy data_1586 beta12orEarlier beta12orEarlier Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid melting temperature true data_1587 beta12orEarlier 1.21 Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid stitch profile true data_1588 beta12orEarlier DNA base pair stacking energies data. DNA base pair stacking energies data data_1589 beta12orEarlier DNA base pair twist angle data. DNA base pair twist angle data data_1590 beta12orEarlier DNA base trimer roll angles data. DNA base trimer roll angles data data_1591 beta12orEarlier beta12orEarlier RNA parameters used by the Vienna package. Vienna RNA parameters true data_1592 beta12orEarlier beta12orEarlier Structure constraints used by the Vienna package. Vienna RNA structure constraints true data_1593 beta12orEarlier beta12orEarlier RNA concentration data used by the Vienna package. Vienna RNA concentration data true data_1594 beta12orEarlier beta12orEarlier RNA calculated energy data generated by the Vienna package. Vienna RNA calculated energy true data_1595 beta12orEarlier Dotplot of RNA base pairing probability matrix. Such as generated by the Vienna package. Base pairing probability matrix dotplot data_1596 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 data_1597 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 data_1598 beta12orEarlier A genetic code for an organism. A genetic code need not include detailed codon usage information. Genetic code data_1599 beta12orEarlier beta12orEarlier A simple measure of synonymous codon usage bias often used to predict gene expression levels. Codon adaptation index true data_1600 beta12orEarlier A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. Synonymous codon usage statistic plot Codon usage bias plot data_1601 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 data_1602 beta12orEarlier The differences in codon usage fractions between two codon usage tables. Codon usage fraction difference data_1621 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 data_1622 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 data_1634 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 data_1636 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 data_1642 beta12orEarlier beta12orEarlier Affymetrix library file of information about which probes belong to which probe set. Affymetrix probe sets library file true data_1643 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 data_1646 beta12orEarlier 1.12 Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. Molecular weights standard fingerprint true data_1656 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 data_1657 beta12orEarlier 1.8 genetic information processing pathways. Genetic information processing pathway report true data_1658 beta12orEarlier 1.8 environmental information processing pathways. Environmental information processing pathway report true data_1659 beta12orEarlier 1.8 A report typically including a map (diagram) of a signal transduction pathway. Signal transduction pathway report true data_1660 beta12orEarlier 1.8 Topic concernning cellular process pathways. Cellular process pathways report true data_1661 beta12orEarlier 1.8 disease pathways, typically of human disease. Disease pathway or network report true data_1662 beta12orEarlier 1.21 A report typically including a map (diagram) of drug structure relationships. Drug structure relationship map true data_1663 beta12orEarlier 1.8 networks of protein interactions. Protein interaction networks true data_1664 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 data_1667 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 data_1668 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 data_1669 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 data_1670 beta12orEarlier 1.5 Information on a database (or ontology) version, for example name, version number and release date. Database version information true data_1671 beta12orEarlier 1.5 Information on an application version, for example name, version number and release date. Tool version information true data_1672 beta12orEarlier beta12orEarlier Information on a version of the CATH database. CATH version information true data_1673 beta12orEarlier beta12orEarlier Cross-mapping of Swiss-Prot codes to PDB identifiers. Swiss-Prot to PDB mapping true data_1674 beta12orEarlier beta12orEarlier Cross-references from a sequence record to other databases. Sequence database cross-references true data_1675 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 data_1676 beta12orEarlier 1.0 The (typically numeric) unique identifier of a submitted job. Job ID true data_1677 beta12orEarlier 1.5 A label (text token) describing the type of job, for example interactive or non-interactive. Job type true data_1678 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 data_1679 beta12orEarlier beta12orEarlier DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. DaliLite log file true data_1680 beta12orEarlier beta12orEarlier STRIDE log file. STRIDE log file true data_1681 beta12orEarlier beta12orEarlier NACCESS log file. NACCESS log file true data_1682 beta12orEarlier beta12orEarlier EMBOSS wordfinder log file. EMBOSS wordfinder log file true data_1683 beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) domainatrix application log file. EMBOSS domainatrix log file true data_1684 beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) sites application log file. EMBOSS sites log file true data_1685 beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. EMBOSS supermatcher error file true data_1686 beta12orEarlier beta12orEarlier EMBOSS megamerger log file. EMBOSS megamerger log file true data_1687 beta12orEarlier beta12orEarlier EMBOSS megamerger log file. EMBOSS whichdb log file true data_1688 beta12orEarlier beta12orEarlier EMBOSS vectorstrip log file. EMBOSS vectorstrip log file true data_1689 beta12orEarlier A username on a computer system or a website. Username data_1690 beta12orEarlier A password on a computer system, or a website. Password data_1691 beta12orEarlier Moby:Email Moby:EmailAddress A valid email address of an end-user. Email address data_1692 beta12orEarlier The name of a person. Person name data_1693 beta12orEarlier 1.5 Number of iterations of an algorithm. Number of iterations true data_1694 beta12orEarlier 1.5 Number of entities (for example database hits, sequences, alignments etc) to write to an output file. Number of output entities true data_1695 beta12orEarlier beta12orEarlier Controls the order of hits (reported matches) in an output file from a database search. Hit sort order true data_1696 beta12orEarlier A human-readable collection of information about a specific drug. Drug annotation Drug structure relationship map A drug structure relationship map is report (typically a map diagram) of drug structure relationships. Drug report data_1707 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 data_1708 beta12orEarlier Image of RNA secondary structure, knots, pseudoknots etc. RNA secondary structure image data_1709 beta12orEarlier Image of protein secondary structure. Protein secondary structure image data_1710 beta12orEarlier Image of one or more molecular tertiary (3D) structures. Structure image data_1711 beta12orEarlier Image of two or more aligned molecular sequences possibly annotated with alignment features. Sequence alignment image data_1712 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 data_1713 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 data_1714 beta12orEarlier An image of spots from a microarray experiment. Microarray spots image data_1715 beta12orEarlier beta12orEarlier A term from the BioPax ontology. BioPax term true data_1716 beta12orEarlier beta12orEarlier A term definition from The Gene Ontology (GO). GO true data_1717 beta12orEarlier beta12orEarlier A term from the MeSH vocabulary. MeSH true data_1718 beta12orEarlier beta12orEarlier A term from the HGNC controlled vocabulary. HGNC true data_1719 beta12orEarlier beta12orEarlier A term from the NCBI taxonomy vocabulary. NCBI taxonomy vocabulary true data_1720 beta12orEarlier beta12orEarlier A term from the Plant Ontology (PO). Plant ontology term true data_1721 beta12orEarlier beta12orEarlier A term from the UMLS vocabulary. UMLS true data_1722 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 data_1723 beta12orEarlier beta12orEarlier A term from the EMAP mouse ontology. EMAP true data_1724 beta12orEarlier beta12orEarlier A term from the ChEBI ontology. ChEBI true data_1725 beta12orEarlier beta12orEarlier A term from the MGED ontology. MGED true data_1726 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 data_1727 beta12orEarlier beta12orEarlier A term definition for a biological process from the Gene Ontology (GO). Data Type is an enumerated string. GO (biological process) true data_1728 beta12orEarlier beta12orEarlier A term definition for a molecular function from the Gene Ontology (GO). Data Type is an enumerated string. GO (molecular function) true data_1729 beta12orEarlier beta12orEarlier A term definition for a cellular component from the Gene Ontology (GO). Data Type is an enumerated string. GO (cellular component) true data_1730 beta12orEarlier 1.5 A relation type defined in an ontology. Ontology relation type true data_1731 beta12orEarlier The definition of a concept from an ontology. Ontology class definition Ontology concept definition data_1732 beta12orEarlier 1.4 A comment on a concept from an ontology. Ontology concept comment true data_1733 beta12orEarlier beta12orEarlier Reference for a concept from an ontology. Ontology concept reference true data_1738 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 data_1742 beta12orEarlier PDBML:PDB_residue_no WHATIF: pdb_number A residue identifier (a string) from a PDB file. PDB residue number data_1743 beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). Cartesian coordinate Atomic coordinate data_1744 beta12orEarlier 1.21 Cartesian x coordinate of an atom (in a molecular structure). Atomic x coordinate true data_1745 beta12orEarlier 1.21 Cartesian y coordinate of an atom (in a molecular structure). Atomic y coordinate true data_1746 beta12orEarlier 1.21 Cartesian z coordinate of an atom (in a molecular structure). Atomic z coordinate true data_1748 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 data_1755 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 data_1756 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 data_1757 beta12orEarlier Name of an atom. Atom name data_1758 beta12orEarlier WHATIF: type Three-letter amino acid residue names as used in PDB files. PDB residue name data_1759 beta12orEarlier PDBML:pdbx_PDB_model_num WHATIF: model_number Identifier of a model structure from a PDB file. Model number PDB model number data_1762 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 data_1764 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 data_1765 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 data_1766 beta12orEarlier beta12orEarlier FASTA sequence database for all CATH domains (based on PDB ATOM records). CATH domain sequences (ATOM) true data_1767 beta12orEarlier beta12orEarlier FASTA sequence database for all CATH domains (based on COMBS sequence data). CATH domain sequences (COMBS) true data_1771 beta12orEarlier Information on an molecular sequence version. Sequence version information Sequence version data_1772 beta12orEarlier A numerical value, that is some type of scored value arising for example from a prediction method. Score data_1776 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 data_1783 beta12orEarlier 1.3 Name of a gene from Aspergillus Genome Database. Gene name (ASPGD) true data_1784 beta12orEarlier 1.3 Name of a gene from Candida Genome Database. Gene name (CGD) true data_1785 beta12orEarlier 1.3 Name of a gene from dictyBase database. Gene name (dictyBase) true data_1786 beta12orEarlier 1.3 Primary name of a gene from EcoGene Database. Gene name (EcoGene primary) true data_1787 beta12orEarlier 1.3 Name of a gene from MaizeGDB (maize genes) database. Gene name (MaizeGDB) true data_1788 beta12orEarlier 1.3 Name of a gene from Saccharomyces Genome Database. Gene name (SGD) true data_1789 beta12orEarlier 1.3 Name of a gene from Tetrahymena Genome Database. Gene name (TGD) true data_1790 beta12orEarlier 1.3 Symbol of a gene from E.coli Genetic Stock Center. Gene name (CGSC) true data_1791 beta12orEarlier 1.3 Symbol of a gene approved by the HUGO Gene Nomenclature Committee. Gene name (HGNC) true data_1792 beta12orEarlier 1.3 Symbol of a gene from the Mouse Genome Database. Gene name (MGD) true data_1793 beta12orEarlier 1.3 Symbol of a gene from Bacillus subtilis Genome Sequence Project. Gene name (Bacillus subtilis) true data_1794 beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB Identifier of a gene from PlasmoDB Plasmodium Genome Resource. Gene ID (PlasmoDB) data_1795 beta12orEarlier Identifier of a gene from EcoGene Database. EcoGene Accession EcoGene ID Gene ID (EcoGene) data_1796 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) data_1797 beta12orEarlier beta13 Gene identifier from Glossina morsitans GeneDB database. Gene ID (GeneDB Glossina morsitans) true data_1798 beta12orEarlier beta13 Gene identifier from Leishmania major GeneDB database. Gene ID (GeneDB Leishmania major) true data_1799 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 data_1800 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 data_1801 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 data_1802 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) data_1803 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) data_1804 beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: SGN Gene identifier from Sol Genomics Network. Gene ID (SGN) data_1805 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) data_1806 beta12orEarlier beta12orEarlier Any name (other than the recommended one) for a gene. Gene synonym true data_1807 beta12orEarlier The name of an open reading frame attributed by a sequencing project. ORF name data_1852 beta12orEarlier beta12orEarlier A component of a larger sequence assembly. Sequence assembly component true data_1853 beta12orEarlier beta12orEarlier A report on a chromosome aberration such as abnormalities in chromosome structure. Chromosome annotation (aberration) true data_1855 beta12orEarlier true An identifier of a clone (cloned molecular sequence) from a database. Clone ID data_1856 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 data_1857 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 data_1858 beta12orEarlier WHATIF: PDBx_B_iso_or_equiv Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. Isotropic B factor data_1859 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 data_1860 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 data_1863 beta12orEarlier Moby:Haplotyping_Study_obj A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. Haplotype map data_1864 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 data_1865 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 data_1866 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 data_1867 beta12orEarlier The name of a protein fold. Protein fold name data_1868 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 data_1869 beta12orEarlier true A unique identifier of a (group of) organisms. Organism identifier data_1870 beta12orEarlier The name of a genus of organism. Genus name data_1872 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 data_1873 beta12orEarlier Moby_namespace:iHOPorganism A unique identifier for an organism used in the iHOP database. iHOP organism ID data_1874 beta12orEarlier Common name for an organism as used in the GenBank database. Genbank common name data_1875 beta12orEarlier The name of a taxon from the NCBI taxonomy database. NCBI taxon data_1877 beta12orEarlier beta12orEarlier An alternative for a word. Synonym true data_1878 beta12orEarlier beta12orEarlier A common misspelling of a word. Misspelling true data_1879 beta12orEarlier beta12orEarlier An abbreviation of a phrase or word. Acronym true data_1880 beta12orEarlier beta12orEarlier A term which is likely to be misleading of its meaning. Misnomer true data_1881 beta12orEarlier Moby:Author Information on the authors of a published work. Author ID data_1882 beta12orEarlier An identifier representing an author in the DragonDB database. DragonDB author identifier data_1883 beta12orEarlier Moby:DescribedLink A URI along with annotation describing the data found at the address. Annotated URI data_1884 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 data_1885 beta12orEarlier Moby_namespace:GENEFARM_GeneID Identifier of a gene from the GeneFarm database. Gene ID (GeneFarm) data_1886 beta12orEarlier Moby_namespace:Blattner_number The blattner identifier for a gene. Blattner number data_1887 beta12orEarlier beta13 Moby_namespace:MIPS_GE_Maize Identifier for genetic elements in MIPS Maize database. Gene ID (MIPS Maize) true data_1888 beta12orEarlier beta13 Moby_namespace:MIPS_GE_Medicago Identifier for genetic elements in MIPS Medicago database. Gene ID (MIPS Medicago) true data_1889 beta12orEarlier 1.3 The name of an Antirrhinum Gene from the DragonDB database. Gene name (DragonDB) true data_1890 beta12orEarlier 1.3 A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. Gene name (Arabidopsis) true data_1891 beta12orEarlier Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. iHOP symbol data_1892 beta12orEarlier 1.3 Name of a gene from the GeneFarm database. Gene name (GeneFarm) true data_1893 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 data_1895 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) data_1896 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) data_1897 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) data_1898 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) data_1899 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) data_1900 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 data_1901 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) data_1902 beta12orEarlier Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. Locus ID (MMP) data_1903 beta12orEarlier Moby_namespace:DDB_gene Identifier of locus from DictyBase (Dictyostelium discoideum). Locus ID (DictyBase) data_1904 beta12orEarlier Moby_namespace:EntrezGene_EntrezGeneID Moby_namespace:EntrezGene_ID Identifier of a locus from EntrezGene database. Locus ID (EntrezGene) data_1905 beta12orEarlier Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). Locus ID (MaizeGDB) data_1906 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 data_1907 beta12orEarlier Moby_namespace:GeneId Identifier of a gene from the KOME database. Gene ID (KOME) data_1908 beta12orEarlier Moby:Tropgene_locus Identifier of a locus from the Tropgene database. Locus ID (Tropgene) data_1916 beta12orEarlier true An alignment of molecular sequences, structures or profiles derived from them. Alignment data_1917 beta12orEarlier Data for an atom (in a molecular structure). General atomic property Atomic property data_2007 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 data_2009 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 data_2012 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 data_2016 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 data_2018 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 data_2019 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 data_2022 beta12orEarlier beta12orEarlier Data used by the Vienna RNA analysis package. Vienna RNA structural data true data_2023 beta12orEarlier 1.5 Data used to replace (mask) characters in a molecular sequence. Sequence mask parameter true data_2024 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 data_2025 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 data_2026 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 data_2028 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 data_2041 beta12orEarlier 1.5 Information on a genome version. Genome version information true data_2042 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 data_2043 beta12orEarlier 1.8 A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Sequence record lite true data_2044 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 data_2046 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 data_2047 beta12orEarlier 1.8 A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Protein sequence record (lite) true data_2048 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 data_2050 beta12orEarlier General data for a molecule. General molecular property Molecular property (general) data_2053 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 data_2070 beta12orEarlier A nucleotide sequence motif. Nucleic acid sequence motif DNA sequence motif RNA sequence motif Sequence motif (nucleic acid) data_2071 beta12orEarlier An amino acid sequence motif. Protein sequence motif Sequence motif (protein) data_2079 beta12orEarlier 1.5 Some simple value controlling a search operation, typically a search of a database. Search parameter true data_2080 beta12orEarlier A report of hits from searching a database of some type. Database hits Search results Database search results data_2081 beta12orEarlier 1.5 The secondary structure assignment (predicted or real) of a nucleic acid or protein. Secondary structure true data_2082 beta12orEarlier An array of numerical values. Array This is a broad data type and is used a placeholder for other, more specific types. Matrix data_2083 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 data_2084 beta12orEarlier A human-readable collection of information about one or more specific nucleic acid molecules. Nucleic acid report data_2085 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 data_2086 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 data_2087 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 data_2088 beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. DNA base structural data data_2090 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 data_2091 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 data_2092 beta12orEarlier 1.8 single nucleotide polymorphism (SNP) in a DNA sequence. SNP true data_2093 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 data_2098 beta12orEarlier true An identifier of a submitted job. Job identifier http://wsio.org/data_009 data_2099 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. data_2100 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 data_2101 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 data_2102 beta12orEarlier A three-letter code used in the KEGG databases to uniquely identify organisms. KEGG organism code data_2103 beta12orEarlier 1.3 Name of an entry (gene) from the KEGG GENES database. Gene name (KEGG GENES) true data_2104 beta12orEarlier Identifier of an object from one of the BioCyc databases. BioCyc ID data_2105 beta12orEarlier Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound ID BioCyc compound identifier Compound ID (BioCyc) data_2106 beta12orEarlier Identifier of a biological reaction from the BioCyc reactions database. Reaction ID (BioCyc) data_2107 beta12orEarlier Identifier of an enzyme from the BioCyc enzymes database. BioCyc enzyme ID Enzyme ID (BioCyc) data_2108 beta12orEarlier true Identifier of a biological reaction from a database. Reaction ID data_2109 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) data_2110 beta12orEarlier true Identifier of a molecular property. Molecular property identifier data_2111 beta12orEarlier true Identifier of a codon usage table, for example a genetic code. Codon usage table identifier Codon usage table ID data_2112 beta12orEarlier Primary identifier of an object from the FlyBase database. FlyBase primary identifier data_2113 beta12orEarlier Identifier of an object from the WormBase database. WormBase identifier data_2114 beta12orEarlier CE[0-9]{5} Protein identifier used by WormBase database. WormBase wormpep ID data_2116 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 data_2117 beta12orEarlier true An identifier of a map of a molecular sequence. Map identifier data_2118 beta12orEarlier true An identifier of a software end-user on a website or a database (typically a person or an entity). Person identifier data_2119 beta12orEarlier true Name or other identifier of a nucleic acid molecule. Nucleic acid identifier data_2126 beta12orEarlier 1.20 Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). Translation frame specification true data_2127 beta12orEarlier true An identifier of a genetic code. Genetic code identifier data_2128 beta12orEarlier Informal name for a genetic code, typically an organism name. Genetic code name data_2129 beta12orEarlier Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. File format name data_2130 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 data_2131 beta12orEarlier Name of a computer operating system such as Linux, PC or Mac. Operating system name data_2132 beta12orEarlier beta12orEarlier A type of point or block mutation, including insertion, deletion, change, duplication and moves. Mutation type true data_2133 beta12orEarlier A logical operator such as OR, AND, XOR, and NOT. Logical operator data_2134 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 data_2135 beta12orEarlier beta12orEarlier A simple parameter that is a toggle (boolean value), typically a control for a modal tool. Toggle true data_2136 beta12orEarlier beta12orEarlier The width of an output sequence or alignment. Sequence width true data_2137 beta12orEarlier A penalty for introducing or extending a gap in an alignment. Gap penalty data_2139 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 data_2140 beta12orEarlier The concentration of a chemical compound. Concentration data_2141 beta12orEarlier 1.5 Size of the incremental 'step' a sequence window is moved over a sequence. Window step size true data_2142 beta12orEarlier beta12orEarlier An image of a graph generated by the EMBOSS suite. EMBOSS graph true data_2143 beta12orEarlier beta12orEarlier An application report generated by the EMBOSS suite. EMBOSS report true data_2145 beta12orEarlier 1.5 An offset for a single-point sequence position. Sequence offset true data_2146 beta12orEarlier 1.5 A value that serves as a threshold for a tool (usually to control scoring or output). Threshold true data_2147 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 data_2149 beta12orEarlier beta12orEarlier The name of a category of biological or bioinformatics database. Database category name true data_2150 beta12orEarlier beta12orEarlier Name of a sequence profile. Sequence profile name true data_2151 beta12orEarlier beta12orEarlier Specification of one or more colors. Color true data_2152 beta12orEarlier 1.5 A parameter that is used to control rendering (drawing) to a device or image. Rendering parameter true data_2154 beta12orEarlier Any arbitrary name of a molecular sequence. Sequence name data_2156 beta12orEarlier 1.5 A temporal date. Date true data_2157 beta12orEarlier beta12orEarlier Word composition data for a molecular sequence. Word composition true data_2160 beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. Fickett testcode plot data_2161 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 data_2162 beta12orEarlier An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. Helical wheel data_2163 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 data_2164 beta12orEarlier beta12orEarlier A plot of general physicochemical properties of a protein sequence. Protein sequence properties plot true data_2165 beta12orEarlier A plot of pK versus pH for a protein. Protein ionisation curve data_2166 beta12orEarlier A plot of character or word composition / frequency of a molecular sequence. Sequence composition plot data_2167 beta12orEarlier Density plot (of base composition) for a nucleotide sequence. Nucleic acid density plot data_2168 beta12orEarlier Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). Sequence trace image data_2169 beta12orEarlier 1.5 A report on siRNA duplexes in mRNA. Nucleic acid features (siRNA) true data_2173 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 data_2174 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 data_2176 beta12orEarlier beta12orEarlier The number of a certain thing. Cardinality true data_2177 beta12orEarlier beta12orEarlier A single thing. Exactly 1 true data_2178 beta12orEarlier beta12orEarlier One or more things. 1 or more true data_2179 beta12orEarlier beta12orEarlier Exactly two things. Exactly 2 true data_2180 beta12orEarlier beta12orEarlier Two or more things. 2 or more true data_2190 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 data_2191 beta12orEarlier 1.8 chemical modification of a protein. Protein features report (chemical modifications) true data_2192 beta12orEarlier 1.5 Data on an error generated by computer system or tool. Error true data_2193 beta12orEarlier Basic information on any arbitrary database entry. Database entry metadata data_2198 beta12orEarlier beta13 A cluster of similar genes. Gene cluster true data_2201 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 data_2208 beta12orEarlier true An identifier of a plasmid in a database. Plasmid identifier data_2209 beta12orEarlier true A unique identifier of a specific mutation catalogued in a database. Mutation ID data_2212 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 data_2213 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 data_2214 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 data_2215 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 data_2216 beta12orEarlier The number of a codon, for instance, at which a mutation is located. Codon number data_2217 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 data_2218 beta12orEarlier 1.5 Basic information about a server on the web, such as an SRS server. Server metadata true data_2219 beta12orEarlier The name of a field in a database. Database field name data_2220 beta12orEarlier Unique identifier of a sequence cluster from the SYSTERS database. SYSTERS cluster ID Sequence cluster ID (SYSTERS) data_2223 beta12orEarlier Data concerning a biological ontology. Ontology metadata data_2235 beta12orEarlier beta13 Raw SCOP domain classification data files. These are the parsable data files provided by SCOP. Raw SCOP domain classification true data_2236 beta12orEarlier beta13 Raw CATH domain classification data files. These are the parsable data files provided by CATH. Raw CATH domain classification true data_2240 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 data_2242 beta12orEarlier beta12orEarlier Phylogenetic property values data. Phylogenetic property values true data_2245 beta12orEarlier 1.5 A collection of sequences output from a bootstrapping (resampling) procedure. Bootstrapping is often performed in phylogenetic analysis. Sequence set (bootstrapped) true data_2247 beta12orEarlier beta12orEarlier A consensus phylogenetic tree derived from comparison of multiple trees. Phylogenetic consensus tree true data_2248 beta12orEarlier 1.5 A data schema for organising or transforming data of some type. Schema true data_2249 beta12orEarlier 1.5 A DTD (document type definition). DTD true data_2250 beta12orEarlier 1.5 An XML Schema. XML Schema true data_2251 beta12orEarlier 1.5 A relax-NG schema. Relax-NG schema true data_2252 beta12orEarlier 1.5 An XSLT stylesheet. XSLT stylesheet true data_2253 beta12orEarlier The name of a data type. Data resource definition name data_2254 beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. OBO file format name data_2285 beta12orEarlier Identifier for genetic elements in MIPS database. MIPS genetic element identifier Gene ID (MIPS) data_2288 beta12orEarlier beta12orEarlier An identifier of protein sequence(s) or protein sequence database entries. Sequence identifier (protein) true data_2289 beta12orEarlier beta12orEarlier An identifier of nucleotide sequence(s) or nucleotide sequence database entries. Sequence identifier (nucleic acid) true data_2290 beta12orEarlier An accession number of an entry from the EMBL sequence database. EMBL ID EMBL accession number EMBL identifier EMBL accession data_2291 beta12orEarlier An identifier of a polypeptide in the UniProt database. UniProt entry name UniProt identifier UniProtKB entry name UniProtKB identifier UniProt ID data_2292 beta12orEarlier Accession number of an entry from the GenBank sequence database. GenBank ID GenBank accession number GenBank identifier GenBank accession data_2293 beta12orEarlier Secondary (internal) identifier of a Gramene database entry. Gramene internal ID Gramene internal identifier Gramene secondary ID Gramene secondary identifier data_2294 beta12orEarlier true An identifier of an entry from a database of molecular sequence variation. Sequence variation ID data_2295 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 data_2296 beta12orEarlier 1.3 Name of an entry (gene) from the AceView genes database. Gene name (AceView) true data_2297 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) data_2298 beta12orEarlier Identifier for a gene approved by the HUGO Gene Nomenclature Committee. HGNC ID Gene ID (HGNC) data_2299 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 data_2300 beta12orEarlier 1.3 Name of an entry (gene) from the NCBI genes database. Gene name (NCBI) true data_2301 beta12orEarlier A specification of a chemical structure in SMILES format. SMILES string data_2302 beta12orEarlier Unique identifier of an entry from the STRING database of protein-protein interactions. STRING ID data_2307 beta12orEarlier 1.4 An informative report on a specific virus. Virus annotation true data_2308 beta12orEarlier 1.4 An informative report on the taxonomy of a specific virus. Virus annotation (taxonomy) true data_2309 beta12orEarlier [0-9]+ Identifier of a biological reaction from the SABIO-RK reactions database. Reaction ID (SABIO-RK) data_2313 beta12orEarlier A human-readable collection of information about one or more specific carbohydrate 3D structure(s). Carbohydrate report data_2314 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 data_2315 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 data_2316 beta12orEarlier The name of a cell line. Cell line name data_2317 beta12orEarlier The exact name of a cell line. Cell line name (exact) data_2318 beta12orEarlier The truncated name of a cell line. Cell line name (truncated) data_2319 beta12orEarlier The name of a cell line without any punctuation. Cell line name (no punctuation) data_2320 beta12orEarlier The assonant name of a cell line. Cell line name (assonant) data_2321 beta12orEarlier true A unique, persistent identifier of an enzyme. Enzyme accession Enzyme ID data_2325 beta12orEarlier Identifier of an enzyme from the REBASE enzymes database. REBASE enzyme number data_2326 beta12orEarlier DB[0-9]{5} Unique identifier of a drug from the DrugBank database. DrugBank ID data_2327 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) data_2335 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 data_2336 beta12orEarlier 1.20 Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. Translation phase specification true data_2337 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 data_2338 beta12orEarlier Any arbitrary identifier of an ontology. Ontology identifier data_2339 beta12orEarlier The name of a concept in an ontology. Ontology concept name data_2340 beta12orEarlier An identifier of a build of a particular genome. Genome build identifier data_2342 beta12orEarlier The name of a biological pathway or network. Pathway or network name data_2343 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) data_2344 beta12orEarlier [a-zA-Z_0-9]+ Identifier of a pathway from the NCI-Nature pathway database. Pathway ID (NCI-Nature) data_2345 beta12orEarlier Identifier of a pathway from the ConsensusPathDB pathway database. Pathway ID (ConsensusPathDB) data_2346 beta12orEarlier Unique identifier of an entry from the UniRef database. UniRef cluster id UniRef entry accession Sequence cluster ID (UniRef) data_2347 beta12orEarlier Unique identifier of an entry from the UniRef100 database. UniRef100 cluster id UniRef100 entry accession Sequence cluster ID (UniRef100) data_2348 beta12orEarlier Unique identifier of an entry from the UniRef90 database. UniRef90 cluster id UniRef90 entry accession Sequence cluster ID (UniRef90) data_2349 beta12orEarlier Unique identifier of an entry from the UniRef50 database. UniRef50 cluster id UniRef50 entry accession Sequence cluster ID (UniRef50) data_2353 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 data_2354 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 data_2355 beta12orEarlier true Identifier of an RNA family, typically an entry from a RNA sequence classification database. RNA family identifier data_2356 beta12orEarlier Stable accession number of an entry (RNA family) from the RFAM database. RFAM accession data_2357 beta12orEarlier 1.5 A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. Protein signature type true data_2358 beta12orEarlier 1.5 An informative report on protein domain-DNA/RNA interaction(s). Domain-nucleic acid interaction report true data_2359 beta12orEarlier 1.8 An informative report on protein domain-protein domain interaction(s). Domain-domain interactions true data_2360 beta12orEarlier beta12orEarlier Data on indirect protein domain-protein domain interaction(s). Domain-domain interaction (indirect) true data_2362 beta12orEarlier true Accession number of a nucleotide or protein sequence database entry. Sequence accession (hybrid) data_2363 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 data_2364 beta12orEarlier 1.8 two-dimensional gel electrophoresis experiments, gels or spots in a gel. 2D PAGE report true data_2365 beta12orEarlier true A persistent, unique identifier of a biological pathway or network (typically a database entry). Pathway or network accession data_2366 beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more molecules. Secondary structure alignment data_2367 beta12orEarlier Identifier of an object from the ASTD database. ASTD ID data_2368 beta12orEarlier Identifier of an exon from the ASTD database. ASTD ID (exon) data_2369 beta12orEarlier Identifier of an intron from the ASTD database. ASTD ID (intron) data_2370 beta12orEarlier Identifier of a polyA signal from the ASTD database. ASTD ID (polya) data_2371 beta12orEarlier Identifier of a transcription start site from the ASTD database. ASTD ID (tss) data_2372 beta12orEarlier 1.8 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. 2D PAGE spot report true data_2373 beta12orEarlier true Unique identifier of a spot from a two-dimensional (protein) gel. Spot ID data_2374 beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. Spot serial number data_2375 beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. Spot ID (HSC-2DPAGE) data_2378 beta12orEarlier beta13 Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. Protein-motif interaction true data_2379 beta12orEarlier true Identifier of a strain of an organism variant, typically a plant, virus or bacterium. Strain identifier data_2380 beta12orEarlier A unique identifier of an item from the CABRI database. CABRI accession data_2381 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 data_2382 beta12orEarlier true Identifier of an entry from a database of genotype experiment metadata. Genotype experiment ID data_2383 beta12orEarlier Identifier of an entry from the EGA database. EGA accession data_2384 beta12orEarlier IPI[0-9]{8} Identifier of a protein entry catalogued in the International Protein Index (IPI) database. IPI protein ID data_2385 beta12orEarlier Accession number of a protein from the RefSeq database. RefSeq protein ID RefSeq accession (protein) data_2386 beta12orEarlier Identifier of an entry (promoter) from the EPD database. EPD identifier EPD ID data_2387 beta12orEarlier Identifier of an entry from the TAIR database. TAIR accession data_2388 beta12orEarlier Identifier of an Arabidopsis thaliana gene from the TAIR database. TAIR accession (At gene) data_2389 beta12orEarlier Identifier of an entry from the UniSTS database. UniSTS accession data_2390 beta12orEarlier Identifier of an entry from the UNITE database. UNITE accession data_2391 beta12orEarlier Identifier of an entry from the UTR database. UTR accession data_2392 beta12orEarlier UPI[A-F0-9]{10} Accession number of a UniParc (protein sequence) database entry. UPI UniParc ID UniParc accession data_2393 beta12orEarlier Identifier of an entry from the Rouge or HUGE databases. mFLJ/mKIAA number data_2395 beta12orEarlier 1.4 An informative report on a specific fungus. Fungi annotation true data_2396 beta12orEarlier 1.4 An informative report on a specific fungus anamorph. Fungi annotation (anamorph) true data_2398 beta12orEarlier Unique identifier for a protein from the Ensembl database. Ensembl ID (protein) Protein ID (Ensembl) Ensembl protein ID data_2400 beta12orEarlier 1.4 An informative report on a specific toxin. Toxin annotation true data_2401 beta12orEarlier beta12orEarlier An informative report on a membrane protein. Protein report (membrane protein) true data_2402 beta12orEarlier 1.12 An informative report on tentative or known protein-drug interaction(s). Protein-drug interaction report true data_2522 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 data_2523 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 data_2524 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 data_2525 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 data_2526 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 data_2527 beta12orEarlier 1.16 Typically a simple numerical or string value that controls the operation of a tool. Parameter true data_2528 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 data_2529 beta12orEarlier 1.5 An informative report on a specific molecule. Molecule report true data_2530 beta12orEarlier A human-readable collection of information about a specific organism. Organism annotation Organism report data_2531 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 data_2534 beta12orEarlier An attribute of a molecular sequence, possibly in reference to some other sequence. Sequence parameter Sequence attribute data_2535 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 data_2536 beta12orEarlier Data concerning a mass spectrometry measurement. Mass spectrometry data data_2537 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 data_2538 beta12orEarlier true An identifier of a mutation. Mutation identifier data_2539 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 data_2540 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 data_2563 beta12orEarlier Single letter amino acid identifier, e.g. G. Amino acid name (single letter) data_2564 beta12orEarlier Three letter amino acid identifier, e.g. GLY. Amino acid name (three letter) data_2565 beta12orEarlier Full name of an amino acid, e.g. Glycine. Amino acid name (full name) data_2576 beta12orEarlier true Identifier of a toxin. Toxin identifier data_2578 beta12orEarlier Unique identifier of a toxin from the ArachnoServer database. ArachnoServer ID data_2579 beta12orEarlier 1.5 A simple summary of expressed genes. Expressed gene list true data_2580 beta12orEarlier Unique identifier of a monomer from the BindingDB database. BindingDB Monomer ID data_2581 beta12orEarlier beta12orEarlier The name of a concept from the GO ontology. GO concept name true data_2582 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) data_2583 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) data_2584 beta12orEarlier beta12orEarlier The name of a concept for a cellular component from the GO ontology. GO concept name (cellular component) true data_2586 beta12orEarlier An image arising from a Northern Blot experiment. Northern blot image data_2587 beta12orEarlier true Unique identifier of a blot from a Northern Blot. Blot ID data_2588 beta12orEarlier Unique identifier of a blot from a Northern Blot from the BlotBase database. BlotBase blot ID data_2589 beta12orEarlier Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. Hierarchy annotation Hierarchy data_2590 beta12orEarlier beta12orEarlier Identifier of an entry from a database of biological hierarchies. Hierarchy identifier true data_2591 beta12orEarlier Identifier of an entry from the Brite database of biological hierarchies. Brite hierarchy ID data_2592 beta12orEarlier beta12orEarlier A type (represented as a string) of cancer. Cancer type true data_2593 beta12orEarlier A unique identifier for an organism used in the BRENDA database. BRENDA organism ID data_2594 beta12orEarlier The name of a taxon using the controlled vocabulary of the UniGene database. UniGene organism abbreviation UniGene taxon data_2595 beta12orEarlier The name of a taxon using the controlled vocabulary of the UTRdb database. UTRdb taxon data_2596 beta12orEarlier true An identifier of a catalogue of biological resources. Catalogue identifier Catalogue ID data_2597 beta12orEarlier The name of a catalogue of biological resources from the CABRI database. CABRI catalogue name data_2598 beta12orEarlier beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. Secondary structure alignment metadata true data_2599 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 data_2600 beta12orEarlier Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). Network Pathway Pathway or network data_2601 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 data_2602 beta12orEarlier beta13 Data concerning a particular genotype, phenotype or a genotype / phenotype relation. Genotype and phenotype data true data_2603 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 data_2605 beta12orEarlier C[0-9]+ Unique identifier of a chemical compound from the KEGG database. KEGG compound ID KEGG compound identifier Compound ID (KEGG) data_2606 beta12orEarlier Name (not necessarily stable) an entry (RNA family) from the RFAM database. RFAM name data_2608 beta12orEarlier R[0-9]+ Identifier of a biological reaction from the KEGG reactions database. Reaction ID (KEGG) data_2609 beta12orEarlier D[0-9]+ Unique identifier of a drug from the KEGG Drug database. Drug ID (KEGG) data_2610 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 data_2611 beta12orEarlier [A-Z][0-9]+(\.[-[0-9]+])? An identifier of a disease from the International Classification of Diseases (ICD) database. ICD identifier data_2612 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) data_2613 beta12orEarlier G[0-9]+ Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). KEGG Glycan ID data_2614 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 data_2615 beta12orEarlier MINT\-[0-9]{1,5} Unique identifier of an entry from the MINT database of protein-protein interactions. MINT ID data_2616 beta12orEarlier DIP[\:\-][0-9]{3}[EN] Unique identifier of an entry from the DIP database of protein-protein interactions. DIP ID data_2617 beta12orEarlier A[0-9]{6} Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. Signaling Gateway protein ID data_2618 beta12orEarlier true Identifier of a protein modification catalogued in a database. Protein modification ID data_2619 beta12orEarlier AA[0-9]{4} Identifier of a protein modification catalogued in the RESID database. RESID ID data_2620 beta12orEarlier [0-9]{4,7} Identifier of an entry from the RGD database. RGD ID data_2621 beta12orEarlier AASequence:[0-9]{10} Identifier of a protein sequence from the TAIR database. TAIR accession (protein) data_2622 beta12orEarlier HMDB[0-9]{5} Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). HMDB ID Compound ID (HMDB) data_2625 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 data_2626 beta12orEarlier PAp[0-9]{8} PDBML:pdbx_PDB_strand_id Identifier of a peptide from the PeptideAtlas peptide databases. PeptideAtlas ID data_2627 beta12orEarlier 1.7 Identifier of a report of molecular interactions from a database (typically). Molecular interaction ID true data_2628 beta12orEarlier [0-9]+ A unique identifier of an interaction from the BioGRID database. BioGRID interaction ID data_2629 beta12orEarlier S[0-9]{2}\.[0-9]{3} Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID Enzyme ID (MEROPS) data_2630 beta12orEarlier true An identifier of a mobile genetic element. Mobile genetic element ID data_2631 beta12orEarlier mge:[0-9]+ An identifier of a mobile genetic element from the Aclame database. ACLAME ID data_2632 beta12orEarlier PWY[a-zA-Z_0-9]{2}\-[0-9]{3} Identifier of an entry from the Saccharomyces genome database (SGD). SGD ID data_2633 beta12orEarlier true Unique identifier of a book. Book ID data_2634 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 data_2635 beta12orEarlier B[0-9]{5} Identifier of a metabolite from the 3DMET database. 3DMET ID Compound ID (3DMET) data_2636 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 data_2637 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 data_2638 beta12orEarlier true [0-9]+ Identifier of an assay from the PubChem database. PubChem bioassay ID data_2639 beta12orEarlier Identifier of an entry from the PubChem database. PubChem identifier PubChem ID data_2641 beta12orEarlier M[0-9]{4} Identifier of an enzyme reaction mechanism from the MACie database. MACie entry number Reaction ID (MACie) data_2642 beta12orEarlier MI[0-9]{7} Identifier for a gene from the miRBase database. miRNA ID miRNA identifier miRNA name Gene ID (miRBase) data_2643 beta12orEarlier ZDB\-GENE\-[0-9]+\-[0-9]+ Identifier for a gene from the Zebrafish information network genome (ZFIN) database. Gene ID (ZFIN) data_2644 beta12orEarlier [0-9]{5} Identifier of an enzyme-catalysed reaction from the Rhea database. Reaction ID (Rhea) data_2645 beta12orEarlier UPA[0-9]{5} Identifier of a biological pathway from the Unipathway database. upaid Pathway ID (Unipathway) data_2646 beta12orEarlier [0-9]+ Identifier of a small molecular from the ChEMBL database. ChEMBL ID Compound ID (ChEMBL) data_2647 beta12orEarlier [a-zA-Z_0-9]+ Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. LGICdb identifier data_2648 beta12orEarlier [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. Reaction kinetics ID (SABIO-RK) data_2649 beta12orEarlier PA[0-9]+ Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). PharmGKB ID data_2650 beta12orEarlier PA[0-9]+ Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Pathway ID (PharmGKB) data_2651 beta12orEarlier PA[0-9]+ Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Disease ID (PharmGKB) data_2652 beta12orEarlier PA[0-9]+ Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Drug ID (PharmGKB) data_2653 beta12orEarlier DAP[0-9]+ Identifier of a drug from the Therapeutic Target Database (TTD). Drug ID (TTD) data_2654 beta12orEarlier TTDS[0-9]+ Identifier of a target protein from the Therapeutic Target Database (TTD). Target ID (TTD) data_2655 beta12orEarlier true A unique identifier of a type or group of cells. Cell type identifier data_2656 beta12orEarlier [0-9]+ A unique identifier of a neuron from the NeuronDB database. NeuronDB ID data_2657 beta12orEarlier [a-zA-Z_0-9]+ A unique identifier of a neuron from the NeuroMorpho database. NeuroMorpho ID data_2658 beta12orEarlier [0-9]+ Identifier of a chemical from the ChemIDplus database. ChemIDplus ID Compound ID (ChemIDplus) data_2659 beta12orEarlier SMP[0-9]{5} Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). Pathway ID (SMPDB) data_2660 beta12orEarlier [0-9]+ Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. BioNumbers ID data_2662 beta12orEarlier T3D[0-9]+ Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. T3DB ID data_2663 beta12orEarlier true Identifier of a carbohydrate. Carbohydrate identifier data_2664 beta12orEarlier [0-9]+ Identifier of an entry from the GlycomeDB database. GlycomeDB ID data_2665 beta12orEarlier [a-zA-Z_0-9]+[0-9]+ Identifier of an entry from the LipidBank database. LipidBank ID data_2666 beta12orEarlier cd[0-9]{5} Identifier of a conserved domain from the Conserved Domain Database. CDD ID data_2667 beta12orEarlier [0-9]{1,5} An identifier of an entry from the MMDB database. MMDB accession MMDB ID data_2668 beta12orEarlier [0-9]+ Unique identifier of an entry from the iRefIndex database of protein-protein interactions. iRefIndex ID data_2669 beta12orEarlier [0-9]+ Unique identifier of an entry from the ModelDB database. ModelDB ID data_2670 beta12orEarlier [0-9]+ Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). Pathway ID (DQCS) data_2671 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). Ensembl ID (Homo sapiens) true data_2672 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). Ensembl ID ('Bos taurus') true data_2673 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). Ensembl ID ('Canis familiaris') true data_2674 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). Ensembl ID ('Cavia porcellus') true data_2675 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). Ensembl ID ('Ciona intestinalis') true data_2676 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). Ensembl ID ('Ciona savignyi') true data_2677 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). Ensembl ID ('Danio rerio') true data_2678 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). Ensembl ID ('Dasypus novemcinctus') true data_2679 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). Ensembl ID ('Echinops telfairi') true data_2680 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). Ensembl ID ('Erinaceus europaeus') true data_2681 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). Ensembl ID ('Felis catus') true data_2682 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). Ensembl ID ('Gallus gallus') true data_2683 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). Ensembl ID ('Gasterosteus aculeatus') true data_2684 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). Ensembl ID ('Homo sapiens') true data_2685 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). Ensembl ID ('Loxodonta africana') true data_2686 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). Ensembl ID ('Macaca mulatta') true data_2687 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). Ensembl ID ('Monodelphis domestica') true data_2688 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). Ensembl ID ('Mus musculus') true data_2689 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). Ensembl ID ('Myotis lucifugus') true data_2690 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). Ensembl ID ("Ornithorhynchus anatinus") true data_2691 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). Ensembl ID ('Oryctolagus cuniculus') true data_2692 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). Ensembl ID ('Oryzias latipes') true data_2693 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). Ensembl ID ('Otolemur garnettii') true data_2694 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). Ensembl ID ('Pan troglodytes') true data_2695 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). Ensembl ID ('Rattus norvegicus') true data_2696 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). Ensembl ID ('Spermophilus tridecemlineatus') true data_2697 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). Ensembl ID ('Takifugu rubripes') true data_2698 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). Ensembl ID ('Tupaia belangeri') true data_2699 beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). Ensembl ID ('Xenopus tropicalis') true data_2700 beta12orEarlier Identifier of a protein domain (or other node) from the CATH database. CATH identifier data_2701 beta12orEarlier 2.10.10.10 A code number identifying a family from the CATH database. CATH node ID (family) data_2702 beta12orEarlier Identifier of an enzyme from the CAZy enzymes database. CAZy ID Enzyme ID (CAZy) data_2704 beta12orEarlier A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). I.M.A.G.E. cloneID IMAGE cloneID Clone ID (IMAGE) data_2705 beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a 'cellular component' concept from the Gene Ontology. GO concept identifier (cellular compartment) GO concept ID (cellular component) data_2706 beta12orEarlier Name of a chromosome as used in the BioCyc database. Chromosome name (BioCyc) data_2709 beta12orEarlier An identifier of a gene expression profile from the CleanEx database. CleanEx entry name data_2710 beta12orEarlier An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. CleanEx dataset code data_2711 beta12orEarlier A human-readable collection of information concerning a genome as a whole. Genome report data_2713 beta12orEarlier Unique identifier for a protein complex from the CORUM database. CORUM complex ID Protein ID (CORUM) data_2714 beta12orEarlier Unique identifier of a position-specific scoring matrix from the CDD database. CDD PSSM-ID data_2715 beta12orEarlier Unique identifier for a protein from the CuticleDB database. CuticleDB ID Protein ID (CuticleDB) data_2716 beta12orEarlier Identifier of a predicted transcription factor from the DBD database. DBD ID data_2717 beta12orEarlier General annotation on an oligonucleotide probe, or a set of probes. Oligonucleotide probe sets annotation Oligonucleotide probe annotation data_2718 beta12orEarlier true Identifier of an oligonucleotide from a database. Oligonucleotide ID data_2719 beta12orEarlier Identifier of an oligonucleotide probe from the dbProbe database. dbProbe ID data_2720 beta12orEarlier Physicochemical property data for one or more dinucleotides. Dinucleotide property data_2721 beta12orEarlier Identifier of an dinucleotide property from the DiProDB database. DiProDB ID data_2722 beta12orEarlier 1.8 disordered structure in a protein. Protein features report (disordered structure) true data_2723 beta12orEarlier Unique identifier for a protein from the DisProt database. DisProt ID Protein ID (DisProt) data_2724 beta12orEarlier 1.5 Annotation on an embryo or concerning embryological development. Embryo report true data_2725 beta12orEarlier Unique identifier for a gene transcript from the Ensembl database. Transcript ID (Ensembl) Ensembl transcript ID data_2726 beta12orEarlier 1.4 An informative report on one or more small molecules that are enzyme inhibitors. Inhibitor annotation true data_2727 beta12orEarlier true Moby:GeneAccessionList An identifier of a promoter of a gene that is catalogued in a database. Promoter ID data_2728 beta12orEarlier Identifier of an EST sequence. EST accession data_2729 beta12orEarlier Identifier of an EST sequence from the COGEME database. COGEME EST ID data_2730 beta12orEarlier Identifier of a unisequence from the COGEME database. A unisequence is a single sequence assembled from ESTs. COGEME unisequence ID data_2731 beta12orEarlier Accession number of an entry (protein family) from the GeneFarm database. GeneFarm family ID Protein family ID (GeneFarm) data_2732 beta12orEarlier The name of a family of organism. Family name data_2733 beta12orEarlier beta13 The name of a genus of viruses. Genus name (virus) true data_2734 beta12orEarlier beta13 The name of a family of viruses. Family name (virus) true data_2735 beta12orEarlier beta13 The name of a SwissRegulon database. Database name (SwissRegulon) true data_2736 beta12orEarlier A feature identifier as used in the SwissRegulon database. This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". Sequence feature ID (SwissRegulon) data_2737 beta12orEarlier A unique identifier of gene in the NMPDR database. A FIG ID consists of four parts: a prefix, genome id, locus type and id number. FIG ID data_2738 beta12orEarlier A unique identifier of gene in the Xenbase database. Gene ID (Xenbase) data_2739 beta12orEarlier A unique identifier of gene in the Genolist database. Gene ID (Genolist) data_2740 beta12orEarlier 1.3 Name of an entry (gene) from the Genolist genes database. Gene name (Genolist) true data_2741 beta12orEarlier Identifier of an entry (promoter) from the ABS database. ABS identifier ABS ID data_2742 beta12orEarlier Identifier of a transcription factor from the AraC-XylS database. AraC-XylS ID data_2743 beta12orEarlier beta12orEarlier Name of an entry (gene) from the HUGO database. Gene name (HUGO) true data_2744 beta12orEarlier Identifier of a locus from the PseudoCAP database. Locus ID (PseudoCAP) data_2745 beta12orEarlier Identifier of a locus from the UTR database. Locus ID (UTR) data_2746 beta12orEarlier Unique identifier of a monosaccharide from the MonosaccharideDB database. MonosaccharideDB ID data_2747 beta12orEarlier beta13 The name of a subdivision of the Collagen Mutation Database (CMD) database. Database name (CMD) true data_2748 beta12orEarlier beta13 The name of a subdivision of the Osteogenesis database. Database name (Osteogenesis) true data_2749 beta12orEarlier true An identifier of a particular genome. Genome identifier data_2751 beta12orEarlier 1.26 An identifier of a particular genome. GenomeReviews ID true data_2752 beta12orEarlier [0-9]+ Identifier of an entry from the GlycoMapsDB (Glycosciences.de) database. GlycoMap ID data_2753 beta12orEarlier A conformational energy map of the glycosidic linkages in a carbohydrate molecule. Carbohydrate conformational map data_2755 beta12orEarlier The name of a transcription factor. Transcription factor name data_2756 beta12orEarlier Identifier of a membrane transport proteins from the transport classification database (TCDB). TCID data_2757 beta12orEarlier PF[0-9]{5} Name of a domain from the Pfam database. Pfam domain name data_2758 beta12orEarlier CL[0-9]{4} Accession number of a Pfam clan. Pfam clan ID data_2759 beta12orEarlier Identifier for a gene from the VectorBase database. VectorBase ID Gene ID (VectorBase) data_2761 beta12orEarlier Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. UTRSite ID data_2762 beta12orEarlier An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. Sequence motif report Sequence profile report Sequence signature report data_2763 beta12orEarlier beta12orEarlier An informative report on a particular locus. Locus annotation true data_2764 beta12orEarlier Official name of a protein as used in the UniProt database. Protein name (UniProt) data_2765 beta12orEarlier 1.5 One or more terms from one or more controlled vocabularies which are annotations on an entity. The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. Term ID list true data_2766 beta12orEarlier Name of a protein family from the HAMAP database. HAMAP ID data_2767 beta12orEarlier 1.12 Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. Identifier with metadata true data_2768 beta12orEarlier beta12orEarlier Annotation about a gene symbol. Gene symbol annotation true data_2769 beta12orEarlier true Identifier of a RNA transcript. Transcript ID data_2770 beta12orEarlier Identifier of an RNA transcript from the H-InvDB database. HIT ID data_2771 beta12orEarlier A unique identifier of gene cluster in the H-InvDB database. HIX ID data_2772 beta12orEarlier Identifier of a antibody from the HPA database. HPA antibody id data_2773 beta12orEarlier Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. IMGT/HLA ID data_2774 beta12orEarlier A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). Gene ID (JCVI) data_2775 beta12orEarlier The name of a kinase protein. Kinase name data_2776 beta12orEarlier Identifier of a physical entity from the ConsensusPathDB database. ConsensusPathDB entity ID data_2777 beta12orEarlier Name of a physical entity from the ConsensusPathDB database. ConsensusPathDB entity name data_2778 beta12orEarlier The number of a strain of algae and protozoa from the CCAP database. CCAP strain number data_2779 beta12orEarlier true An identifier of stock from a catalogue of biological resources. Stock number data_2780 beta12orEarlier A stock number from The Arabidopsis information resource (TAIR). Stock number (TAIR) data_2781 beta12orEarlier Identifier of an entry from the RNA editing database (REDIdb). REDIdb ID data_2782 beta12orEarlier Name of a domain from the SMART database. SMART domain name data_2783 beta12orEarlier Accession number of an entry (family) from the PANTHER database. Panther family ID Protein family ID (PANTHER) data_2784 beta12orEarlier A unique identifier for a virus from the RNAVirusDB database. Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. RNAVirusDB ID data_2785 beta12orEarlier true An accession of annotation on a (group of) viruses (catalogued in a database). Virus ID Virus identifier data_2786 beta12orEarlier An identifier of a genome project assigned by NCBI. NCBI Genome Project ID data_2787 beta12orEarlier A unique identifier of a whole genome assigned by the NCBI. NCBI genome accession data_2788 beta12orEarlier 1.8 Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. Sequence profile data true data_2789 beta12orEarlier Unique identifier for a membrane protein from the TopDB database. TopDB ID Protein ID (TopDB) data_2790 beta12orEarlier true Identifier of a two-dimensional (protein) gel. Gel identifier Gel ID data_2791 beta12orEarlier Name of a reference map gel from the SWISS-2DPAGE database. Reference map name (SWISS-2DPAGE) data_2792 beta12orEarlier Unique identifier for a peroxidase protein from the PeroxiBase database. PeroxiBase ID Protein ID (PeroxiBase) data_2793 beta12orEarlier Identifier of an entry from the SISYPHUS database of tertiary structure alignments. SISYPHUS ID data_2794 beta12orEarlier true Accession of an open reading frame (catalogued in a database). ORF ID data_2795 beta12orEarlier true An identifier of an open reading frame. ORF identifier data_2796 beta12orEarlier [1-9][0-9]* Identifier of an entry from the GlycosciencesDB database. LInear Notation for Unique description of Carbohydrate Sequences ID LINUCS ID data_2797 beta12orEarlier Unique identifier for a ligand-gated ion channel protein from the LGICdb database. LGICdb ID Protein ID (LGICdb) data_2798 beta12orEarlier Identifier of an EST sequence from the MaizeDB database. MaizeDB ID data_2799 beta12orEarlier A unique identifier of gene in the MfunGD database. Gene ID (MfunGD) data_2800 beta12orEarlier An identifier of a disease from the Orpha database. Orpha number data_2802 beta12orEarlier Unique identifier for a protein from the EcID database. Protein ID (EcID) data_2803 beta12orEarlier A unique identifier of a cDNA molecule catalogued in the RefSeq database. Clone ID (RefSeq) data_2804 beta12orEarlier Unique identifier for a cone snail toxin protein from the ConoServer database. Protein ID (ConoServer) data_2805 beta12orEarlier Identifier of a GeneSNP database entry. GeneSNP ID data_2812 beta12orEarlier true Identifier of a lipid. Lipid identifier data_2831 beta12orEarlier beta12orEarlier A flat-file (textual) data archive. Databank true data_2832 beta12orEarlier beta12orEarlier A web site providing data (web pages) on a common theme to a HTTP client. Web portal true data_2835 beta12orEarlier Identifier for a gene from the VBASE2 database. VBASE2 ID Gene ID (VBASE2) data_2836 beta12orEarlier A unique identifier for a virus from the DPVweb database. DPVweb virus ID DPVweb ID data_2837 beta12orEarlier [0-9]+ Identifier of a pathway from the BioSystems pathway database. Pathway ID (BioSystems) data_2838 beta12orEarlier beta12orEarlier Data concerning a proteomics experiment. Experimental data (proteomics) true data_2849 beta12orEarlier An abstract of a scientific article. Abstract data_2850 beta12orEarlier 3D coordinate and associated data for a lipid structure. Lipid structure data_2851 beta12orEarlier 3D coordinate and associated data for the (3D) structure of a drug. Drug structure data_2852 beta12orEarlier 3D coordinate and associated data for the (3D) structure of a toxin. Toxin structure data_2854 beta12orEarlier A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. PSSM Position-specific scoring matrix data_2855 beta12orEarlier A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. Distance matrix data_2856 beta12orEarlier Distances (values representing similarity) between a group of molecular structures. Structural distance matrix data_2857 beta12orEarlier 1.5 Bibliographic data concerning scientific article(s). Article metadata true data_2858 beta12orEarlier A concept from a biological ontology. This includes any fields from the concept definition such as concept name, definition, comments and so on. Ontology concept data_2865 beta12orEarlier A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. Codon usage bias data_2866 beta12orEarlier 1.8 Northern Blot experiments. Northern blot report true data_2870 beta12orEarlier A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. RH map The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. Radiation hybrid map data_2872 beta12orEarlier A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. ID list data_2873 beta12orEarlier Gene frequencies data that may be read during phylogenetic tree calculation. Phylogenetic gene frequencies data data_2874 beta12orEarlier beta13 A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. Sequence set (polymorphic) true data_2875 beta12orEarlier 1.5 An entry (resource) from the DRCAT bioinformatics resource catalogue. DRCAT resource true data_2877 beta12orEarlier 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. Protein complex data_2878 beta12orEarlier 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. Protein structural motif data_2879 beta12orEarlier A human-readable collection of information about one or more specific lipid 3D structure(s). Lipid report data_2880 beta12orEarlier 1.4 Image of one or more molecular secondary structures. Secondary structure image true data_2881 beta12orEarlier 1.5 An informative report on general information, properties or features of one or more molecular secondary structures. Secondary structure report true data_2882 beta12orEarlier beta12orEarlier DNA sequence-specific feature annotation (not in a feature table). DNA features true data_2883 beta12orEarlier 1.5 Features concerning RNA or regions of DNA that encode an RNA molecule. RNA features report true data_2884 beta12orEarlier Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph. Graph data Plot data_2886 beta12orEarlier A protein sequence and associated metadata. Sequence record (protein) Protein sequence record data_2887 beta12orEarlier A nucleic acid sequence and associated metadata. Nucleotide sequence record Sequence record (nucleic acid) DNA sequence record RNA sequence record Nucleic acid sequence record data_2888 beta12orEarlier 1.8 A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. Protein sequence record (full) true data_2889 beta12orEarlier 1.8 A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. Nucleic acid sequence record (full) true data_2891 beta12orEarlier true Accession of a mathematical model, typically an entry from a database. Biological model accession data_2892 beta12orEarlier The name of a type or group of cells. Cell type name data_2893 beta12orEarlier true Accession of a type or group of cells (catalogued in a database). Cell type ID Cell type accession data_2894 beta12orEarlier true Accession of an entry from a database of chemicals. Chemical compound accession Small molecule accession Compound accession data_2895 beta12orEarlier true Accession of a drug. Drug accession data_2896 beta12orEarlier Name of a toxin. Toxin name data_2897 beta12orEarlier true Accession of a toxin (catalogued in a database). Toxin accession data_2898 beta12orEarlier true Accession of a monosaccharide (catalogued in a database). Monosaccharide accession data_2899 beta12orEarlier Common name of a drug. Drug name data_2900 beta12orEarlier true Accession of an entry from a database of carbohydrates. Carbohydrate accession data_2901 beta12orEarlier true Accession of a specific molecule (catalogued in a database). Molecule accession data_2902 beta12orEarlier true Accession of a data definition (catalogued in a database). Data resource definition accession data_2903 beta12orEarlier true An accession of a particular genome (in a database). Genome accession data_2904 beta12orEarlier true An accession of a map of a molecular sequence (deposited in a database). Map accession data_2905 beta12orEarlier true Accession of an entry from a database of lipids. Lipid accession data_2906 beta12orEarlier true Accession of a peptide deposited in a database. Peptide ID data_2907 beta12orEarlier true Accession of a protein deposited in a database. Protein accessions Protein accession data_2908 beta12orEarlier true An accession of annotation on a (group of) organisms (catalogued in a database). Organism accession data_2909 beta12orEarlier Moby:BriefOccurrenceRecord Moby:FirstEpithet Moby:InfraspecificEpithet Moby:OccurrenceRecord Moby:Organism_Name Moby:OrganismsLongName Moby:OrganismsShortName The name of an organism (or group of organisms). Organism name data_2910 beta12orEarlier true Accession of a protein family (that is deposited in a database). Protein family accession data_2911 beta12orEarlier true Accession of an entry from a database of transcription factors or binding sites. Transcription factor accession data_2912 beta12orEarlier true Accession number of a strain of an organism variant, typically a plant, virus or bacterium. Strain accession data_2913 beta12orEarlier true 1.26 An accession of annotation on a (group of) viruses (catalogued in a database). Virus identifier true data_2914 beta12orEarlier Metadata on sequence features. Sequence features metadata data_2915 beta12orEarlier Identifier of a Gramene database entry. Gramene identifier data_2916 beta12orEarlier An identifier of an entry from the DDBJ sequence database. DDBJ ID DDBJ accession number DDBJ identifier DDBJ accession data_2917 beta12orEarlier An identifier of an entity from the ConsensusPathDB database. ConsensusPathDB identifier data_2925 beta12orEarlier 1.8 Data concerning, extracted from, or derived from the analysis of molecular sequence(s). This is a broad data type and is used a placeholder for other, more specific types. Sequence data true data_2927 beta12orEarlier beta13 Data concerning codon usage. This is a broad data type and is used a placeholder for other, more specific types. Codon usage true data_2954 beta12orEarlier 1.5 Data derived from the analysis of a scientific text such as a full text article from a scientific journal. Article report true data_2955 beta12orEarlier An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. Sequence-derived report Sequence report data_2956 beta12orEarlier Data concerning the properties or features of one or more protein secondary structures. Protein secondary structure data_2957 beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. Hopp and Woods plot data_2958 beta12orEarlier 1.21 A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Nucleic acid melting curve true data_2959 beta12orEarlier 1.21 A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Nucleic acid probability profile true data_2960 beta12orEarlier 1.21 A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Nucleic acid temperature profile true data_2961 beta12orEarlier 1.8 A report typically including a map (diagram) of a gene regulatory network. Gene regulatory network report true data_2965 beta12orEarlier 1.8 An informative report on a two-dimensional (2D PAGE) gel. 2D PAGE gel report true data_2966 beta12orEarlier 1.14 General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. Oligonucleotide probe sets annotation true data_2967 beta12orEarlier 1.5 An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. Microarray image true data_2968 beta12orEarlier Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen. Image data Image http://semanticscience.org/resource/SIO_000079 http://semanticscience.org/resource/SIO_000081 data_2969 beta12orEarlier Image of a molecular sequence, possibly with sequence features or properties shown. Sequence image data_2970 beta12orEarlier A report on protein properties concerning hydropathy. Protein hydropathy report Protein hydropathy data data_2971 beta12orEarlier beta13 Data concerning a computational workflow. Workflow data true data_2972 beta12orEarlier 1.5 A computational workflow. Workflow true data_2973 beta12orEarlier beta13 Data concerning molecular secondary structure data. Secondary structure data true data_2974 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 protein sequence (string of characters). Protein sequence (raw) true data_2975 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 nucleic acid sequence. Nucleic acid sequence (raw) true data_2976 beta12orEarlier One or more protein sequences, possibly with associated annotation. Amino acid sequence Amino acid sequences Protein sequences Protein sequence http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation data_2977 beta12orEarlier One or more nucleic acid sequences, possibly with associated annotation. Nucleic acid sequences Nucleotide sequence Nucleotide sequences DNA sequence Nucleic acid sequence http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation data_2978 beta12orEarlier Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. Enzyme kinetics annotation Reaction annotation This is a broad data type and is used a placeholder for other, more specific types. Reaction data data_2979 beta12orEarlier Data concerning small peptides. Peptide data Peptide property data_2980 beta12orEarlier Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19. 1.5 An informative report concerning the classification of protein sequences or structures. This is a broad data type and is used a placeholder for other, more specific types. Protein classification true data_2981 beta12orEarlier 1.8 Data concerning specific or conserved pattern in molecular sequences. This is a broad data type and is used a placeholder for other, more specific types. Sequence motif data true data_2982 beta12orEarlier beta13 Data concerning models representing a (typically multiple) sequence alignment. This is a broad data type and is used a placeholder for other, more specific types. Sequence profile data true data_2983 beta12orEarlier beta13 Data concerning a specific biological pathway or network. Pathway or network data true data_2984 beta12orEarlier An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. Pathway or network report data_2985 beta12orEarlier A thermodynamic or kinetic property of a nucleic acid molecule. Nucleic acid property (thermodynamic or kinetic) Nucleic acid thermodynamic property Nucleic acid thermodynamic data data_2986 beta12orEarlier Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19. 1.5 Data concerning the classification of nucleic acid sequences or structures. This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid classification true data_2987 beta12orEarlier 1.5 A report on a classification of molecular sequences, structures or other entities. This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. Classification report true data_2989 beta12orEarlier 1.8 key residues involved in protein folding. Protein features report (key folding sites) true data_2991 beta12orEarlier Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. Torsion angle data Protein geometry data data_2992 beta12orEarlier An image of protein structure. Structure image (protein) Protein structure image data_2994 beta12orEarlier Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. Phylogenetic character weights data_3002 beta12orEarlier Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. Genome annotation track Genome track Genome-browser track Genomic track Sequence annotation track Annotation track data_3021 beta12orEarlier P43353|Q7M1G0|Q9C199|A5A6J6 [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} Accession number of a UniProt (protein sequence) database entry. UniProt accession number UniProt entry accession UniProtKB accession UniProtKB accession number Swiss-Prot entry accession TrEMBL entry accession UniProt accession data_3022 beta12orEarlier 16 [1-9][0-9]? Identifier of a genetic code in the NCBI list of genetic codes. NCBI genetic code ID data_3025 beta12orEarlier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. Ontology concept identifier data_3026 beta12orEarlier beta12orEarlier The name of a concept for a biological process from the GO ontology. GO concept name (biological process) true data_3027 beta12orEarlier beta12orEarlier The name of a concept for a molecular function from the GO ontology. GO concept name (molecular function) true data_3028 beta12orEarlier Data concerning the classification, identification and naming of organisms. Taxonomic data This is a broad data type and is used a placeholder for other, more specific types. Taxonomy data_3029 beta13 EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. Protein ID (EMBL/GenBank/DDBJ) data_3031 beta13 1.5 A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. Core data entities typically have a format and may be identified by an accession number. Core data true data_3034 beta13 true Name or other identifier of molecular sequence feature(s). Sequence feature identifier data_3035 beta13 true An identifier of a molecular tertiary structure, typically an entry from a structure database. Structure identifier data_3036 beta13 true An identifier of an array of numerical values, such as a comparison matrix. Matrix identifier data_3085 beta13 1.8 A report (typically a table) on character or word composition / frequency of protein sequence(s). Protein sequence composition true data_3086 beta13 1.8 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). Nucleic acid sequence composition (report) true data_3101 beta13 1.5 A node from a classification of protein structural domain(s). Protein domain classification node true data_3102 beta13 Duplicates http://edamontology.org/data_1002, hence deprecated. 1.23 Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. CAS number true data_3103 beta13 Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). ATC code data_3104 beta13 A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). Unique Ingredient Identifier UNII data_3105 beta13 1.5 Basic information concerning geographical location or time. Geotemporal metadata true data_3106 beta13 Metadata concerning the software, hardware or other aspects of a computer system. System metadata data_3107 beta13 1.15 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Sequence feature name true data_3108 beta13 Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. Experimental measurement data Experimentally measured data Measured data Measurement Measurement data Measurement metadata Raw experimental 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. Experimental measurement data_3110 beta13 Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. Such data as found in Affymetrix CEL or GPR files. Raw microarray data data_3111 beta13 Data generated from processing and analysis of probe set data from a microarray experiment. Gene annotation (expression) Gene expression report Microarray probe set data Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. Processed microarray data data_3112 beta13 The final processed (normalised) data for a set of hybridisations in a microarray experiment. Gene expression data matrix Normalised microarray data This combines data from all hybridisations. Gene expression matrix data_3113 beta13 Annotation on a biological sample, for example experimental factors and their values. This might include compound and dose in a dose response experiment. Sample annotation data_3115 beta13 Annotation on the array itself used in a microarray experiment. This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. Microarray metadata data_3116 beta13 1.8 Annotation on laboratory and/or data processing protocols used in an microarray experiment. This might describe e.g. the normalisation methods used to process the raw data. Microarray protocol annotation true data_3117 beta13 Data concerning the hybridisations measured during a microarray experiment. Microarray hybridisation data data_3119 beta13 1.5 A report of regions in a molecular sequence that are biased to certain characters. Sequence features (compositionally-biased regions) true data_3122 beta13 1.5 A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. Nucleic acid features (difference and change) true data_3128 beta13 A human-readable collection of information about regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. Nucleic acid features (structure) Quadruplexes (report) Stem loop (report) d-loop (report) The report may be based on analysis of nucleic acid sequence or structural data, or any annotation or information about specific nucleic acid 3D structure(s) or such structures in general. Nucleic acid structure report data_3129 beta13 1.8 short repetitive subsequences (repeat sequences) in a protein sequence. Protein features report (repeats) true data_3130 beta13 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. Sequence motif matches (protein) true data_3131 beta13 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. Sequence motif matches (nucleic acid) true data_3132 beta13 1.5 A report on displacement loops in a mitochondrial DNA sequence. A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. Nucleic acid features (d-loop) true data_3133 beta13 1.5 A report on stem loops in a DNA sequence. A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. Nucleic acid features (stem loop) true data_3134 beta13 An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. Clone or EST (report) Gene transcript annotation Nucleic acid features (mRNA features) Transcript (report) mRNA (report) mRNA features This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). Gene transcript report data_3137 beta13 1.8 features of non-coding or functional RNA molecules, including tRNA and rRNA. Non-coding RNA true data_3138 beta13 1.5 Features concerning transcription of DNA into RNA including the regulation of transcription. This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. Transcriptional features (report) true data_3140 beta13 1.5 A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. Nucleic acid features (immunoglobulin gene structure) true data_3141 beta13 1.5 Information on a 'class' node from the SCOP database. SCOP class true data_3142 beta13 1.5 Information on a 'fold' node from the SCOP database. SCOP fold true data_3143 beta13 1.5 Information on a 'superfamily' node from the SCOP database. SCOP superfamily true data_3144 beta13 1.5 Information on a 'family' node from the SCOP database. SCOP family true data_3145 beta13 1.5 Information on a 'protein' node from the SCOP database. SCOP protein true data_3146 beta13 1.5 Information on a 'species' node from the SCOP database. SCOP species true data_3147 beta13 1.8 mass spectrometry experiments. Mass spectrometry experiment true data_3148 beta13 Nucleic acid classification A human-readable collection of information about a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure. Gene annotation (homology information) Gene annotation (homology) Gene family annotation Gene homology (report) Homology information This includes reports on on gene homologues between species. Gene family report data_3153 beta13 An image of a protein. Protein image data_3154 beta13 1.24 An alignment of protein sequences and/or structures. Protein alignment true data_3165 1.0 1.8 sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. NGS experiment true data_3181 1.1 An informative report about a DNA sequence assembly. Assembly report This might include an overall quality assessment of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. Sequence assembly report data_3210 1.1 An index of a genome sequence. Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. Genome index data_3231 1.1 1.8 Report concerning genome-wide association study experiments. GWAS report true data_3236 1.2 The position of a cytogenetic band in a genome. Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. Cytoband position data_3238 1.2 CL_[0-9]{7} Cell type ontology concept ID. CL ID Cell type ontology ID data_3241 1.2 Mathematical model of a network, that contains biochemical kinetics. Kinetic model data_3264 1.3 Identifier of a COSMIC database entry. COSMIC identifier COSMIC ID data_3265 1.3 Identifier of a HGMD database entry. HGMD identifier HGMD ID data_3266 1.3 true Unique identifier of sequence assembly. Sequence assembly version Sequence assembly ID data_3268 1.3 1.5 A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. Sequence feature type true data_3269 1.3 1.5 An informative report on gene homologues between species. Gene homology (report) true data_3270 1.3 ENSGT00390000003602 Unique identifier for a gene tree from the Ensembl database. Ensembl ID (gene tree) Ensembl gene tree ID data_3271 1.3 A phylogenetic tree that is an estimate of the character's phylogeny. Gene tree data_3272 1.3 A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. Species tree data_3273 1.3 true Name or other identifier of an entry from a biosample database. Sample accession Sample ID data_3274 1.3 Identifier of an object from the MGI database. MGI accession data_3275 1.3 Name of a phenotype. Phenotype Phenotypes Phenotype name data_3354 1.4 A HMM transition matrix contains the probabilities of switching from one HMM state to another. HMM transition matrix Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. Transition matrix data_3355 1.4 A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. HMM emission matrix Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. Emission matrix data_3356 1.4 1.15 A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. Hidden Markov model true data_3358 1.4 true An identifier of a data format. Format identifier data_3424 1.5 Raw biological or biomedical image generated by some experimental technique. Raw image http://semanticscience.org/resource/SIO_000081 data_3425 1.5 Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. Carbohydrate data Carbohydrate property data_3426 1.5 1.8 Report concerning proteomics experiments. Proteomics experiment report true data_3427 1.5 1.8 RNAi experiments. RNAi report true data_3428 1.5 1.8 biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. Simulation experiment report true data_3442 1.7 An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. MRT image Magnetic resonance imaging image Magnetic resonance tomography image NMRI image Nuclear magnetic resonance imaging image MRI image data_3449 1.7 An image from a cell migration track assay. Cell migration track image data_3451 1.7 Rate of association of a protein with another protein or some other molecule. kon Rate of association data_3479 1.7 Multiple gene identifiers in a specific order. Such data are often used for genome rearrangement tools and phylogenetic tree labeling. Gene order data_3483 1.7 The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. Spectra Spectrum data_3488 1.7 Spectral information for a molecule from a nuclear magnetic resonance experiment. NMR spectra NMR spectrum data_3490 1.8 1.21 A sketch of a small molecule made with some specialised drawing package. Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. Chemical structure sketch true data_3492 1.8 An informative report about a specific or conserved nucleic acid sequence pattern. Nucleic acid signature data_3494 1.8 A DNA sequence. DNA sequences DNA sequence data_3495 1.8 An RNA sequence. RNA sequences RNA sequence data_3496 1.8 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 RNA sequence. RNA sequence (raw) true data_3497 1.8 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 DNA sequence. DNA sequence (raw) true data_3498 1.8 Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. Gene sequence variations Variations are stored along with a reference genome. Sequence variations data_3505 1.8 A list of publications such as scientic papers or books. Bibliography data_3509 1.8 A mapping of supplied textual terms or phrases to ontology concepts (URIs). Ontology mapping data_3546 1.9 Any data concerning a specific biological or biomedical image. Image-associated data Image-related data This can include basic provenance and technical information about the image, scientific annotation and so on. Image metadata data_3558 1.9 A human-readable collection of information concerning a clinical trial. Clinical trial information Clinical trial report data_3567 1.10 A report about a biosample. Biosample report Reference sample report data_3568 1.10 Accession number of an entry from the Gene Expression Atlas. Gene Expression Atlas Experiment ID data_3667 1.12 true Identifier of an entry from a database of disease. Disease identifier data_3668 1.12 The name of some disease. Disease name data_3669 1.12 Learning resource Learning material is a document or another digital object that is designed for learning (educational, training) purposes. Educational material Open educational resource (OER) Teaching material Training material Learning material data_3670 1.12 A training course available for use on the Web. On-line course MOOC Massive open online course Online course data_3671 1.12 Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query. Free text Plain text Textual search query Text data_3707 1.14 Machine-readable biodiversity data. Biodiversity information OTU table Biodiversity data data_3716 1.14 A human-readable collection of information concerning biosafety data. Biosafety information Biosafety report data_3717 1.14 A report about any kind of isolation of biological material. Geographic location Isolation source Isolation report data_3718 1.14 Information about the ability of an organism to cause disease in a corresponding host. Pathogenicity Pathogenicity report data_3719 1.14 Information about the biosafety classification of an organism according to corresponding law. Biosafety level Biosafety classification data_3720 1.14 A report about localisation of the isolaton of biological material e.g. country or coordinates. Geographic location data_3721 1.14 A report about any kind of isolation source of biological material e.g. blood, water, soil. Isolation source data_3722 1.14 Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum. Physiology parameter data_3723 1.14 Experimentally determined parameter of the morphology of an organism, e.g. size & shape. Morphology parameter data_3724 1.14 Experimental determined parameter for the cultivation of an organism. Cultivation conditions Carbon source Culture media composition Nitrogen source Salinity Temperature pH value Cultivation parameter data_3732 1.15 Data concerning a sequencing experiment, that may be specified as an input to some tool. Sequencing metadata name data_3733 1.15 An identifier of a flow cell of a sequencing machine. A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 "lanes" which allows 8 experiments in a single analysis. Flow cell identifier data_3734 1.15 An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced. Lane identifier data_3735 1.15 A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. Run number data_3736 1.15 Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment. This is a broad data type and is used a placeholder for other, more specific types. Ecological data data_3737 1.15 The mean species diversity in sites or habitats at a local scale. α-diversity Alpha diversity data data_3738 1.15 The ratio between regional and local species diversity. True beta diversity β-diversity Beta diversity data data_3739 1.15 The total species diversity in a landscape. ɣ-diversity Gamma diversity data data_3743 1.15 A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart. Ordination plot data_3753 1.16 A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data. Enrichment report Over-representation report Functional enrichment report Over-representation data data_3754 1.16 GO-term report A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins. GO-term enrichment report Gene ontology concept over-representation report Gene ontology enrichment report Gene ontology term enrichment report GO-term enrichment data data_3756 1.16 Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. False localisation rate PTM localisation PTM score Localisation score data_3757 1.16 Identifier of a protein modification catalogued in the Unimod database. Unimod ID data_3759 1.16 Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. ProteomeXchange ID data_3768 1.16 Groupings of expression profiles according to a clustering algorithm. Clustered gene expression profiles Clustered expression profiles data_3769 1.16 An identifier of a concept from the BRENDA ontology. BRENDA ontology concept ID data_3779 1.16 A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations. Annotated text data_3786 1.16 A structured query, in form of a script, that defines a database search task. Query script data_3805 1.19 Structural 3D model (volume map) from electron microscopy. 3D EM Map data_3806 1.19 Annotation on a structural 3D EM Map from electron microscopy. This might include one or several locations in the map of the known features of a particular macromolecule. 3D EM Mask data_3807 1.19 Raw DDD movie acquisition from electron microscopy. EM Movie data_3808 1.19 Raw acquisition from electron microscopy or average of an aligned DDD movie. EM Micrograph data_3842 1.21 Data coming from molecular simulations, computer "experiments" on model molecules. Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic). Molecular simulation data data_3856 1.21 Identifier of an entry from the RNA central database of annotated human miRNAs. There are canonical and taxon-specific forms of RNAcentral ID. Canonical form e.g. urs_9or10digits identifies an RNA sequence (within the RNA central database) which may appear in multiple sequences. Taxon-specific form identifies a sequence in the specific taxon (e.g. urs_9or10digits_taxonID). RNA central ID data_3861 1.21 A human-readable systematic collection of patient (or population) health information in a digital format. EHR EMR Electronic medical record Electronic health record data_3869 1.22 Data coming from molecular simulations, computer "experiments" on model molecules. Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic). Simulation data_3870 1.22 Dynamic information of a structure molecular system coming from a molecular simulation: XYZ 3D coordinates (sometimes with their associated velocities) for every atom along time. Trajectory data data_3871 1.22 Force field parameters: charges, masses, radii, bond lengths, bond dihedrals, etc. define the structural molecular system, and are essential for the proper description and simulation of a molecular system. Forcefield parameters data_3872 1.22 Static information of a structure molecular system that is needed for a molecular simulation: the list of atoms, their non-bonded parameters for Van der Waals and electrostatic interactions, and the complete connectivity in terms of bonds, angles and dihedrals. Topology data data_3905 1.22 Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots. Density plot Histogram data_3914 1.23 Report of the quality control review that was made of factors involved in a procedure. QC metrics QC report Quality control metrics Quality control report data_3917 1.23 A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak). Read count matrix Count matrix data_3924 1.24 Alignment (superimposition) of DNA tertiary (3D) structures. Structure alignment (DNA) DNA structure alignment data_3932 1.24 A score derived from the P-value to ensure correction for multiple tests. The Q-value provides an estimate of the positive False Discovery Rate (pFDR), i.e. the rate of false positives among all the cases reported positive: pFDR = FP / (FP + TP). Adjusted P-value FDR Padj pFDR Q-values are widely used in high-throughput data analysis (e.g. detection of differentially expressed genes from transcriptome data). Q-value data_3949 1.24 A profile HMM is a variant of a Hidden Markov model that is derived specifically from a set of (aligned) biological sequences. Profile HMMs provide the basis for a position-specific scoring system, which can be used to align sequences and search databases for related sequences. Profile HMM data_3952 1.24 WP[0-9]+ Identifier of a pathway from the WikiPathways pathway database. WikiPathways ID WikiPathways pathway ID Pathway ID (WikiPathways) data_3953 1.24 A ranked list of pathways, each associated with z-score, p-value or similar, concerning or derived from the analysis of e.g. a set of genes or proteins. Pathway analysis results Pathway enrichment report Pathway over-representation report Pathway report Pathway term enrichment report Pathway overrepresentation data data_4022 1.26 \d{4}-\d{4}-\d{4}-\d{3}(\d|X) Identifier of a researcher registered with the ORCID database. Used to identify author IDs. ORCID Identifier data_4040 1.26 Data management plan is a document describing the data management of a project or an organisation, including acquisition, reuse, structure, processing, storage, documentation, sharing, and preservation of data. This may include budgeting for these operations. DMP Data management plan format_1196 beta12orEarlier Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. SMILES format_1197 beta12orEarlier Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. InChI format_1198 beta12orEarlier Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. The general MF query format consists of a series of valid atomic symbols, with an optional number or range. mf format_1199 beta12orEarlier The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification. InChIKey format_1200 beta12orEarlier SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. smarts format_1206 beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. unambiguous pure format_1207 beta12orEarlier Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. Non-sequence characters may be used for example for gaps. nucleotide http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence format_1208 beta12orEarlier Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. Non-sequence characters may be used for gaps and translation stop. protein http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence format_1209 beta12orEarlier Alphabet for the consensus of two or more molecular sequences. consensus format_1210 beta12orEarlier Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. pure nucleotide format_1211 beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . unambiguous pure nucleotide format_1212 beta12orEarlier Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. dna http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence format_1213 beta12orEarlier Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. rna http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence format_1214 beta12orEarlier Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. unambiguous pure dna format_1215 beta12orEarlier Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. pure dna format_1216 beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. unambiguous pure rna sequence format_1217 beta12orEarlier Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. pure rna format_1218 beta12orEarlier Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. unambiguous pure protein format_1219 beta12orEarlier Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. pure protein format_1228 beta12orEarlier beta12orEarlier Format of an entry from UniGene. A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. UniGene entry format true format_1247 beta12orEarlier beta12orEarlier Format of an entry from the COG database of clusters of (related) protein sequences. COG sequence cluster format true format_1248 beta12orEarlier Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. Feature location EMBL feature location format_1295 beta12orEarlier Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). quicktandem format_1296 beta12orEarlier Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). Sanger inverted repeats format_1297 beta12orEarlier Report format for tandem repeats in a sequence (an EMBOSS report format). EMBOSS repeat format_1316 beta12orEarlier Format of a report on exon-intron structure generated by EMBOSS est2genome. est2genome format format_1318 beta12orEarlier Report format for restriction enzyme recognition sites used by EMBOSS restrict program. restrict format format_1319 beta12orEarlier Report format for restriction enzyme recognition sites used by EMBOSS restover program. restover format format_1320 beta12orEarlier Report format for restriction enzyme recognition sites used by REBASE database. REBASE restriction sites format_1332 beta12orEarlier Format of results of a sequence database search using FASTA. This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) FASTA search results format format_1333 beta12orEarlier Format of results of a sequence database search using some variant of BLAST. This includes score data, alignment data and summary table. BLAST results format_1334 beta12orEarlier Format of results of a sequence database search using some variant of MSPCrunch. mspcrunch format_1335 beta12orEarlier Format of results of a sequence database search using some variant of Smith Waterman. Smith-Waterman format format_1336 beta12orEarlier Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. dhf format_1337 beta12orEarlier Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. The hits are putative ligand-binding sequences and are found from a search of a sequence database. lhf format_1341 beta12orEarlier Results format for searches of the InterPro database. InterPro hits format format_1342 beta12orEarlier Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. InterPro protein view report format format_1343 beta12orEarlier Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. InterPro match table format format_1349 beta12orEarlier Dirichlet distribution HMMER format. HMMER Dirichlet prior format_1350 beta12orEarlier Dirichlet distribution MEME format. MEME Dirichlet prior format_1351 beta12orEarlier Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. HMMER emission and transition format_1356 beta12orEarlier Format of a regular expression pattern from the Prosite database. prosite-pattern format_1357 beta12orEarlier Format of an EMBOSS sequence pattern. EMBOSS sequence pattern format_1360 beta12orEarlier A motif in the format generated by the MEME program. meme-motif format_1366 beta12orEarlier Sequence profile (sequence classifier) format used in the PROSITE database. prosite-profile format_1367 beta12orEarlier A profile (sequence classifier) in the format used in the JASPAR database. JASPAR format format_1369 beta12orEarlier Format of the model of random sequences used by MEME. MEME background Markov model format_1370 beta12orEarlier Format of a hidden Markov model representation used by the HMMER package. HMMER format format_1391 beta12orEarlier FASTA-style format for multiple sequences aligned by HMMER package to an HMM. HMMER-aln format_1392 beta12orEarlier Format of multiple sequences aligned by DIALIGN package. DIALIGN format format_1393 beta12orEarlier EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. The format is clustal-like and includes annotation of domain family classification information. daf format_1419 beta12orEarlier Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. Sequence-MEME profile alignment format_1421 beta12orEarlier Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. HMMER profile alignment (sequences versus HMMs) format_1422 beta12orEarlier Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. HMMER profile alignment (HMM versus sequences) format_1423 beta12orEarlier Format of PHYLIP phylogenetic distance matrix data. Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). Phylip distance matrix format_1424 beta12orEarlier Dendrogram (tree file) format generated by ClustalW. ClustalW dendrogram format_1425 beta12orEarlier Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. Phylip tree raw format_1430 beta12orEarlier PHYLIP file format for continuous quantitative character data. Phylip continuous quantitative characters format_1431 beta12orEarlier beta12orEarlier Format of phylogenetic property data. Phylogenetic property values format true format_1432 beta12orEarlier PHYLIP file format for phylogenetics character frequency data. Phylip character frequencies format format_1433 beta12orEarlier Format of PHYLIP discrete states data. Phylip discrete states format format_1434 beta12orEarlier Format of PHYLIP cliques data. Phylip cliques format format_1435 beta12orEarlier Phylogenetic tree data format used by the PHYLIP program. Phylip tree format format_1436 beta12orEarlier The format of an entry from the TreeBASE database of phylogenetic data. TreeBASE format format_1437 beta12orEarlier The format of an entry from the TreeFam database of phylogenetic data. TreeFam format format_1445 beta12orEarlier Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. Phylip tree distance format format_1454 beta12orEarlier Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. dssp format_1455 beta12orEarlier Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). hssp format_1457 beta12orEarlier Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. Vienna RNA format Vienna RNA secondary structure format Dot-bracket format format_1458 beta12orEarlier Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. Vienna local RNA secondary structure format format_1475 beta12orEarlier Format of an entry (or part of an entry) from the PDB database. PDB entry format PDB database entry format format_1476 beta12orEarlier Entry format of PDB database in PDB format. PDB format PDB format_1477 beta12orEarlier Entry format of PDB database in mmCIF format. mmCIF format_1478 beta12orEarlier Entry format of PDB database in PDBML (XML) format. PDBML format_1500 beta12orEarlier beta12orEarlier Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. Domainatrix 3D-1D scoring matrix format true format_1504 beta12orEarlier Amino acid index format used by the AAindex database. aaindex format_1511 beta12orEarlier beta12orEarlier Format of an entry from IntEnz (The Integrated Relational Enzyme Database). IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. IntEnz enzyme report format true format_1512 beta12orEarlier beta12orEarlier Format of an entry from the BRENDA enzyme database. BRENDA enzyme report format true format_1513 beta12orEarlier beta12orEarlier Format of an entry from the KEGG REACTION database of biochemical reactions. KEGG REACTION enzyme report format true format_1514 beta12orEarlier beta12orEarlier Format of an entry from the KEGG ENZYME database. KEGG ENZYME enzyme report format true format_1515 beta12orEarlier beta12orEarlier Format of an entry from the proto section of the REBASE enzyme database. REBASE proto enzyme report format true format_1516 beta12orEarlier beta12orEarlier Format of an entry from the withrefm section of the REBASE enzyme database. REBASE withrefm enzyme report format true format_1551 beta12orEarlier Format of output of the Pcons Model Quality Assessment Program (MQAP). Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. Pcons report format format_1552 beta12orEarlier Format of output of the ProQ protein model quality predictor. ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. ProQ report format format_1563 beta12orEarlier beta12orEarlier Format of SMART domain assignment data. The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. SMART domain assignment report format true format_1568 beta12orEarlier beta12orEarlier Entry format for the BIND database of protein interaction. BIND entry format true format_1569 beta12orEarlier beta12orEarlier Entry format for the IntAct database of protein interaction. IntAct entry format true format_1570 beta12orEarlier beta12orEarlier Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. InterPro entry format true format_1571 beta12orEarlier beta12orEarlier Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. References are included and a functional inference is made where possible. InterPro entry abstract format true format_1572 beta12orEarlier beta12orEarlier Entry format for the Gene3D protein secondary database. Gene3D entry format true format_1573 beta12orEarlier beta12orEarlier Entry format for the PIRSF protein secondary database. PIRSF entry format true format_1574 beta12orEarlier beta12orEarlier Entry format for the PRINTS protein secondary database. PRINTS entry format true format_1575 beta12orEarlier beta12orEarlier Entry format for the Panther library of protein families and subfamilies. Panther Families and HMMs entry format true format_1576 beta12orEarlier beta12orEarlier Entry format for the Pfam protein secondary database. Pfam entry format true format_1577 beta12orEarlier beta12orEarlier Entry format for the SMART protein secondary database. SMART entry format true format_1578 beta12orEarlier beta12orEarlier Entry format for the Superfamily protein secondary database. Superfamily entry format true format_1579 beta12orEarlier beta12orEarlier Entry format for the TIGRFam protein secondary database. TIGRFam entry format true format_1580 beta12orEarlier beta12orEarlier Entry format for the ProDom protein domain classification database. ProDom entry format true format_1581 beta12orEarlier beta12orEarlier Entry format for the FSSP database. FSSP entry format true format_1582 beta12orEarlier A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). findkm format_1603 beta12orEarlier beta12orEarlier Entry format of Ensembl genome database. Ensembl gene report format true format_1604 beta12orEarlier beta12orEarlier Entry format of DictyBase genome database. DictyBase gene report format true format_1605 beta12orEarlier beta12orEarlier Entry format of Candida Genome database. CGD gene report format true format_1606 beta12orEarlier beta12orEarlier Entry format of DragonDB genome database. DragonDB gene report format true format_1607 beta12orEarlier beta12orEarlier Entry format of EcoCyc genome database. EcoCyc gene report format true format_1608 beta12orEarlier beta12orEarlier Entry format of FlyBase genome database. FlyBase gene report format true format_1609 beta12orEarlier beta12orEarlier Entry format of Gramene genome database. Gramene gene report format true format_1610 beta12orEarlier beta12orEarlier Entry format of KEGG GENES genome database. KEGG GENES gene report format true format_1611 beta12orEarlier beta12orEarlier Entry format of the Maize genetics and genomics database (MaizeGDB). MaizeGDB gene report format true format_1612 beta12orEarlier beta12orEarlier Entry format of the Mouse Genome Database (MGD). MGD gene report format true format_1613 beta12orEarlier beta12orEarlier Entry format of the Rat Genome Database (RGD). RGD gene report format true format_1614 beta12orEarlier beta12orEarlier Entry format of the Saccharomyces Genome Database (SGD). SGD gene report format true format_1615 beta12orEarlier beta12orEarlier Entry format of the Sanger GeneDB genome database. GeneDB gene report format true format_1616 beta12orEarlier beta12orEarlier Entry format of The Arabidopsis Information Resource (TAIR) genome database. TAIR gene report format true format_1617 beta12orEarlier beta12orEarlier Entry format of the WormBase genomes database. WormBase gene report format true format_1618 beta12orEarlier beta12orEarlier Entry format of the Zebrafish Information Network (ZFIN) genome database. ZFIN gene report format true format_1619 beta12orEarlier beta12orEarlier Entry format of the TIGR genome database. TIGR gene report format true format_1620 beta12orEarlier beta12orEarlier Entry format for the dbSNP database. dbSNP polymorphism report format true format_1623 beta12orEarlier beta12orEarlier Format of an entry from the OMIM database of genotypes and phenotypes. OMIM entry format true format_1624 beta12orEarlier beta12orEarlier Format of a record from the HGVbase database of genotypes and phenotypes. HGVbase entry format true format_1625 beta12orEarlier beta12orEarlier Format of a record from the HIVDB database of genotypes and phenotypes. HIVDB entry format true format_1626 beta12orEarlier beta12orEarlier Format of an entry from the KEGG DISEASE database. KEGG DISEASE entry format true format_1627 beta12orEarlier Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. Primer3 primer format_1628 beta12orEarlier A format of raw sequence read data from an Applied Biosystems sequencing machine. ABI format_1629 beta12orEarlier Format of MIRA sequence trace information file. mira format_1630 beta12orEarlier caf Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. CAF format_1631 beta12orEarlier Sequence assembly project file EXP format. Affymetrix EXP format EXP format_1632 beta12orEarlier Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. SCF format_1633 beta12orEarlier PHD sequence trace format to store serialised chromatogram data (reads). PHD format_1637 beta12orEarlier Format of Affymetrix data file of raw image data. Affymetrix image data file format dat format_1638 beta12orEarlier Format of Affymetrix data file of information about (raw) expression levels of the individual probes. Affymetrix probe raw data format cel format_1639 beta12orEarlier Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. affymetrix format_1640 beta12orEarlier beta12orEarlier Entry format for the ArrayExpress microarrays database. ArrayExpress entry format true format_1641 beta12orEarlier Affymetrix data file format for information about experimental conditions and protocols. Affymetrix experimental conditions data file format affymetrix-exp format_1644 beta12orEarlier chp Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. Affymetrix probe normalised data format CHP format_1645 beta12orEarlier beta12orEarlier Format of an entry from the Electron Microscopy DataBase (EMDB). EMDB entry format true format_1647 beta12orEarlier beta12orEarlier The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. KEGG PATHWAY entry format true format_1648 beta12orEarlier beta12orEarlier The format of an entry from the MetaCyc metabolic pathways database. MetaCyc entry format true format_1649 beta12orEarlier beta12orEarlier The format of a report from the HumanCyc metabolic pathways database. HumanCyc entry format true format_1650 beta12orEarlier beta12orEarlier The format of an entry from the INOH signal transduction pathways database. INOH entry format true format_1651 beta12orEarlier beta12orEarlier The format of an entry from the PATIKA biological pathways database. PATIKA entry format true format_1652 beta12orEarlier beta12orEarlier The format of an entry from the reactome biological pathways database. Reactome entry format true format_1653 beta12orEarlier beta12orEarlier The format of an entry from the aMAZE biological pathways and molecular interactions database. aMAZE entry format true format_1654 beta12orEarlier beta12orEarlier The format of an entry from the CPDB database. CPDB entry format true format_1655 beta12orEarlier beta12orEarlier The format of an entry from the Panther Pathways database. Panther Pathways entry format true format_1665 beta12orEarlier Format of Taverna workflows. Taverna workflow format format_1666 beta12orEarlier beta12orEarlier Format of mathematical models from the BioModel database. Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. BioModel mathematical model format true format_1697 beta12orEarlier beta12orEarlier The format of an entry from the KEGG LIGAND chemical database. KEGG LIGAND entry format true format_1698 beta12orEarlier beta12orEarlier The format of an entry from the KEGG COMPOUND database. KEGG COMPOUND entry format true format_1699 beta12orEarlier beta12orEarlier The format of an entry from the KEGG PLANT database. KEGG PLANT entry format true format_1700 beta12orEarlier beta12orEarlier The format of an entry from the KEGG GLYCAN database. KEGG GLYCAN entry format true format_1701 beta12orEarlier beta12orEarlier The format of an entry from PubChem. PubChem entry format true format_1702 beta12orEarlier beta12orEarlier The format of an entry from a database of chemical structures and property predictions. ChemSpider entry format true format_1703 beta12orEarlier beta12orEarlier The format of an entry from Chemical Entities of Biological Interest (ChEBI). ChEBI includes an ontological classification defining relations between entities or classes of entities. ChEBI entry format true format_1704 beta12orEarlier beta12orEarlier The format of an entry from the MSDchem ligand dictionary. MSDchem ligand dictionary entry format true format_1705 beta12orEarlier The format of an entry from the HET group dictionary (HET groups from PDB files). HET group dictionary entry format format_1706 beta12orEarlier beta12orEarlier The format of an entry from the KEGG DRUG database. KEGG DRUG entry format true format_1734 beta12orEarlier Format of bibliographic reference as used by the PubMed database. PubMed citation format_1735 beta12orEarlier Format for abstracts of scientific articles from the Medline database. Bibliographic reference information including citation information is included Medline Display Format format_1736 beta12orEarlier CiteXplore 'core' citation format including title, journal, authors and abstract. CiteXplore-core format_1737 beta12orEarlier CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. CiteXplore-all format_1739 beta12orEarlier Article format of the PubMed Central database. pmc format_1740 beta12orEarlier The format of iHOP (Information Hyperlinked over Proteins) text-mining result. iHOP format format_1741 beta12orEarlier OSCAR format of annotated chemical text. OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document. OSCAR format format_1747 beta12orEarlier beta13 Format of an ATOM record (describing data for an individual atom) from a PDB file. PDB atom record format true format_1760 beta12orEarlier beta12orEarlier Format of CATH domain classification information for a polypeptide chain. The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. CATH chain report format true format_1761 beta12orEarlier beta12orEarlier Format of CATH domain classification information for a protein PDB file. The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. CATH PDB report format true format_1782 beta12orEarlier beta12orEarlier Entry (gene) format of the NCBI database. NCBI gene report format true format_1808 beta12orEarlier beta12orEarlier Moby:GI_Gene Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. GeneIlluminator gene report format true format_1809 beta12orEarlier beta12orEarlier Moby:BacMapGeneCard Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. BacMap gene card format true format_1810 beta12orEarlier beta12orEarlier Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). ColiCard report format true format_1861 beta12orEarlier Map of a plasmid (circular DNA) in PlasMapper TextMap format. PlasMapper TextMap format_1910 beta12orEarlier Phylogenetic tree Newick (text) format. nh newick format_1911 beta12orEarlier Phylogenetic tree TreeCon (text) format. TreeCon format format_1912 beta12orEarlier Phylogenetic tree Nexus (text) format. Nexus format format_1915 beta12orEarlier true A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. Data format Data model Exchange format File format The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. Format Data model A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models, however, do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) File format File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. format_1918 beta12orEarlier beta13 Data format for an individual atom. Atomic data format true format_1919 beta12orEarlier true Data format for a molecular sequence record. Sequence record format format_1920 beta12orEarlier true Data format for molecular sequence feature information. Sequence feature annotation format format_1921 beta12orEarlier true Data format for molecular sequence alignment information. Alignment format format_1923 beta12orEarlier ACEDB sequence format. acedb format_1924 beta12orEarlier beta12orEarlier Clustalw output format. clustal sequence format true format_1925 beta12orEarlier Codata entry format. codata format_1926 beta12orEarlier Fasta format variant with database name before ID. dbid format_1927 beta12orEarlier EMBL entry format. EMBL EMBL sequence format EMBL format format_1928 beta12orEarlier Staden experiment file format. Staden experiment format format_1929 beta12orEarlier FASTA format including NCBI-style IDs. FASTA format FASTA sequence format FASTA format_1930 beta12orEarlier fastq fq FASTQ short read format ignoring quality scores. FASTAQ fq FASTQ format_1931 beta12orEarlier FASTQ Illumina 1.3 short read format. FASTQ-illumina format_1932 beta12orEarlier FASTQ short read format with phred quality. FASTQ-sanger format_1933 beta12orEarlier FASTQ Solexa/Illumina 1.0 short read format. FASTQ-solexa format_1934 beta12orEarlier Fitch program format. fitch program format_1935 beta12orEarlier GCG sequence file format. GCG SSF GCG SSF (single sequence file) file format. GCG format_1936 beta12orEarlier Genbank entry format. GenBank GenBank format format_1937 beta12orEarlier Genpept protein entry format. Currently identical to refseqp format genpept format_1938 beta12orEarlier GFF feature file format with sequence in the header. GFF2-seq format_1939 beta12orEarlier GFF3 feature file format with sequence. GFF3-seq format_1940 beta12orEarlier FASTA sequence format including NCBI-style GIs. giFASTA format format_1941 beta12orEarlier Hennig86 output sequence format. hennig86 format_1942 beta12orEarlier Intelligenetics sequence format. ig format_1943 beta12orEarlier Intelligenetics sequence format (strict version). igstrict format_1944 beta12orEarlier Jackknifer interleaved and non-interleaved sequence format. jackknifer format_1945 beta12orEarlier Mase program sequence format. mase format format_1946 beta12orEarlier Mega interleaved and non-interleaved sequence format. mega-seq format_1947 beta12orEarlier GCG MSF (multiple sequence file) file format. GCG MSF format_1948 beta12orEarlier pir NBRF/PIR entry sequence format. nbrf pir nbrf/pir format_1949 beta12orEarlier Nexus/paup interleaved sequence format. nexus-seq format_1950 beta12orEarlier PDB sequence format (ATOM lines). pdb format in EMBOSS. pdbatom format_1951 beta12orEarlier PDB nucleotide sequence format (ATOM lines). pdbnuc format in EMBOSS. pdbatomnuc format_1952 beta12orEarlier PDB nucleotide sequence format (SEQRES lines). pdbnucseq format in EMBOSS. pdbseqresnuc format_1953 beta12orEarlier PDB sequence format (SEQRES lines). pdbseq format in EMBOSS. pdbseqres format_1954 beta12orEarlier Plain old FASTA sequence format (unspecified format for IDs). Pearson format format_1955 beta12orEarlier beta12orEarlier Phylip interleaved sequence format. phylip sequence format true format_1956 beta12orEarlier beta12orEarlier PHYLIP non-interleaved sequence format. phylipnon sequence format true format_1957 beta12orEarlier Raw sequence format with no non-sequence characters. raw format_1958 beta12orEarlier Refseq protein entry sequence format. Currently identical to genpept format refseqp format_1959 beta12orEarlier beta12orEarlier Selex sequence format. selex sequence format true format_1960 beta12orEarlier Staden suite sequence format. Staden format format_1961 beta12orEarlier Stockholm multiple sequence alignment format (used by Pfam and Rfam). Stockholm format format_1962 beta12orEarlier DNA strider output sequence format. strider format format_1963 beta12orEarlier UniProtKB entry sequence format. SwissProt format UniProt format UniProtKB format format_1964 beta12orEarlier txt Plain text sequence format (essentially unformatted). plain text format (unformatted) format_1965 beta12orEarlier beta12orEarlier Treecon output sequence format. treecon sequence format true format_1966 beta12orEarlier NCBI ASN.1-based sequence format. ASN.1 sequence format format_1967 beta12orEarlier DAS sequence (XML) format (any type). das sequence format DAS format format_1968 beta12orEarlier DAS sequence (XML) format (nucleotide-only). The use of this format is deprecated. dasdna format_1969 beta12orEarlier EMBOSS debugging trace sequence format of full internal data content. debug-seq format_1970 beta12orEarlier Jackknifer output sequence non-interleaved format. jackknifernon format_1971 beta12orEarlier beta12orEarlier Mega non-interleaved output sequence format. meganon sequence format true format_1972 beta12orEarlier NCBI FASTA sequence format with NCBI-style IDs. There are several variants of this. NCBI format format_1973 beta12orEarlier Nexus/paup non-interleaved sequence format. nexusnon format_1974 beta12orEarlier General Feature Format (GFF) of sequence features. GFF2 format_1975 beta12orEarlier Generic Feature Format version 3 (GFF3) of sequence features. GFF3 format_1976 beta12orEarlier 1.7 PIR feature format. pir true format_1977 beta12orEarlier beta12orEarlier Swiss-Prot feature format. swiss feature true format_1978 beta12orEarlier DAS GFF (XML) feature format. DASGFF feature das feature DASGFF format_1979 beta12orEarlier EMBOSS debugging trace feature format of full internal data content. debug-feat format_1980 beta12orEarlier beta12orEarlier EMBL feature format. EMBL feature true format_1981 beta12orEarlier beta12orEarlier Genbank feature format. GenBank feature true format_1982 beta12orEarlier ClustalW format for (aligned) sequences. clustal ClustalW format format_1983 beta12orEarlier EMBOSS alignment format for debugging trace of full internal data content. debug format_1984 beta12orEarlier Fasta format for (aligned) sequences. FASTA-aln format_1985 beta12orEarlier Pearson MARKX0 alignment format. markx0 format_1986 beta12orEarlier Pearson MARKX1 alignment format. markx1 format_1987 beta12orEarlier Pearson MARKX10 alignment format. markx10 format_1988 beta12orEarlier Pearson MARKX2 alignment format. markx2 format_1989 beta12orEarlier Pearson MARKX3 alignment format. markx3 format_1990 beta12orEarlier Alignment format for start and end of matches between sequence pairs. match format_1991 beta12orEarlier Mega format for (typically aligned) sequences. mega format_1992 beta12orEarlier Mega non-interleaved format for (typically aligned) sequences. meganon format_1993 beta12orEarlier beta12orEarlier MSF format for (aligned) sequences. msf alignment format true format_1994 beta12orEarlier beta12orEarlier Nexus/paup format for (aligned) sequences. nexus alignment format true format_1995 beta12orEarlier beta12orEarlier Nexus/paup non-interleaved format for (aligned) sequences. nexusnon alignment format true format_1996 beta12orEarlier EMBOSS simple sequence pairwise alignment format. pair format_1997 beta12orEarlier http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format Phylip format for (aligned) sequences. PHYLIP PHYLIP interleaved format ph phy PHYLIP format format_1998 beta12orEarlier http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format Phylip non-interleaved format for (aligned) sequences. PHYLIP sequential format phylipnon PHYLIP sequential format_1999 beta12orEarlier Alignment format for score values for pairs of sequences. scores format format_2000 beta12orEarlier SELEX format for (aligned) sequences. selex format_2001 beta12orEarlier EMBOSS simple multiple alignment format. EMBOSS simple format format_2002 beta12orEarlier Simple multiple sequence (alignment) format for SRS. srs format format_2003 beta12orEarlier Simple sequence pair (alignment) format for SRS. srspair format_2004 beta12orEarlier T-Coffee program alignment format. T-Coffee format format_2005 beta12orEarlier Treecon format for (aligned) sequences. TreeCon-seq format_2006 beta12orEarlier true Data format for a phylogenetic tree. Phylogenetic tree format format_2013 beta12orEarlier true Data format for a biological pathway or network. Biological pathway or network format format_2014 beta12orEarlier true Data format for a sequence-profile alignment. Sequence-profile alignment format format_2015 beta12orEarlier beta12orEarlier Data format for a sequence-HMM profile alignment. Sequence-profile alignment (HMM) format true format_2017 beta12orEarlier Data format for an amino acid index. Amino acid index format format_2020 beta12orEarlier true Data format for a full-text scientific article. Literature format Article format format_2021 beta12orEarlier true Data format of a report from text mining. Text mining report format format_2027 beta12orEarlier true Data format for reports on enzyme kinetics. Enzyme kinetics report format format_2030 beta12orEarlier true Format of a report on a chemical compound. Chemical compound annotation format Chemical structure format Small molecule report format Small molecule structure format Chemical data format format_2031 beta12orEarlier true Format of a report on a particular locus, gene, gene system or groups of genes. Gene features format Gene annotation format format_2032 beta12orEarlier true Format of a workflow. Programming language Script format Workflow format format_2033 beta12orEarlier true Data format for a molecular tertiary structure. Tertiary structure format format_2034 beta12orEarlier 1.2 Data format for a biological model. Biological model format true format_2035 beta12orEarlier true Text format of a chemical formula. Chemical formula format format_2036 beta12orEarlier true Format of raw (unplotted) phylogenetic data. Phylogenetic character data format format_2037 beta12orEarlier Format of phylogenetic continuous quantitative character data. Phylogenetic continuous quantitative character format format_2038 beta12orEarlier Format of phylogenetic discrete states data. Phylogenetic discrete states format format_2039 beta12orEarlier Format of phylogenetic cliques data. Phylogenetic tree report (cliques) format format_2040 beta12orEarlier Format of phylogenetic invariants data. Phylogenetic tree report (invariants) format format_2045 beta12orEarlier beta12orEarlier Annotation format for electron microscopy models. Electron microscopy model format true format_2049 beta12orEarlier true Format for phylogenetic tree distance data. Phylogenetic tree report (tree distances) format format_2051 beta12orEarlier 1.0 Format for sequence polymorphism data. Polymorphism report format true format_2052 beta12orEarlier true Format for reports on a protein family. Protein family report format format_2054 beta12orEarlier true Format for molecular interaction data. Molecular interaction format Protein interaction format format_2055 beta12orEarlier true Format for sequence assembly data. Sequence assembly format format_2056 beta12orEarlier Format for information about a microarray experimental per se (not the data generated from that experiment). Microarray experiment data format format_2057 beta12orEarlier Format for sequence trace data (i.e. including base call information). Sequence trace format format_2058 beta12orEarlier true Format of a file of gene expression data, e.g. a gene expression matrix or profile. Gene expression data format Gene expression report format format_2059 beta12orEarlier beta12orEarlier Format of a report on genotype / phenotype information. Genotype and phenotype annotation format true format_2060 beta12orEarlier true Format of a map of (typically one) molecular sequence annotated with features. Map format format_2061 beta12orEarlier true Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. Nucleic acid features (primers) format format_2062 beta12orEarlier true Format of a report of general information about a specific protein. Protein report format format_2063 beta12orEarlier beta12orEarlier Format of a report of general information about a specific enzyme. Protein report (enzyme) format true format_2064 beta12orEarlier Format of a matrix of 3D-1D scores (amino acid environment probabilities). 3D-1D scoring matrix format format_2065 beta12orEarlier true Format of a report on the quality of a protein three-dimensional model. Protein structure report (quality evaluation) format format_2066 beta12orEarlier true Format of a report on sequence hits and associated data from searching a sequence database. Database hits (sequence) format format_2067 beta12orEarlier true Format of a matrix of genetic distances between molecular sequences. Sequence distance matrix format format_2068 beta12orEarlier true Format of a sequence motif. Sequence motif format format_2069 beta12orEarlier true Format of a sequence profile. Sequence profile format format_2072 beta12orEarlier Format of a hidden Markov model. Hidden Markov model format format_2074 beta12orEarlier true Data format of a dirichlet distribution. Dirichlet distribution format format_2075 beta12orEarlier true Data format for the emission and transition counts of a hidden Markov model. HMM emission and transition counts format format_2076 beta12orEarlier true Format for secondary structure (predicted or real) of an RNA molecule. RNA secondary structure format format_2077 beta12orEarlier true Format for secondary structure (predicted or real) of a protein molecule. Protein secondary structure format format_2078 beta12orEarlier true Format used to specify range(s) of sequence positions. Sequence range format format_2094 beta12orEarlier Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. pure format_2095 beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. unpure format_2096 beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. unambiguous sequence format_2097 beta12orEarlier Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. ambiguous format_2155 beta12orEarlier true Format used for map of repeats in molecular (typically nucleotide) sequences. Sequence features (repeats) format format_2158 beta12orEarlier true Format used for report on restriction enzyme recognition sites in nucleotide sequences. Nucleic acid features (restriction sites) format format_2159 beta12orEarlier 1.10 Format used for report on coding regions in nucleotide sequences. Gene features (coding region) format true format_2170 beta12orEarlier true Format used for clusters of molecular sequences. Sequence cluster format format_2171 beta12orEarlier Format used for clusters of protein sequences. Sequence cluster format (protein) format_2172 beta12orEarlier Format used for clusters of nucleotide sequences. Sequence cluster format (nucleic acid) format_2175 beta12orEarlier beta13 Format used for clusters of genes. Gene cluster format true format_2181 beta12orEarlier A text format resembling EMBL entry format. This concept may be used for the many non-standard EMBL-like text formats. EMBL-like (text) format_2182 beta12orEarlier A text format resembling FASTQ short read format. This concept may be used for non-standard FASTQ short read-like formats. FASTQ-like format (text) format_2183 beta12orEarlier true XML format for EMBL entries. EMBLXML https://fairsharing.org/bsg-s001452/ format_2184 beta12orEarlier true Specific XML format for EMBL entries (only uses certain sections). cdsxml https://fairsharing.org/bsg-s001452/ format_2185 beta12orEarlier INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/DDBJ-style flatfile formats, with a small amount of additional structure. INSD XML INSDC XML INSDSeq format_2186 beta12orEarlier Geneseq sequence format. geneseq format_2187 beta12orEarlier A text sequence format resembling uniprotkb entry format. UniProt-like (text) format_2188 beta12orEarlier 1.8 UniProt entry sequence format. UniProt format true format_2189 beta12orEarlier 1.8 ipi sequence format. ipi true format_2194 beta12orEarlier Abstract format used by MedLine database. medline format_2195 beta12orEarlier true Format used for ontologies. Ontology format format_2196 beta12orEarlier A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. OBO format format_2200 beta12orEarlier A text format resembling FASTA format. This concept may also be used for the many non-standard FASTA-like formats. FASTA-like (text) http://filext.com/file-extension/FASTA format_2202 beta12orEarlier 1.8 Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. Sequence record full format true format_2203 beta12orEarlier 1.8 Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. Sequence record lite format true format_2204 beta12orEarlier An XML format for EMBL entries. This is a placeholder for other more specific concepts. It should not normally be used for annotation. EMBL format (XML) format_2205 beta12orEarlier A text format resembling GenBank entry (plain text) format. This concept may be used for the non-standard GenBank-like text formats. GenBank-like format (text) format_2206 beta12orEarlier Text format for a sequence feature table. Sequence feature table format (text) format_2210 beta12orEarlier 1.0 Format of a report on organism strain data / cell line. Strain data format true format_2211 beta12orEarlier beta12orEarlier Format for a report of strain data as used for CIP database entries. CIP strain data format true format_2243 beta12orEarlier beta12orEarlier PHYLIP file format for phylogenetic property data. phylip property values true format_2303 beta12orEarlier beta12orEarlier Entry format (HTML) for the STRING database of protein interaction. STRING entry format (HTML) true format_2304 beta12orEarlier Entry format (XML) for the STRING database of protein interaction. STRING entry format (XML) format_2305 beta12orEarlier GFF feature format (of indeterminate version). GFF format_2306 beta12orEarlier Gene Transfer Format (GTF), a restricted version of GFF. GTF format_2310 beta12orEarlier FASTA format wrapped in HTML elements. FASTA-HTML format_2311 beta12orEarlier EMBL entry format wrapped in HTML elements. EMBL-HTML format_2322 beta12orEarlier beta12orEarlier Format of an entry from the BioCyc enzyme database. BioCyc enzyme report format true format_2323 beta12orEarlier beta12orEarlier Format of an entry from the Enzyme nomenclature database (ENZYME). ENZYME enzyme report format true format_2328 beta12orEarlier beta12orEarlier Format of a report on a gene from the PseudoCAP database. PseudoCAP gene report format true format_2329 beta12orEarlier beta12orEarlier Format of a report on a gene from the GeneCards database. GeneCards gene report format true format_2330 beta12orEarlier Textual format. Plain text format txt Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). Textual format http://filext.com/file-extension/TXT http://www.iana.org/assignments/media-types/media-types.xhtml#text http://www.iana.org/assignments/media-types/text/plain format_2331 beta12orEarlier HTML format. Hypertext Markup Language HTML http://filext.com/file-extension/HTML format_2332 beta12orEarlier xml eXtensible Markup Language (XML) format. eXtensible Markup Language Data in XML format can be serialised into text, or binary format. XML format_2333 beta12orEarlier true Binary format. Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. Binary format format_2334 beta12orEarlier beta13 Typical textual representation of a URI. URI format true format_2341 beta12orEarlier beta12orEarlier The format of an entry from the NCI-Nature pathways database. NCI-Nature pathway entry format true format_2350 beta12orEarlier true A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented. Format (typed) This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. Format (by type of data) format_2352 beta12orEarlier Any ontology allowed, none mandatory. Preferably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology. BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming. BioJSON BioXSD BioXSD XML BioXSD XML format BioXSD data model BioXSD format BioXSD in XML BioXSD in XML format BioXSD+XML BioXSD/GTrack BioXSD|GTrack BioYAML 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. BioXSD (XML) format_2376 beta12orEarlier A serialisation format conforming to the Resource Description Framework (RDF) model. Resource Description Framework format RDF Resource Description Framework RDF format format_2532 beta12orEarlier Genbank entry format wrapped in HTML elements. GenBank-HTML format_2542 beta12orEarlier beta12orEarlier Format of a report on protein features (domain composition). Protein features (domains) format true format_2543 beta12orEarlier A format resembling EMBL entry (plain text) format. This concept may be used for the many non-standard EMBL-like formats. EMBL-like format format_2545 beta12orEarlier A format resembling FASTQ short read format. This concept may be used for non-standard FASTQ short read-like formats. FASTQ-like format format_2546 beta12orEarlier A format resembling FASTA format. This concept may be used for the many non-standard FASTA-like formats. FASTA-like format_2547 beta12orEarlier A sequence format resembling uniprotkb entry format. uniprotkb-like format format_2548 beta12orEarlier Format for a sequence feature table. Sequence feature table format format_2549 beta12orEarlier OBO ontology text format. OBO format_2550 beta12orEarlier OBO ontology XML format. OBO-XML format_2551 beta12orEarlier Data format for a molecular sequence record (text). Sequence record format (text) format_2552 beta12orEarlier Data format for a molecular sequence record (XML). Sequence record format (XML) format_2553 beta12orEarlier XML format for a sequence feature table. Sequence feature table format (XML) format_2554 beta12orEarlier Text format for molecular sequence alignment information. Alignment format (text) format_2555 beta12orEarlier XML format for molecular sequence alignment information. Alignment format (XML) format_2556 beta12orEarlier Text format for a phylogenetic tree. Phylogenetic tree format (text) format_2557 beta12orEarlier XML format for a phylogenetic tree. Phylogenetic tree format (XML) format_2558 beta12orEarlier An XML format resembling EMBL entry format. This concept may be used for the any non-standard EMBL-like XML formats. EMBL-like (XML) format_2559 beta12orEarlier A format resembling GenBank entry (plain text) format. This concept may be used for the non-standard GenBank-like formats. GenBank-like format format_2560 beta12orEarlier beta12orEarlier Entry format for the STRING database of protein interaction. STRING entry format true format_2561 beta12orEarlier Text format for sequence assembly data. Sequence assembly format (text) format_2562 beta12orEarlier beta13 Text format (representation) of amino acid residues. Amino acid identifier format true format_2566 beta12orEarlier Alphabet for a molecular sequence without any unknown positions or ambiguity characters. completely unambiguous format_2567 beta12orEarlier Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. completely unambiguous pure format_2568 beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . completely unambiguous pure nucleotide format_2569 beta12orEarlier Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. completely unambiguous pure dna format_2570 beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. completely unambiguous pure rna sequence format_2571 beta12orEarlier true Format of a raw molecular sequence (i.e. the alphabet used). Raw sequence format http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence format_2572 beta12orEarlier BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. BAM format_2573 beta12orEarlier Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. SAM format_2585 beta12orEarlier Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. SBML format_2607 beta12orEarlier Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. completely unambiguous pure protein format_2848 beta12orEarlier true Format of a bibliographic reference. Bibliographic reference format format_2919 beta12orEarlier Format of a sequence annotation track. Sequence annotation track format format_2920 beta12orEarlier Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. Alignment format (pair only) format_2921 beta12orEarlier true Format of sequence variation annotation. Sequence variation annotation format format_2922 beta12orEarlier Some variant of Pearson MARKX alignment format. markx0 variant format_2923 beta12orEarlier Some variant of Mega format for (typically aligned) sequences. mega variant format_2924 beta12orEarlier Some variant of Phylip format for (aligned) sequences. Phylip format variant format_3000 beta12orEarlier AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). AB1 format_3001 beta12orEarlier ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). ACE format_3003 beta12orEarlier Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). BED format_3004 beta12orEarlier bigBed format for large sequence annotation tracks, similar to textual BED format. bigBed format_3005 beta12orEarlier wig Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. WIG format_3006 beta12orEarlier bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. bigWig format_3007 beta12orEarlier PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. PSL format_3008 beta12orEarlier Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. MAF format_3009 beta12orEarlier 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. 2bit format_3010 beta12orEarlier .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. .nib format_3011 beta12orEarlier gp genePred table format for gene prediction tracks. genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. genePred format_3012 beta12orEarlier Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. pgSnp format_3013 beta12orEarlier axt format of alignments, typically produced from BLASTZ. axt format_3014 beta12orEarlier lav LAV format of alignments generated by BLASTZ and LASTZ. LAV format_3015 beta12orEarlier Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). Pileup format_3016 beta12orEarlier vcf vcf.gz Variant Call Format (VCF) is tabular format for storing genomic sequence variations. 1000 Genomes Project has its own specification for encoding structural variations in VCF (https://www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%20Call%20Format)%20version%204.0/encoding-structural-variants). This is based on VCF version 4.0 and not directly compatible with VCF version 4.3. VCF format_3017 beta12orEarlier Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. SRF format_3018 beta12orEarlier ZTR format for storing chromatogram data from DNA sequencing instruments. ZTR format_3019 beta12orEarlier Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. GVF format_3020 beta12orEarlier bcf bcf.gz BCF is the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). BCF format_3033 beta13 true Format of a matrix (array) of numerical values. Matrix format format_3097 beta13 true Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). Protein domain classification format format_3098 beta13 Format of raw SCOP domain classification data files. These are the parsable data files provided by SCOP. Raw SCOP domain classification format format_3099 beta13 Format of raw CATH domain classification data files. These are the parsable data files provided by CATH. Raw CATH domain classification format format_3100 beta13 Format of summary of domain classification information for a CATH domain. The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. CATH domain report format format_3155 1.0 Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. SBRML format_3156 1.0 BioPAX is an exchange format for pathway data, with its data model defined in OWL. BioPAX format_3157 1.0 EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. EBI Application Result XML format_3158 1.0 XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. MIF PSI MI XML (MIF) format_3159 1.0 phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. phyloXML format_3160 1.0 NeXML is a standardised XML format for rich phyloinformatic data. NeXML format_3161 1.0 MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). MAGE-ML format_3162 1.0 MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). MAGE-TAB format_3163 1.0 GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). GCDML format_3164 1.0 GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability"). BioXSD/GTrack GTrack BioXSD|GTrack GTrack GTrack ecosystem of formats GTrack format GTrack|BTrack|GSuite GTrack GTrack|GSuite|BTrack GTrack 'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes. GTrack format_3166 1.0 true Data format for a report of information derived from a biological pathway or network. Biological pathway or network report format format_3167 1.0 true Data format for annotation on a laboratory experiment. Experiment annotation format format_3235 1.2 Cytoband format for chromosome cytobands. Reflects a UCSC Browser DB table. Cytoband format format_3239 1.2 CopasiML, the native format of COPASI. CopasiML format_3240 1.2 CellML, the format for mathematical models of biological and other networks. CellML format_3242 1.2 Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. PSI MI TAB (MITAB) format_3243 1.2 Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. PSI-PAR format_3244 1.2 mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. mzML format_3245 1.2 true Format for mass pectra and derived data, include peptide sequences etc. Mass spectrometry data format format_3246 1.2 TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. TraML format_3247 1.2 mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. mzIdentML format_3248 1.2 mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. mzQuantML format_3249 1.2 GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. GelML format_3250 1.2 spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. spML format_3252 1.2 A human-readable encoding for the Web Ontology Language (OWL). OWL Functional Syntax format_3253 1.2 A syntax for writing OWL class expressions. This format was influenced by the OWL Abstract Syntax and the DL style syntax. Manchester OWL Syntax format_3254 1.2 A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". This format is used in Protege 4. KRSS2 Syntax format_3255 1.2 The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. The SPARQL Query Language incorporates a very similar syntax. Turtle format_3256 1.2 nt A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. N-Triples should not be confused with Notation 3 which is a superset of Turtle. N-Triples format_3257 1.2 n3 A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind. N3 Notation3 format_3262 1.2 OWL ontology XML serialisation format. OWL OWL/XML format_3281 1.3 The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. A2M format_3284 1.3 Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. Standard flowgram format SFF format_3285 1.3 The MAP file describes SNPs and is used by the Plink package. Plink MAP MAP format_3286 1.3 The PED file describes individuals and genetic data and is used by the Plink package. Plink PED PED format_3287 1.3 true Data format for a metadata on an individual and their genetic data. Individual genetic data format format_3288 1.3 The PED/MAP file describes data used by the Plink package. Plink PED/MAP PED/MAP format_3309 1.3 File format of a CT (Connectivity Table) file from the RNAstructure package. Connect format Connectivity Table file format CT format_3310 1.3 XRNA old input style format. SS format_3311 1.3 RNA Markup Language. RNAML format_3312 1.3 Format for the Genetic Data Environment (GDE). GDE format_3313 1.3 A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) package. Block file format BLC format_3326 1.3 true Format of a data index of some type. Data index format format_3327 1.3 BAM indexing format. BAI format_3328 1.3 HMMER profile HMM file for HMMER versions 2.x. HMMER2 format_3329 1.3 HMMER profile HMM file for HMMER versions 3.x. HMMER3 format_3330 1.3 PO is the output format of Partial Order Alignment program (POA) performing Multiple Sequence Alignment (MSA). PO format_3331 1.3 XML format as produced by the NCBI Blast package. BLAST XML results format format_3462 1.7 http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf Reference-based compression of alignment format. CRAM format_3464 1.7 json JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs. JavaScript Object Notation JSON format_3466 1.7 Encapsulated PostScript format. EPS format_3467 1.7 Graphics Interchange Format. GIF format_3468 1.7 Microsoft Excel spreadsheet format. Microsoft Excel format xls format_3475 1.7 tab tsv Tabular data represented as tab-separated values in a text file. Tab-delimited Tab-separated values tab TSV format_3476 1.7 1.10 Format of a file of gene expression data, e.g. a gene expression matrix or profile. Gene expression data format true format_3477 1.7 Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. Cytoscape input file format format_3484 1.7 https://github.com/BenLangmead/bowtie/blob/master/MANUAL Bowtie format for indexed reference genome for "small" genomes. Bowtie index format ebwt format_3485 1.7 http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf Rich sequence format. GCG RSF RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). RSF format_3486 1.7 Some format based on the GCG format. GCG format variant format_3487 1.7 http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc Bioinformatics Sequence Markup Language format. BSML format_3491 1.7 https://github.com/BenLangmead/bowtie/blob/master/MANUAL Bowtie format for indexed reference genome for "large" genomes. Bowtie long index format ebwtl format_3499 1.8 Ensembl standard format for variation data. Ensembl variation file format format_3506 1.8 Microsoft Word format. Microsoft Word format doc docx format_3507 1.8 true Format of documents including word processor, spreadsheet and presentation. Document format format_3508 1.8 Portable Document Format. PDF format_3547 1.9 true Format used for images and image metadata. Image format format_3548 1.9 Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. DICOM format format_3549 1.9 nii An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI) commonly used to store brain imaging data obtained using Magnetic Resonance Imaging (MRI) methods. NIFTI format NIfTI-1 format nii format_3550 1.9 Text-based tagged file format for medical images generated using the MetaImage software package. Metalmage format mhd format_3551 1.9 Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. nrrd format_3554 1.9 File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. R file format format_3555 1.9 File format used for scripts for the Statistical Package for the Social Sciences. SPSS format_3556 1.9 eml mht mhtml MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. HTML email format HTML email message format MHT MHT format MHTML format MIME HTML MIME HTML format eml MIME multipart MIME multipart format MIME multipart message MIME multipart message format MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons included in EDAM as a specialisation of 'HTML'. MHTML format_3578 1.10 Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. IDAT format_3579 1.10 Joint Picture Group file format for lossy graphics file. JPEG jpeg Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. JPG format_3580 1.10 Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts. rcc format_3581 1.11 ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes. This file format is for machine learning. arff format_3582 1.11 AFG is a single text-based file assembly format that holds read and consensus information together. afg format_3583 1.11 The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. Holds a tab-delimited chromosome /start /end / datavalue dataset. bedgraph format_3584 1.11 Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. bedstrict format_3585 1.11 BED file format where each feature is described by chromosome, start, end, name, score, and strand. Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6 bed6 format_3586 1.11 A BED file where each feature is described by all twelve columns. Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12 bed12 format_3587 1.11 Tabular format of chromosome names and sizes used by Galaxy. Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. chrominfo format_3588 1.11 Custom Sequence annotation track format used by Galaxy. Used for tracks/track views within galaxy. customtrack format_3589 1.11 Color space FASTA format sequence variant. FASTA format extended for color space information. csfasta format_3590 1.11 HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF). h5 An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package. HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF. HDF5 format_3591 1.11 A versatile bitmap format. The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs. TIFF format_3592 1.11 Standard bitmap storage format in the Microsoft Windows environment. Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications. BMP format_3593 1.11 IM is a format used by LabEye and other applications based on the IFUNC image processing library. IFUNC library reads and writes most uncompressed interchange versions of this format. im format_3594 1.11 pcd Photo CD format, which is the highest resolution format for images on a CD. PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications. pcd format_3595 1.11 PCX is an image file format that uses a simple form of run-length encoding. It is lossless. pcx format_3596 1.11 The PPM format is a lowest common denominator color image file format. ppm format_3597 1.11 PSD (Photoshop Document) is a proprietary file that allows the user to work with the images' individual layers even after the file has been saved. psd format_3598 1.11 X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. The XBM format was replaced by XPM for X11 in 1989. xbm format_3599 1.11 X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. xpm format_3600 1.11 RGB file format is the native raster graphics file format for Silicon Graphics workstations. rgb format_3601 1.11 The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. pbm format_3602 1.11 The PGM format is a lowest common denominator grayscale file format. It is designed to be extremely easy to learn and write programs for. pgm format_3603 1.11 png PNG is a file format for image compression. It iis expected to replace the Graphics Interchange Format (GIF). PNG format_3604 1.11 Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. Scalable Vector Graphics The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. SVG format_3605 1.11 Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems. The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. rast format_3606 1.11 true Textual report format for sequence quality for reports from sequencing machines. Sequence quality report format (text) format_3607 1.11 http://en.wikipedia.org/wiki/Phred_quality_score FASTQ format subset for Phred sequencing quality score data only (no sequences). Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities. qual format_3608 1.11 FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format. Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected) qualsolexa format_3609 1.11 http://en.wikipedia.org/wiki/Phred_quality_score FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8. Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator. qualillumina format_3610 1.11 http://en.wikipedia.org/wiki/Phred_quality_score FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data. For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format. qualsolid format_3611 1.11 http://en.wikipedia.org/wiki/Phred_quality_score FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. qual454 format_3612 1.11 Human ENCODE peak format. Format that covers both the broad peak format and narrow peak format from ENCODE. ENCODE peak format format_3613 1.11 Human ENCODE narrow peak format. Format that covers both the broad peak format and narrow peak format from ENCODE. ENCODE narrow peak format format_3614 1.11 Human ENCODE broad peak format. ENCODE broad peak format format_3615 1.11 bgz Blocked GNU Zip format. BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format). bgzip format_3616 1.11 TAB-delimited genome position file index format. tabix format_3617 1.11 true Data format for graph data. Graph format format_3618 1.11 XML-based format used to store graph descriptions within Galaxy. xgmml format_3619 1.11 SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. sif format_3620 1.11 MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. xlsx format_3621 1.11 Data format used by the SQLite database. SQLite format format_3622 1.11 Data format used by the SQLite database conformant to the Gemini schema. Gemini SQLite format format_3623 1.11 Duplicate of http://edamontology.org/format_3326 1.20 Format of a data index of some type. Index format true format_3624 1.11 An index of a genome database, indexed for use by the snpeff tool. snpeffdb format_3626 1.12 Binary format used by MATLAB files to store workspace variables. .mat file format MAT file format MATLAB file format MAT format_3650 1.12 Format used by netCDF software library for writing and reading chromatography-MS data files. Also used to store trajectory atom coordinates information, such as the ones obtained by Molecular Dynamics simulations. ANDI-MS Network Common Data Form (NetCDF) library is supported by AMBER MD package from version 9. NetCDF format_3651 1.12 mgf Mascot Generic Format. Encodes multiple MS/MS spectra in a single file. Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions. MGF format_3652 1.12 Spectral data format file where each spectrum is written to a separate file. Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum. dta format_3653 1.12 Spectral data file similar to dta. Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to. pkl format_3654 1.12 https://dx.doi.org/10.1038%2Fnbt1031 Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. mzXML format_3655 1.12 http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. pepXML format_3657 1.12 Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways. GPML format_3665 1.12 oxlicg A list of k-mers and their occurrences in a dataset. Can also be used as an implicit De Bruijn graph. K-mer countgraph format_3681 1.13 mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results. mzTab format_3682 1.13 imzml imzML metadata is a data format for mass spectrometry imaging metadata. imzML data are recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. This entry is for the metadata XML file imzML metadata file format_3683 1.13 qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements. The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well. qcML format_3684 1.13 PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment. PRIDE XML format_3685 1.13 Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements. SED-ML format_3686 1.13 Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network). COMBINE OMEX format_3687 1.13 The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from experiments employing a combination of technologies. ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata). ISA-TAB format_3688 1.13 SBtab is a tabular format for biochemical network models. SBtab format_3689 1.13 Biological Connection Markup Language (BCML) is an XML format for biological pathways. BCML format_3690 1.13 Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. BDML format_3691 1.13 Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. BEL format_3692 1.13 SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. SBGN-ML format_3693 1.13 agp AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome). AGP format_3696 1.13 PostScript format. PostScript PS format_3698 1.13 sra SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. SRA SRA archive format SRA format format_3699 1.13 VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. SRA native format VDB format_3700 1.13 Index file format used by the samtools package to index TAB-delimited genome position files. Tabix index file format format_3701 1.13 A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). Sequin format format_3702 1.14 Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. Magellan storage file format This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. MSF format_3706 1.14 true Data format for biodiversity data. Biodiversity data format format_3708 1.14 Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). ABCD ABCD format format_3709 1.14 Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample. GCT format Res format GCT/Res format format_3710 1.14 wiff Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex). wiff WIFF format format_3711 1.14 Output format used by X! series search engines that is based on the XML language BIOML. X!Tandem XML format_3712 1.14 Proprietary file format for mass spectrometry data from Thermo Scientific. Proprietary format for which documentation is not available. Thermo RAW format_3713 1.14 "Raw" result file from Mascot database search. Mascot .dat file format_3714 1.14 Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. MaxQuant APL MaxQuant APL peaklist format format_3725 1.14 Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs. SBOL format_3726 1.14 PMML uses XML to represent mining models. The structure of the models is described by an XML Schema. One or more mining models can be contained in a PMML document. PMML format_3727 1.14 Image file format used by the Open Microscopy Environment (OME). An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file's first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions. OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. OME-TIFF format_3728 1.14 The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record. Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs. LocARNA PP format_3729 1.14 Input format used by the Database of Genotypes and Phenotypes (dbGaP). The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. dbGaP format format_3746 1.15 biom The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables. BIological Observation Matrix format biom BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. BIOM format format_3747 1.15 A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data. No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML). protXML http://doi.org/10.1038/msb4100024 http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v3.xsd format_3748 1.15 true A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries. Semantic Web format Linked data format format_3749 1.15 jsonld JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON. JavaScript Object Notation for Linked Data jsonld JSON-LD format_3750 1.15 yaml yml YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. YAML Ain't Markup Language yml Data in YAML format can be serialised into text, or binary format. YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible". YAML format_3751 1.16 Tabular data represented as values in a text file delimited by some character. Delimiter-separated values Tabular format DSV format_3752 1.16 csv Tabular data represented as comma-separated values in a text file. Comma-separated values CSV format_3758 1.16 out "Raw" result file from SEQUEST database search. SEQUEST .out file format_3764 1.16 http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1IdXMLFile.html http://open-ms.sourceforge.net/schemas/ XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. idXML format_3765 1.16 Data table formatted such that it can be passed/streamed within the KNIME platform. KNIME datatable format format_3770 1.16 UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. UniProt XML UniProt XML format UniProtKB XML format UniProtKB XML format_3771 1.16 UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). UniProt RDF UniProt RDF format UniProt RDF/XML UniProt RDF/XML format UniProtKB RDF format UniProtKB RDF/XML UniProtKB RDF/XML format UniProtKB RDF format_3772 1.16 BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming. BioJSON (BioXSD data model) BioJSON format (BioXSD) BioXSD BioJSON BioXSD BioJSON format BioXSD JSON BioXSD JSON format BioXSD in JSON BioXSD in JSON format BioXSD+JSON BioXSD/GTrack BioJSON BioXSD|BioJSON|BioYAML BioJSON BioXSD|GTrack BioJSON Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. BioJSON (BioXSD) format_3773 1.16 BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editing, and object-oriented programming. BioXSD BioYAML BioXSD BioYAML format BioXSD YAML BioXSD YAML format BioXSD in YAML BioXSD in YAML format BioXSD+YAML BioXSD/GTrack BioYAML BioXSD|BioJSON|BioYAML BioYAML BioXSD|GTrack BioYAML BioYAML (BioXSD data model) BioYAML (BioXSD) BioYAML format BioYAML format (BioXSD) Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. BioYAML format_3774 1.16 BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench. BioJSON format (Jalview) JSON (Jalview) JSON format (Jalview) Jalview BioJSON Jalview BioJSON format Jalview JSON Jalview JSON format BioJSON (Jalview) format_3775 1.16 GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata. BioXSD/GTrack GSuite BioXSD|GTrack GSuite GSuite (GTrack ecosystem of formats) GSuite format GTrack|BTrack|GSuite GSuite GTrack|GSuite|BTrack GSuite 'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files. GSuite format_3776 1.16 BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats. BTrack (GTrack ecosystem of formats) BTrack format BioXSD/GTrack BTrack BioXSD|GTrack BTrack GTrack|BTrack|GSuite BTrack GTrack|GSuite|BTrack BTrack 'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats. BTrack format_3777 1.16 The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. Bioversity MCPD FAO MCPD IPGRI MCPD MCPD V.1 MCPD V.2 MCPD format Multi-Crop Passport Descriptors Multi-Crop Passport Descriptors format Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012). MCPD format_3780 1.16 true Data format of an annotated text, e.g. with recognised entities, concepts, and relations. Annotated text format format_3781 1.16 JSON format of annotated scientific text used by PubAnnotations and other tools. PubAnnotation format format_3782 1.16 BioC is a standardised XML format for sharing and integrating text data and annotations. BioC format_3783 1.16 Native textual export format of annotated scientific text from PubTator. PubTator format format_3784 1.16 A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD. Open Annotation format format_3785 1.16 A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar. BRAT format BRAT standoff format BioNLP Shared Task format format_3787 1.16 true A query language (format) for structured database queries. Query format Query language format_3788 1.16 sql SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. Structured Query Language SQL format_3789 1.16 xq xquery xqy XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.). XML Query xq xqy XQuery format_3790 1.16 SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. SPARQL Protocol and RDF Query Language SPARQL format_3804 1.17 XML format for XML Schema. xsd format_3811 1.20 XMFA format stands for eXtended Multi-FastA format and is used to store collinear sub-alignments that constitute a single genome alignment. eXtended Multi-FastA format XMFA format_3812 1.20 The GEN file format contains genetic data and describes SNPs. Genotype file format GEN format_3813 1.20 The SAMPLE file format contains information about each individual i.e. individual IDs, covariates, phenotypes and missing data proportions, from a GWAS study. SAMPLE file format format_3814 1.20 SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information. SDF format_3815 1.20 An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. Molfile format_3816 1.20 Complete, portable representation of a SYBYL molecule. ASCII file which contains all the information needed to reconstruct a SYBYL molecule. Mol2 format_3817 1.20 format for the LaTeX document preparation system. LaTeX format uses the TeX typesetting program format latex format_3818 1.20 Tab-delimited text file format used by Eland - the read-mapping program distributed by Illumina with its sequencing analysis pipeline - which maps short Solexa sequence reads to the human reference genome. ELAND eland ELAND format format_3819 1.20 Phylip multiple alignment sequence format, less stringent than PHYLIP format. PHYLIP Interleaved format It differs from Phylip Format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length. Relaxed PHYLIP Interleaved format_3820 1.20 Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998). Relaxed PHYLIP non-interleaved Relaxed PHYLIP non-interleaved format Relaxed PHYLIP sequential format It differs from Phylip sequential format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length. Relaxed PHYLIP Sequential format_3821 1.20 Default XML format of VisANT, containing all the network information. VisANT xml VisANT xml format VisML format_3822 1.20 GML (Graph Modeling Language) is a text file format supporting network data with a very easy syntax. It is used by Graphlet, Pajek, yEd, LEDA and NetworkX. GML format GML format_3823 1.20 FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. FASTG assembly graph format It is called FASTG, like FASTA, but the G stands for "graph". FASTG format_3824 1.20 true Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment. NMR peak assignment data format NMR processed data format NMR raw data format Nuclear magnetic resonance spectroscopy data format Processed NMR data format Raw NMR data format NMR data format format_3825 1.20 nmrML is an MSI supported XML-based open access format for metabolomics NMR raw and processed spectral data. It is accompanies by an nmrCV (controlled vocabulary) to allow ontology-based annotations. nmrML format_3826 1.20 . proBAM is an adaptation of BAM (format_2572), which was extended to meet specific requirements entailed by proteomics data. proBAM format_3827 1.20 . proBED is an adaptation of BED (format_3003), which was extended to meet specific requirements entailed by proteomics data. proBED format_3828 1.20 true Data format for raw microarray data. Microarray data format Raw microarray data format format_3829 1.20 GenePix Results (GPR) text file format developed by Axon Instruments that is used to save GenePix Results data. GPR format_3830 1.20 Binary format used by the ARB software suite. ARB binary format ARB format_3832 1.20 http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1ConsensusXMLFile.html OpenMS format for grouping features in one map or across several maps. consensusXML format_3833 1.20 http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1FeatureXMLFile.html OpenMS format for quantitation results (LC/MS features). featureXML format_3834 1.20 http://www.psidev.info/mzdata-1_0_5-docs Now deprecated data format of the HUPO Proteomics Standards Initiative. Replaced by mzML (format_3244). mzData format_3835 1.20 http://cruxtoolkit.sourceforge.net/tide-search.html Format supported by the Tide tool for identifying peptides from tandem mass spectra. TIDE TXT format_3836 1.20 ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/ProposedBLASTXMLChanges.pdf ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf http://www.ncbi.nlm.nih.gov/data_specs/schema/NCBI_BlastOutput2.mod.xsd XML format as produced by the NCBI Blast package v2. BLAST XML v2 results format format_3838 1.20 Microsoft Powerpoint format. pptx format_3839 1.20 ibd ibd is a data format for mass spectrometry imaging data. imzML data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. ibd format_3841 1.21 Data format used in Natural Language Processing. Natural Language Processing format NLP format format_3843 1.21 XML input file format for BEAST Software (Bayesian Evolutionary Analysis Sampling Trees). BEAST format_3844 1.21 Chado-XML format is a direct mapping of the Chado relational schema into XML. Chado-XML format_3845 1.21 An alignment format generated by PRANK/PRANKSTER consisting of four elements: newick, nodes, selection and model. HSAML format_3846 1.21 Output xml file from the InterProScan sequence analysis application. InterProScan XML format_3847 1.21 The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KEGG Markup Language KGML format_3848 1.21 XML format for collected entries from bibliographic databases MEDLINE and PubMed. MEDLINE XML PubMed XML format_3849 1.21 A set of XML compliant markup components for describing multiple sequence alignments. MSAML format_3850 1.21 OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format. OrthoXML format_3851 1.21 Tree structure of Protein Sequence Database Markup Language generated using Matra software. PSDML format_3852 1.21 SeqXML is an XML Schema to describe biological sequences, developed by the Stockholm Bioinformatics Centre. SeqXML format_3853 1.21 XML format for the UniParc database. UniParc XML format_3854 1.21 XML format for the UniRef reference clusters. UniRef XML format_3857 1.21 cwl Common Workflow Language (CWL) format for description of command-line tools and workflows. Common Workflow Language CommonWL CWL format_3858 1.21 Proprietary file format for mass spectrometry data from Waters. Proprietary format for which documentation is not available, but used by multiple tools. Waters RAW format_3859 1.21 A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry. JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression. JCAMP-DX format_3862 1.21 An NLP format used for annotated textual documents. NLP annotation format format_3863 1.21 NLP format used by a specific type of corpus (collection of texts). NLP corpus format format_3864 1.21 mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq workflows. miRTop format mirGFF3 is a specialisation of GFF3; produced by small-RNA-Seq analysis workflows, usable and convertible with the miRTop API (https://mirtop.readthedocs.io/en/latest/), and consumable by tools for downstream analysis. mirGFF3 format_3865 1.21 A "placeholder" concept for formats of annotated RNA data, including e.g. microRNA and RNA-Seq data. RNA data format miRNA data format microRNA data format RNA annotation format format_3866 1.22 true File format to store trajectory information for a 3D structure . CG trajectory formats MD trajectory formats NA trajectory formats Protein trajectory formats Formats differ on what they are able to store (coordinates, velocities, topologies) and how they are storing it (raw, compressed, textual, binary). Trajectory format format_3867 1.22 true Binary file format to store trajectory information for a 3D structure . Trajectory format (binary) format_3868 1.22 true Textual file format to store trajectory information for a 3D structure . Trajectory format (text) format_3873 1.22 HDF is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data, originally developed at the National Center for Supercomputing Applications at the University of Illinois. HDF is currently supported by many commercial and non-commercial software platforms such as Java, MATLAB/Scilab, Octave, Python and R. HDF format_3874 1.22 PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA). The compression is made projecting the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the most relevant eigenvectors obtained by diagonalization of the covariance matrix (PCA). In the compression/decompression process, part of the original information is lost, depending on the final number of eigenvectors chosen. However, with a reasonable choice of the set of eigenvectors the compression typically reduces the trajectory file to less than one tenth of their original size with very acceptable loss of information. Compression with PCAZip can only be applied to unsolvated structures. PCAzip format_3875 1.22 Portable binary format for trajectories produced by GROMACS package. XTC uses the External Data Representation (xdr) routines for writing and reading data which were created for the Unix Network File System (NFS). XTC files use a reduced precision (lossy) algorithm which works multiplying the coordinates by a scaling factor (typically 1000), so converting them to pm (GROMACS standard distance unit is nm). This allows an integer rounding of the values. Several other tricks are performed, such as making use of atom proximity information: atoms close in sequence are usually close in space (e.g. water molecules). That makes XTC format the most efficient in terms of disk usage, in most cases reducing by a factor of 2 the size of any other binary trajectory format. XTC format_3876 1.22 Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format. Trajectory Next Generation format Fully architecture-independent format, regarding both endianness and the ability to mix single/double precision trajectories and I/O libraries. Self-sufficient, it should not require any other files for reading, and all the data should be contained in a single file for easy transport. Temporal compression of data, improving the compression rate of the previous XTC format. Possibility to store meta-data with information about the simulation. Direct access to a particular frame. Efficient parallel I/O. TNG format_3877 1.22 The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number. XYZ files are structured in this way: First line contains the number of atoms in the file. Second line contains a title, comment, or filename. Remaining lines contain atom information. Each line starts with the element symbol, followed by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules or frames can be contained within one file, so it supports trajectory storage. XYZ files can be directly represented by a molecular viewer, as they contain all the basic information needed to build the 3D model. XYZ format_3878 1.22 AMBER trajectory (also called mdcrd), with 10 coordinates per line and format F8.3 (fixed point notation with field width 8 and 3 decimal places). AMBER trajectory format inpcrd mdcrd format_3879 1.22 true Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation. CG topology format MD topology format NA topology format Protein topology format Many different file formats exist describing structural molecular topology. Typically, each MD package or simulation software works with their own implementation (e.g. GROMACS top, CHARMM psf, AMBER prmtop). Topology format format_3880 1.22 GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files. There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package. GROMACS top format_3881 1.22 AMBER Prmtop file (version 7) is a structure topology text file divided in several sections designed to be parsed easily using simple Fortran code. Each section contains particular topology information, such as atom name, charge, mass, angles, dihedrals, etc. AMBER Parm AMBER Parm7 Parm7 Prmtop Prmtop7 It can be modified manually, but as the size of the system increases, the hand-editing becomes increasingly complex. AMBER Parameter-Topology file format is used extensively by the AMBER software suite and is referred to as the Prmtop file for short. version 7 is written to distinguish it from old versions of AMBER Prmtop. Similarly to HDF5, it is a completely different format, according to AMBER group: a drastic change to the file format occurred with the 2004 release of Amber 7 (http://ambermd.org/prmtop.pdf) AMBER top format_3882 1.22 X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD and CHARMM molecular simulations programs. PSF files contain six main sections of interest: atoms, bonds, angles, dihedrals, improper dihedrals (force terms used to maintain planarity) and cross-terms. The high similarity in the functional form of the two potential energy functions used by AMBER and CHARMM force-fields gives rise to the possible use of one force-field within the other MD engine. Therefore, the conversion of PSF files to AMBER Prmtop format is possible with the use of AMBER chamber (CHARMM - AMBER) program. PSF format_3883 1.22 GROMACS itp files (include topology) contain structure topology information, and are typically included in GROMACS topology files (GROMACS top). Itp files are used to define individual (or multiple) components of a topology as a separate file. This is particularly useful if there is a molecule that is used frequently, and also reduces the size of the system topology file, splitting it in different parts. GROMACS itp files are used also to define position restrictions on the molecule, or to define the force field parameters for a particular ligand. GROMACS itp format_3884 1.22 Format of force field parameter files, which store the set of parameters (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential for the proper description and simulation of a molecular system. Many different file formats exist describing force field parameters. Typically, each MD package or simulation software works with their own implementation (e.g. GROMACS itp, CHARMM rtf, AMBER off / frcmod). FF parameter format format_3885 1.22 Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates. Scripps Research Institute BinPos It is basically a translation of the ASCII atom coordinate format to binary code. The only additional information stored is a magic number that identifies the BinPos format and the number of atoms per snapshot. The remainder is the chain of coordinates binary encoded. A drawback of this format is its architecture dependency. Integers and floats codification depends on the architecture, thus it needs to be converted if working in different platforms (little endian, big endian). BinPos format_3886 1.22 AMBER coordinate/restart file with 6 coordinates per line and decimal format F12.7 (fixed point notation with field width 12 and 7 decimal places). restrt rst7 RST format_3887 1.22 Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information. There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package. CHARMM rtf format_3888 1.22 AMBER frcmod (Force field Modification) is a file format to store any modification to the standard force field needed for a particular molecule to be properly represented in the simulation. AMBER frcmod format_3889 1.22 AMBER Object File Format library files (OFF library files) store residue libraries (forcefield residue parameters). AMBER Object File Format AMBER lib AMBER off format_3906 1.22 MReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc. NMReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc. Find more in the paper at https://doi.org/10.1002/mrc.4527. NMReDATA format_3909 1.22 BpForms is a string format for concretely representing the primary structures of biopolymers, including DNA, RNA, and proteins that include non-canonical nucleic and amino acids. See https://www.bpforms.org for more information. BpForms format_3910 1.22 Format of trr files that contain the trajectory of a simulation experiment used by GROMACS. The first 4 bytes of any trr file containing 1993. See https://github.com/galaxyproject/galaxy/pull/6597/files#diff-409951594551183dbf886e24de6cb129R760 trr format_3911 1.22 msh Mash sketch is a format for sequence / sequence checksum information. To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random identifier. By sorting these hashes, a small subset from the top of the sorted list can represent the entire sequence. Mash sketch min-hash sketch msh format_3913 1.23 loom The Loom file format is based on HDF5, a standard for storing large numerical datasets. The Loom format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns. Loom format_3915 1.23 zarray zgroup The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data. Zarr format_3916 1.23 mtx The Matrix Market matrix (MTX) format stores numerical or pattern matrices in a dense (array format) or sparse (coordinate format) representation. MTX format_3951 1.24 text/plain BcForms is a format for abstractly describing the molecular structure (atoms and bonds) of macromolecular complexes as a collection of subunits and crosslinks. Each subunit can be described with BpForms (http://edamontology.org/format_3909) or SMILES (http://edamontology.org/data_2301). BcForms uses an ontology of crosslinks to abstract the chemical details of crosslinks from the descriptions of complexes (see https://bpforms.org/crosslink.html). BcForms is related to http://edamontology.org/format_3909. (BcForms uses BpForms to describe subunits which are DNA, RNA, or protein polymers.) However, that format isn't the parent of BcForms. BcForms is similarly related to SMILES (http://edamontology.org/data_2301). BcForms format_3956 1.24 nq N-Quads is a line-based, plain text format for encoding an RDF dataset. It includes information about the graph each triple belongs to. N-Quads should not be confused with N-Triples which does not contain graph information. N-Quads format_3969 1.25 json application/json Vega is a visualization grammar, a declarative language for creating, saving, and sharing interactive visualization designs. With Vega, you can describe the visual appearance and interactive behavior of a visualization in a JSON format, and generate web-based views using Canvas or SVG. Vega format_3970 1.25 json application/json Vega-Lite is a high-level grammar of interactive graphics. It provides a concise JSON syntax for rapidly generating visualizations to support analysis. Vega-Lite specifications can be compiled to Vega specifications. Vega-lite format_3971 1.25 application/xml A model description language for computational neuroscience. NeuroML format_3972 1.25 bngl application/xml plain/text BioNetGen is a format for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. BioNetGen Language BNGL format_3973 1.25 A Docker image is a file, comprised of multiple layers, that is used to execute code in a Docker container. An image is essentially built from the instructions for a complete and executable version of an application, which relies on the host OS kernel. Docker image format_3975 1.25 gfa Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. Graphical Fragment Assembly (GFA) 1.0 GFA 1 format_3976 1.25 gfa Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. GFA2 is an update of GFA1 which is not compatible with GFA1. Graphical Fragment Assembly (GFA) 2.0 GFA 2 format_3977 1.25 xlsx application/vnd.openxmlformats-officedocument.spreadsheetml.sheet ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a syntax for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables format_3978 1.25 contig The CONTIG format used for output of the SOAPdenovo alignment program. It contains contig sequences generated without using mate pair information. CONTIG format_3979 1.25 wego WEGO native format used by the Web Gene Ontology Annotation Plot application. Tab-delimited format with gene names and others GO IDs (columns) with one annotation record per line. WEGO format_3980 1.25 rpkm Tab-delimited format for gene expression levels table, calculated as Reads Per Kilobase per Million (RPKM) mapped reads. Gene expression levels table format For example a 1kb transcript with 1000 alignments in a sample of 10 million reads (out of which 8 million reads can be mapped) will have RPKM = 1000/(1 * 8) = 125 RPKM format_3981 1.25 tar TAR archive file format generated by the Unix-based utility tar. TAR Tarball tar For example a 1kb transcript with 1000 alignments in a sample of 10 million reads (out of which 8 million reads can be mapped) will have RPKM = 1000/(1 * 8) = 125 TAR format format_3982 1.25 chain The CHAIN format describes a pairwise alignment that allow gaps in both sequences simultaneously and is used by the UCSC Genome Browser. CHAIN https://genome.ucsc.edu/goldenPath/help/chain.html format_3983 1.25 net The NET file format is used to describe the data that underlie the net alignment annotations in the UCSC Genome Browser. NET https://genome.ucsc.edu/goldenPath/help/net.html format_3984 1.25 qmap Format of QMAP files generated for methylation data from an internal BGI pipeline. QMAP format_3985 1.25 ga An emerging format for high-level Galaxy workflow description. Galaxy workflow format GalaxyWF ga gxformat2 https://github.com/galaxyproject/gxformat2 format_3986 1.25 wmv The proprietary native video format of various Microsoft programs such as Windows Media Player. Windows Media Video format Windows movie file format WMV format_3987 1.25 zip ZIP is an archive file format that supports lossless data compression. ZIP A ZIP file may contain one or more files or directories that may have been compressed. ZIP format format_3988 1.25 lsm Zeiss' proprietary image format based on TIFF. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. LSM format_3989 1.25 gz gzip GNU zip compressed file format common to Unix-based operating systems. GNU Zip gz gzip GZIP format format_3990 1.25 avi Audio Video Interleaved (AVI) format is a multimedia container format for AVI files, that allows synchronous audio-with-video playback. Audio Video Interleaved AVI format_3991 1.25 trackdb A declaration file format for UCSC browsers track dataset display charateristics. TrackDB format_3992 1.25 cigar Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-length encoded) pairwise alignment format. It is useful for representing long (e.g. genomic) pairwise alignments. CIGAR CIGAR format http://wiki.bits.vib.be/index.php/CIGAR/ format_3993 1.25 stl STL is a file format native to the stereolithography CAD software created by 3D Systems. The format is used to save and share surface-rendered 3D images and also for 3D printing. stl Stereolithography format format_3994 1.25 u3d U3D (Universal 3D) is a compressed file format and data structure for 3D computer graphics. It contains 3D model information such as triangle meshes, lighting, shading, motion data, lines and points with color and structure. Universal 3D Universal 3D format U3D format_3995 1.25 tex Bitmap image format used for storing textures. Texture files can create the appearance of different surfaces and can be applied to both 2D and 3D objects. Note the file extension .tex is also used for LaTex documents which are a completely different format and they are NOT interchangeable. Texture file format format_3996 1.25 py Format for scripts writtenin Python - a widely used high-level programming language for general-purpose programming. Python Python program py Python script format_3997 1.25 mp4 A digital multimedia container format most commonly used to store video and audio. MP4 MPEG-4 format_3998 1.25 pl Format for scripts written in Perl - a family of high-level, general-purpose, interpreted, dynamic programming languages. Perl Perl program pl Perl script format_3999 1.25 r Format for scripts written in the R language - an open source programming language and software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing. R R program R script format_4000 1.25 rmd A file format for making dynamic documents (R Markdown scripts) with the R language. R markdown https://rmarkdown.rstudio.com/articles_intro.html format_4001 1.25 This duplicates an existing concept (http://edamontology.org/format_3549). 1.26 An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI) commonly used to store brain imaging data obtained using Magnetic Resonance Imaging (MRI) methods. NIFTI format true format_4002 1.25 pickle Format used by Python pickle module for serializing and de-serializing a Python object structure. pickle https://docs.python.org/2/library/pickle.html format_4003 1.25 npy The standard binary file format used by NumPy - a fundamental package for scientific computing with Python - for persisting a single arbitrary NumPy array on disk. The format stores all of the shape and dtype information necessary to reconstruct the array correctly. NumPy npy NumPy format format_4004 1.25 repz Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB toolbox for structured illumination fluorescence microscopy) or alternatively extracted with zip file archiver software. SimTools repertoire file format https://pdfs.semanticscholar.org/5f25/f1cc6cdf2225fe22dc6fd4fc0296d486a85c.pdf format_4005 1.25 cfg A configuration file used by various programs to store settings that are specific to their respective software. Configuration file format format_4006 1.25 zst Format used by the Zstandard real-time compression algorithm. Zstandard compression format Zstandard-compressed file format zst Zstandard format https://github.com/facebook/zstd/blob/master/doc/zstd_compression_format.md format_4007 1.25 m The file format for MATLAB scripts or functions. MATLAB m MATLAB script format_4015 1.26 A data format for specifying parameter estimation problems in systems biology. PEtab format_4018 1.26 g.vcf g.vcf.gz Genomic Variant Call Format (gVCF) is a version of VCF that includes not only the positions that are variant when compared to a reference genome, but also the non-variant positions as ranges, including metrics of confidence that the positions in the range are actually non-variant e.g. minimum read-depth and genotype quality. g.vcf g.vcf.gz gVCF format_4023 1.26 cml Chemical Markup Language (CML) is an XML-based format for encoding detailed information about a wide range of chemical concepts. ChemML cml format_4024 1.26 cif Crystallographic Information File (CIF) is a data exchange standard file format for Crystallographic Information and related Structural Science data. cif format_4025 1.26 json Format for describing the capabilities of a biosimulation tool including the modeling frameworks, simulation algorithms, and modeling formats that it supports, as well as metadata such as a list of the interfaces, programming languages, and operating systems supported by the tool; a link to download the tool; a list of the authors of the tool; and the license to the tool. BioSimulators format for the specifications of biosimulation tools format_4026 1.26 Outlines the syntax and semantics of the input and output arguments for command-line interfaces for biosimulation tools. BioSimulators standard for command-line interfaces for biosimulation tools format_4035 1.26 Data format derived from the standard PDB format, which enables user to incorporate parameters for charge and radius to the existing PDB data file. PQR format_4036 1.26 Data format used in AutoDock 4 for storing atomic coordinates, partial atomic charges and AutoDock atom types for both receptors and ligands. PDBQT format_4039 1.26 msp MSP is a data format for mass spectrometry data. NIST Text file format for storing MS∕MS spectra (m∕z and intensity of mass peaks) along with additional annotations for each spectrum. A single MSP file can thus contain single or multiple spectra. This format is frequently used to share spectra libraries. MSP format_4041 1.26 A standard for DMPs developed by the Research Data Alliance Machine-actionable data management plan RDA Common Standard for Machine-Actionable Data Management Plans (maDMPS) RDA DMP maDMP operation_0004 beta12orEarlier true Function A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Computational method Computational operation Computational procedure Computational subroutine Function (programming) Lambda abstraction Mathematical function Mathematical operation Computational tool Process sumo:Function Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. Operation Function Operation is a function that is computational. It typically has input(s) and output(s), which are always data. Computational tool Computational tool provides one or more operations. Process Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. operation_0224 beta12orEarlier Search or query a data resource and retrieve entries and / or annotation. Database retrieval Query Query and retrieval operation_0225 beta12orEarlier beta13 Search database to retrieve all relevant references to a particular entity or entry. Data retrieval (database cross-reference) true operation_0226 beta12orEarlier true Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. This is a broad concept and is used a placeholder for other, more specific concepts. Annotation operation_0227 beta12orEarlier true Generate an index of (typically a file of) biological data. Data indexing Database indexing Indexing operation_0228 beta12orEarlier 1.6 Analyse an index of biological data. Data index analysis true operation_0229 beta12orEarlier beta12orEarlier Retrieve basic information about a molecular sequence. Annotation retrieval (sequence) true operation_0230 beta12orEarlier Generate a molecular sequence by some means. Sequence generation (nucleic acid) Sequence generation (protein) Sequence generation operation_0231 beta12orEarlier Edit or change a molecular sequence, either randomly or specifically. Sequence editing operation_0232 beta12orEarlier Merge two or more (typically overlapping) molecular sequences. Sequence splicing Paired-end merging Paired-end stitching Read merging Read stitching Sequence merging operation_0233 beta12orEarlier Convert a molecular sequence from one type to another. Sequence conversion operation_0234 beta12orEarlier Calculate sequence complexity, for example to find low-complexity regions in sequences. Sequence complexity calculation operation_0235 beta12orEarlier Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. Sequence ambiguity calculation operation_0236 beta12orEarlier Calculate character or word composition or frequency of a molecular sequence. Sequence composition calculation operation_0237 beta12orEarlier Find and/or analyse repeat sequences in (typically nucleotide) sequences. Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. Repeat sequence analysis operation_0238 beta12orEarlier Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). Motif discovery Motifs and patterns might be conserved or over-represented (occur with improbable frequency). Sequence motif discovery operation_0239 beta12orEarlier Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). Motif scanning Sequence signature detection Sequence signature recognition Motif detection Motif recognition Motif search Sequence motif detection Sequence motif search Sequence profile search Sequence motif recognition operation_0240 beta12orEarlier Find motifs shared by molecular sequences. Sequence motif comparison operation_0241 beta12orEarlier beta13 Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. Transcription regulatory sequence analysis true operation_0242 beta12orEarlier 1.19 Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). Conserved transcription regulatory sequence identification true operation_0243 beta12orEarlier 1.18 Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. Protein property calculation (from structure) true operation_0244 beta12orEarlier Analyse flexibility and motion in protein structure. CG analysis MD analysis Protein Dynamics Analysis Trajectory analysis Nucleic Acid Dynamics Analysis Protein flexibility and motion analysis Protein flexibility prediction Protein motion prediction Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. Simulation analysis operation_0245 beta12orEarlier Identify or screen for 3D structural motifs in protein structure(s). Protein structural feature identification Protein structural motif recognition This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. Structural motif discovery operation_0246 beta12orEarlier Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). Protein domain recognition operation_0247 beta12orEarlier Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). Protein architecture analysis operation_0248 beta12orEarlier WHATIF: SymShellFiveXML WHATIF: SymShellOneXML WHATIF: SymShellTenXML WHATIF: SymShellTwoXML WHATIF:ListContactsNormal WHATIF:ListContactsRelaxed WHATIF:ListSideChainContactsNormal WHATIF:ListSideChainContactsRelaxed Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). Residue interaction calculation operation_0249 beta12orEarlier WHATIF:CysteineTorsions WHATIF:ResidueTorsions WHATIF:ResidueTorsionsBB WHATIF:ShowTauAngle Calculate, visualise or analyse phi/psi angles of a protein structure. Backbone torsion angle calculation Cysteine torsion angle calculation Tau angle calculation Torsion angle calculation Protein geometry calculation operation_0250 beta12orEarlier Extract, calculate or predict non-positional (physical or chemical) properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence or 3D structure. Protein property rendering Protein property calculation (from sequence) Protein property calculation (from structure) Protein structural property calculation Structural property calculation This includes methods to render and visualise the properties of a protein sequence, and a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. Protein property calculation operation_0252 beta12orEarlier Immunogen design Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. Antigenicity prediction Immunogenicity prediction B cell peptide immunogenicity prediction Hopp and Woods plotting MHC peptide immunogenicity prediction Immunological system are cellular or humoral. In vaccine design to induces a cellular immune response, methods must search for antigens that can be recognized by the major histocompatibility complex (MHC) molecules present in T lymphocytes. If a humoral response is required, antigens for B cells must be identified. This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot. This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. Peptide immunogenicity prediction operation_0253 beta12orEarlier Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. Sequence feature prediction Sequence feature recognition Motif database search SO:0000110 Look at "Protein feature detection" (http://edamontology.org/operation_3092) and "Nucleic acid feature detection" (http://edamontology.org/operation_0415) in case more specific terms are needed. Sequence feature detection operation_0254 beta12orEarlier beta13 Extract a sequence feature table from a sequence database entry. Data retrieval (feature table) true operation_0255 beta12orEarlier 1.6 Query the features (in a feature table) of molecular sequence(s). Feature table query true operation_0256 beta12orEarlier Compare the feature tables of two or more molecular sequences. Feature comparison Feature table comparison Sequence feature comparison operation_0257 beta12orEarlier beta13 Display basic information about a sequence alignment. Data retrieval (sequence alignment) true operation_0258 beta12orEarlier Analyse a molecular sequence alignment. Sequence alignment analysis operation_0259 beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. See also 'Sequence profile alignment'. Sequence alignment comparison operation_0260 beta12orEarlier Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). Sequence alignment conversion operation_0261 beta12orEarlier beta13 Process (read and / or write) physicochemical property data of nucleic acids. Nucleic acid property processing true operation_0262 beta12orEarlier Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. Nucleic acid property calculation operation_0264 beta12orEarlier Predict splicing alternatives or transcript isoforms from analysis of sequence data. Alternative splicing analysis Alternative splicing detection Differential splicing analysis Splice transcript prediction Alternative splicing prediction operation_0265 beta12orEarlier Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. Frameshift error detection Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. Frameshift detection operation_0266 beta12orEarlier Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. Vector sequence detection operation_0267 beta12orEarlier Predict secondary structure of protein sequences. Secondary structure prediction (protein) Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. Protein secondary structure prediction operation_0268 beta12orEarlier Predict super-secondary structure of protein sequence(s). Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. Protein super-secondary structure prediction operation_0269 beta12orEarlier Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. Transmembrane protein prediction operation_0270 beta12orEarlier Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). Transmembrane protein analysis operation_0271 beta12orEarlier This is a "organisational class" not very useful for annotation per se. 1.19 Predict tertiary structure of a molecular (biopolymer) sequence. Structure prediction true operation_0272 beta12orEarlier Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. Residue interaction prediction Contact map prediction Protein contact map prediction Methods usually involve multiple sequence alignment analysis. Residue contact prediction operation_0273 beta12orEarlier 1.19 Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. Protein interaction raw data analysis true operation_0274 beta12orEarlier 1.12 Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. Protein-protein interaction prediction (from protein sequence) true operation_0275 beta12orEarlier 1.12 Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. Protein-protein interaction prediction (from protein structure) true operation_0276 beta12orEarlier Analyse a network of protein interactions. Protein interaction network comparison Protein interaction network analysis operation_0277 beta12orEarlier Notions of pathway and network were mixed up, EDAM 1.24 disentangles them. 1.24 Compare two or more biological pathways or networks. Pathway or network comparison true operation_0278 beta12orEarlier Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). RNA shape prediction Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). RNA secondary structure prediction operation_0279 beta12orEarlier Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. For example, compute folding energies such as minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. Nucleic acid folding Nucleic acid folding modelling Nucleic acid folding prediction Nucleic acid folding energy calculation Nucleic acid folding analysis operation_0280 beta12orEarlier beta13 Retrieve information on restriction enzymes or restriction enzyme sites. Data retrieval (restriction enzyme annotation) true operation_0281 beta12orEarlier beta13 Identify genetic markers in DNA sequences. A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. Genetic marker identification true operation_0282 beta12orEarlier Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. Functional mapping Genetic cartography Genetic map construction Genetic map generation Linkage mapping QTL mapping Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Genetic mapping operation_0283 beta12orEarlier Analyse genetic linkage. For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. Linkage analysis operation_0284 beta12orEarlier Calculate codon usage statistics and create a codon usage table. Codon usage table construction Codon usage table generation operation_0285 beta12orEarlier Compare two or more codon usage tables. Codon usage table comparison operation_0286 beta12orEarlier Analyse codon usage in molecular sequences or process codon usage data (e.g. a codon usage table). Codon usage data analysis Codon usage table analysis Codon usage analysis operation_0287 beta12orEarlier Identify and plot third base position variability in a nucleotide sequence. Base position variability plotting operation_0288 beta12orEarlier Find exact character or word matches between molecular sequences without full sequence alignment. Sequence word comparison operation_0289 beta12orEarlier Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. Phylogenetic distance matrix generation Sequence distance calculation Sequence distance matrix construction Sequence distance matrix generation operation_0290 beta12orEarlier Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. Sequence redundancy removal operation_0291 beta12orEarlier Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. Sequence cluster construction Sequence cluster generation The clusters may be output or used internally for some other purpose. Sequence clustering operation_0292 beta12orEarlier Align (identify equivalent sites within) molecular sequences. Sequence alignment construction Sequence alignment generation Consensus-based sequence alignment Constrained sequence alignment Multiple sequence alignment (constrained) Sequence alignment (constrained) Includes methods that align sequence profiles (representing sequence alignments): ethods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'. See also "Read mapping" Sequence alignment operation_0293 beta12orEarlier beta13 Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). Hybrid sequence alignment construction true operation_0294 beta12orEarlier Align molecular sequences using sequence and structural information. Sequence alignment (structure-based) Structure-based sequence alignment operation_0295 beta12orEarlier Align (superimpose) molecular tertiary structures. Structural alignment 3D profile alignment 3D profile-to-3D profile alignment Structural profile alignment Includes methods that align structural (3D) profiles or templates (representing structures or structure alignments) - including methods that perform one-to-one, one-to-many or many-to-many comparisons. Structure alignment operation_0296 beta12orEarlier Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. Sequence profile construction Sequence profile generation operation_0297 beta12orEarlier Generate some type of structural (3D) profile or template from a structure or structure alignment. Structural profile construction Structural profile generation 3D profile generation operation_0298 beta12orEarlier 1.19 Align sequence profiles (representing sequence alignments). Profile-profile alignment true operation_0299 beta12orEarlier 1.19 Align structural (3D) profiles or templates (representing structures or structure alignments). 3D profile-to-3D profile alignment true operation_0300 beta12orEarlier Align molecular sequence(s) to sequence profile(s), or profiles to other profiles. A profile typically represents a sequence alignment. Profile-profile alignment Profile-to-profile alignment Sequence-profile alignment Sequence-to-profile alignment A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence profile alignment operation_0301 beta12orEarlier 1.19 Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). Sequence-to-3D-profile alignment true operation_0302 beta12orEarlier Align molecular sequence to structure in 3D space (threading). Sequence-structure alignment Sequence-3D profile alignment Sequence-to-3D-profile alignment This includes sequence-to-3D-profile alignment methods, which align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment) - methods might perform one-to-one, one-to-many or many-to-many comparisons. Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Protein threading operation_0303 beta12orEarlier Recognize (predict and identify) known protein structural domains or folds in protein sequence(s) which (typically) are not accompanied by any significant sequence similarity to know structures. Domain prediction Fold prediction Protein domain prediction Protein fold prediction Protein fold recognition 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. Fold recognition operation_0304 beta12orEarlier (jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved. 1.17 Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. This includes documentation, general information and other metadata on entities such as databases, database entries and tools. Metadata retrieval true operation_0305 beta12orEarlier Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics. Literature search operation_0306 beta12orEarlier Text analysis Process and analyse text (typically scientific literature) to extract information from it. Literature mining Text analytics Text data mining Article analysis Literature analysis Text mining operation_0307 beta12orEarlier Perform in-silico (virtual) PCR. Virtual PCR operation_0308 beta12orEarlier Design or predict oligonucleotide primers for PCR and DNA amplification etc. PCR primer prediction Primer design PCR primer design (based on gene structure) PCR primer design (for conserved primers) PCR primer design (for gene transcription profiling) PCR primer design (for genotyping polymorphisms) PCR primer design (for large scale sequencing) PCR primer design (for methylation PCRs) Primer quality estimation Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. PCR primer design operation_0309 beta12orEarlier Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. Microarray probe prediction Microarray probe design operation_0310 beta12orEarlier Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. Metagenomic assembly Sequence assembly editing For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. Sequence assembly operation_0311 beta12orEarlier 1.16 Standardize or normalize microarray data. Microarray data standardisation and normalisation true operation_0312 beta12orEarlier beta12orEarlier Process (read and / or write) SAGE, MPSS or SBS experimental data. Sequencing-based expression profile data processing true operation_0313 beta12orEarlier Perform cluster analysis of expression data to identify groups with similar expression profiles, for example by clustering. Gene expression clustering Gene expression profile clustering Expression profile clustering operation_0314 beta12orEarlier The measurement of the activity (expression) of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function. Feature expression analysis Functional profiling Gene expression profile construction Gene expression profile generation Gene expression quantification Gene transcription profiling Non-coding RNA profiling Protein profiling RNA profiling mRNA profiling Gene expression profiling generates some sort of gene expression profile, for example from microarray data. Gene expression profiling operation_0315 beta12orEarlier Comparison of expression profiles. Gene expression comparison Gene expression profile comparison Expression profile comparison operation_0316 beta12orEarlier beta12orEarlier Interpret (in functional terms) and annotate gene expression data. Functional profiling true operation_0317 beta12orEarlier beta12orEarlier Analyse EST or cDNA sequences. For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. EST and cDNA sequence analysis true operation_0318 beta12orEarlier beta12orEarlier Identify and select targets for protein structural determination. Methods will typically navigate a graph of protein families of known structure. Structural genomics target selection true operation_0319 beta12orEarlier Assign secondary structure from protein coordinate or experimental data. Includes secondary structure assignment from circular dichroism (CD) spectroscopic data, and from protein coordinate data. Protein secondary structure assignment operation_0320 beta12orEarlier Assign a protein tertiary structure (3D coordinates), or other aspects of protein structure, from raw experimental data. NOE assignment Structure calculation Protein structure assignment operation_0321 beta12orEarlier WHATIF: CorrectedPDBasXML WHATIF: UseFileDB WHATIF: UseResidueDB Evaluate the quality or correctness a protein three-dimensional model. Protein model validation Residue validation Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. This includes methods that calculate poor quality residues. The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). Protein structure validation operation_0322 beta12orEarlier WHATIF: CorrectedPDBasXML Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. Protein model refinement Molecular model refinement operation_0323 beta12orEarlier Construct a phylogenetic tree. Phlyogenetic tree construction Phylogenetic reconstruction Phylogenetic tree generation Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. Phylogenetic inference operation_0324 beta12orEarlier Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. Phylogenetic tree analysis Phylogenetic modelling Phylgenetic modelling is the modelling of trait evolution and prediction of trait values using phylogeny as a basis. Phylogenetic analysis operation_0325 beta12orEarlier Compare two or more phylogenetic trees. For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. Phylogenetic tree comparison operation_0326 beta12orEarlier Edit a phylogenetic tree. Phylogenetic tree editing operation_0327 beta12orEarlier Comparison of a DNA sequence to orthologous sequences in different species and inference of a phylogenetic tree, in order to identify regulatory elements such as transcription factor binding sites (TFBS). Phylogenetic shadowing Phylogenetic shadowing is a type of footprinting where many closely related species are used. A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. Phylogenetic footprinting operation_0328 beta12orEarlier 1.20 Simulate the folding of a protein. Protein folding simulation true operation_0329 beta12orEarlier 1.19 Predict the folding pathway(s) or non-native structural intermediates of a protein. Protein folding pathway prediction true operation_0330 beta12orEarlier 1.12 Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Protein SNP mapping true operation_0331 beta12orEarlier Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. Variant functional prediction Protein SNP mapping Protein mutation modelling Protein stability change prediction Protein SNP mapping maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations. Variant effect prediction operation_0332 beta12orEarlier beta12orEarlier Design molecules that elicit an immune response (immunogens). Immunogen design true operation_0333 beta12orEarlier 1.18 Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). Zinc finger prediction true operation_0334 beta12orEarlier Calculate Km, Vmax and derived data for an enzyme reaction. Enzyme kinetics calculation operation_0335 beta12orEarlier Reformat a file of data (or equivalent entity in memory). Data reformatting File format conversion File formatting File reformatting Format conversion Data formatting operation_0336 beta12orEarlier Test and validate the format and content of a data file. File format validation Format validation operation_0337 beta12orEarlier true Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. Data visualisation Rendering Molecular visualisation Plotting This includes methods to render and visualise molecules. Visualisation operation_0338 beta12orEarlier Search a sequence database by sequence comparison and retrieve similar sequences. Sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. This excludes direct retrieval methods (e.g. the dbfetch program). Sequence database search operation_0339 beta12orEarlier Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. Structure database search operation_0340 beta12orEarlier 1.8 Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. Protein secondary database search true operation_0341 beta12orEarlier 1.8 Screen a sequence against a motif or pattern database. Motif database search true operation_0342 beta12orEarlier 1.4 Search a database of sequence profiles with a query sequence. Sequence profile database search true operation_0343 beta12orEarlier beta12orEarlier Search a database of transmembrane proteins, for example for sequence or structural similarities. Transmembrane protein database search true operation_0344 beta12orEarlier 1.6 Query a database and retrieve sequences with a given entry code or accession number. Sequence retrieval (by code) true operation_0345 beta12orEarlier 1.6 Query a database and retrieve sequences containing a given keyword. Sequence retrieval (by keyword) true operation_0346 beta12orEarlier Search a sequence database and retrieve sequences that are similar to a query sequence. Sequence database search (by sequence) Structure database search (by sequence) Sequence similarity search operation_0347 beta12orEarlier 1.8 Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. Sequence database search (by motif or pattern) true operation_0348 beta12orEarlier 1.6 Search a sequence database and retrieve sequences of a given amino acid composition. Sequence database search (by amino acid composition) true operation_0349 beta12orEarlier Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. Sequence database search (by property) operation_0350 beta12orEarlier 1.6 Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. Sequence database search (by sequence using word-based methods) true operation_0351 beta12orEarlier 1.6 Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. This includes tools based on PSI-BLAST. Sequence database search (by sequence using profile-based methods) true operation_0352 beta12orEarlier 1.6 Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. This includes tools based on the Smith-Waterman algorithm or FASTA. Sequence database search (by sequence using local alignment-based methods) true operation_0353 beta12orEarlier 1.6 Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. This includes tools based on the Needleman and Wunsch algorithm. Sequence database search (by sequence using global alignment-based methods) true operation_0354 beta12orEarlier 1.6 Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. Sequence database search (by sequence for primer sequences) true operation_0355 beta12orEarlier 1.6 Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. Sequence database search (by molecular weight) true operation_0356 beta12orEarlier 1.6 Search sequence(s) or a sequence database for sequences of a given isoelectric point. Sequence database search (by isoelectric point) true operation_0357 beta12orEarlier 1.6 Query a tertiary structure database and retrieve entries with a given entry code or accession number. Structure retrieval (by code) true operation_0358 beta12orEarlier 1.6 Query a tertiary structure database and retrieve entries containing a given keyword. Structure retrieval (by keyword) true operation_0359 beta12orEarlier 1.8 Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. Structure database search (by sequence) true operation_0360 beta12orEarlier Search a database of molecular structure and retrieve structures that are similar to a query structure. Structure database search (by structure) Structure retrieval by structure Structural similarity search operation_0361 beta12orEarlier Annotate a molecular sequence record with terms from a controlled vocabulary. Sequence annotation operation_0362 beta12orEarlier Annotate a genome sequence with terms from a controlled vocabulary. Functional genome annotation Metagenome annotation Structural genome annotation Genome annotation operation_0363 beta12orEarlier Generate the reverse and / or complement of a nucleotide sequence. Nucleic acid sequence reverse and complement Reverse / complement Reverse and complement Reverse complement operation_0364 beta12orEarlier Generate a random sequence, for example, with a specific character composition. Random sequence generation operation_0365 beta12orEarlier Generate digest fragments for a nucleotide sequence containing restriction sites. Nucleic acid restriction digest Restriction digest operation_0366 beta12orEarlier Cleave a protein sequence into peptide fragments (corresponding to enzymatic or chemical cleavage). This is often followed by calculation of protein fragment masses (http://edamontology.org/operation_0398). Protein sequence cleavage operation_0367 beta12orEarlier Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. Sequence mutation and randomisation operation_0368 beta12orEarlier Mask characters in a molecular sequence (replacing those characters with a mask character). For example, SNPs or repeats in a DNA sequence might be masked. Sequence masking operation_0369 beta12orEarlier Cut (remove) characters or a region from a molecular sequence. Sequence cutting operation_0370 beta12orEarlier Create (or remove) restriction sites in sequences, for example using silent mutations. Restriction site creation operation_0371 beta12orEarlier Translate a DNA sequence into protein. DNA translation operation_0372 beta12orEarlier Transcribe a nucleotide sequence into mRNA sequence(s). DNA transcription operation_0377 beta12orEarlier 1.8 Calculate base frequency or word composition of a nucleotide sequence. Sequence composition calculation (nucleic acid) true operation_0378 beta12orEarlier 1.8 Calculate amino acid frequency or word composition of a protein sequence. Sequence composition calculation (protein) true operation_0379 beta12orEarlier Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. Repeat sequence detection operation_0380 beta12orEarlier Analyse repeat sequence organisation such as periodicity. Repeat sequence organisation analysis operation_0383 beta12orEarlier 1.12 Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. Protein hydropathy calculation (from structure) true operation_0384 beta12orEarlier WHATIF:AtomAccessibilitySolvent WHATIF:AtomAccessibilitySolventPlus Calculate solvent accessible or buried surface areas in protein or other molecular structures. Protein solvent accessibility calculation Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Accessible surface calculation operation_0385 beta12orEarlier 1.12 Identify clusters of hydrophobic or charged residues in a protein structure. Protein hydropathy cluster calculation true operation_0386 beta12orEarlier Calculate whether a protein structure has an unusually large net charge (dipole moment). Protein dipole moment calculation operation_0387 beta12orEarlier WHATIF:AtomAccessibilityMolecular WHATIF:AtomAccessibilityMolecularPlus WHATIF:ResidueAccessibilityMolecular WHATIF:ResidueAccessibilitySolvent WHATIF:ResidueAccessibilityVacuum WHATIF:ResidueAccessibilityVacuumMolecular WHATIF:TotAccessibilityMolecular WHATIF:TotAccessibilitySolvent Calculate the molecular surface area in proteins and other macromolecules. Protein atom surface calculation Protein residue surface calculation Protein surface and interior calculation Protein surface calculation Molecular surface calculation operation_0388 beta12orEarlier 1.12 Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. Protein binding site prediction (from structure) true operation_0389 beta12orEarlier Analyse the interaction of protein with nucleic acids, e.g. RNA or DNA-binding sites, interfaces etc. Protein-nucleic acid binding site analysis Protein-DNA interaction analysis Protein-RNA interaction analysis Protein-nucleic acid interaction analysis operation_0390 beta12orEarlier Decompose a structure into compact or globular fragments (protein peeling). Protein peeling operation_0391 beta12orEarlier Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. Protein distance matrix calculation operation_0392 beta12orEarlier Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. Protein contact map calculation Contact map calculation operation_0393 beta12orEarlier Calculate clusters of contacting residues in protein structures. This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role. Residue cluster calculation operation_0394 beta12orEarlier WHATIF:HasHydrogenBonds WHATIF:ShowHydrogenBonds WHATIF:ShowHydrogenBondsM Identify potential hydrogen bonds between amino acids and other groups. The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. Hydrogen bond calculation operation_0395 beta12orEarlier 1.12 Calculate non-canonical atomic interactions in protein structures. Residue non-canonical interaction detection true operation_0396 beta12orEarlier Calculate a Ramachandran plot of a protein structure. Ramachandran plot calculation operation_0397 beta12orEarlier 1.22 Validate a Ramachandran plot of a protein structure. Ramachandran plot validation true operation_0398 beta12orEarlier Calculate the molecular weight of a protein sequence or fragments. Peptide mass calculation Protein molecular weight calculation operation_0399 beta12orEarlier Predict extinction coefficients or optical density of a protein sequence. Protein extinction coefficient calculation operation_0400 beta12orEarlier Calculate pH-dependent properties from pKa calculations of a protein sequence. Protein pH-dependent property calculation Protein pKa calculation operation_0401 beta12orEarlier 1.12 Hydropathy calculation on a protein sequence. Protein hydropathy calculation (from sequence) true operation_0402 beta12orEarlier Plot a protein titration curve. Protein titration curve plotting operation_0403 beta12orEarlier Calculate isoelectric point of a protein sequence. Protein isoelectric point calculation operation_0404 beta12orEarlier Estimate hydrogen exchange rate of a protein sequence. Protein hydrogen exchange rate calculation operation_0405 beta12orEarlier Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. Protein hydrophobic region calculation operation_0406 beta12orEarlier Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. Protein aliphatic index calculation operation_0407 beta12orEarlier Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. Protein hydrophobic moment plotting operation_0408 beta12orEarlier Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. Protein globularity prediction operation_0409 beta12orEarlier Predict the solubility or atomic solvation energy of a protein sequence. Protein solubility prediction operation_0410 beta12orEarlier Predict crystallizability of a protein sequence. Protein crystallizability prediction operation_0411 beta12orEarlier (jison)Too fine-grained. 1.17 Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. Protein signal peptide detection (eukaryotes) true operation_0412 beta12orEarlier (jison)Too fine-grained. 1.17 Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. Protein signal peptide detection (bacteria) true operation_0413 beta12orEarlier 1.12 Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. MHC peptide immunogenicity prediction true operation_0414 beta12orEarlier 1.6 Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. Methods typically involve scanning for known motifs, patterns and regular expressions. Protein feature prediction (from sequence) true operation_0415 beta12orEarlier Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. Sequence feature detection (nucleic acid) Nucleic acid feature prediction Nucleic acid feature recognition Nucleic acid site detection Nucleic acid site prediction Nucleic acid site recognition Methods typically involve scanning for known motifs, patterns and regular expressions. This is placeholder but does not comprehensively include all child concepts - please inspect other concepts under "Nucleic acid sequence analysis" for example "Gene prediction", for other feature detection operations. Nucleic acid feature detection operation_0416 beta12orEarlier Predict antigenic determinant sites (epitopes) in protein sequences. Antibody epitope prediction Epitope prediction B cell epitope mapping B cell epitope prediction Epitope mapping (MHC Class I) Epitope mapping (MHC Class II) T cell epitope mapping T cell epitope prediction Epitope mapping is commonly done during vaccine design. Epitope mapping operation_0417 beta12orEarlier Predict post-translation modification sites in protein sequences. PTM analysis PTM prediction PTM site analysis PTM site prediction Post-translation modification site prediction Post-translational modification analysis Protein post-translation modification site prediction Acetylation prediction Acetylation site prediction Dephosphorylation prediction Dephosphorylation site prediction GPI anchor prediction GPI anchor site prediction GPI modification prediction GPI modification site prediction Glycosylation prediction Glycosylation site prediction Hydroxylation prediction Hydroxylation site prediction Methylation prediction Methylation site prediction N-myristoylation prediction N-myristoylation site prediction N-terminal acetylation prediction N-terminal acetylation site prediction N-terminal myristoylation prediction N-terminal myristoylation site prediction Palmitoylation prediction Palmitoylation site prediction Phosphoglycerylation prediction Phosphoglycerylation site prediction Phosphorylation prediction Phosphorylation site prediction Phosphosite localization Prenylation prediction Prenylation site prediction Pupylation prediction Pupylation site prediction S-nitrosylation prediction S-nitrosylation site prediction S-sulfenylation prediction S-sulfenylation site prediction Succinylation prediction Succinylation site prediction Sulfation prediction Sulfation site prediction Sumoylation prediction Sumoylation site prediction Tyrosine nitration prediction Tyrosine nitration site prediction Ubiquitination prediction Ubiquitination site prediction Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. Post-translational modification site prediction operation_0418 beta12orEarlier Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. Protein signal peptide detection operation_0419 beta12orEarlier 1.12 Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. Protein binding site prediction (from sequence) true operation_0420 beta12orEarlier Predict or detect RNA and DNA-binding binding sites in protein sequences. Protein-nucleic acid binding detection Protein-nucleic acid binding prediction Protein-nucleic acid binding site detection Protein-nucleic acid binding site prediction Zinc finger prediction This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). Nucleic acids-binding site prediction operation_0421 beta12orEarlier 1.20 Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation. Protein folding site prediction true operation_0422 beta12orEarlier Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. Protein cleavage site prediction operation_0423 beta12orEarlier 1.8 Predict epitopes that bind to MHC class I molecules. Epitope mapping (MHC Class I) true operation_0424 beta12orEarlier 1.8 Predict epitopes that bind to MHC class II molecules. Epitope mapping (MHC Class II) true operation_0425 beta12orEarlier 1.12 Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. Whole gene prediction true operation_0426 beta12orEarlier 1.12 Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene component prediction true operation_0427 beta12orEarlier Detect or predict transposons, retrotransposons / retrotransposition signatures etc. Transposon prediction operation_0428 beta12orEarlier Detect polyA signals in nucleotide sequences. PolyA detection PolyA prediction PolyA signal prediction Polyadenylation signal detection Polyadenylation signal prediction PolyA signal detection operation_0429 beta12orEarlier Detect quadruplex-forming motifs in nucleotide sequences. Quadruplex structure prediction Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. Quadruplex formation site detection operation_0430 beta12orEarlier Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. CpG island and isochores detection CpG island and isochores rendering An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. CpG island and isochore detection operation_0431 beta12orEarlier Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. Restriction site recognition operation_0432 beta12orEarlier Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. Nucleosome exclusion sequence prediction Nucleosome formation sequence prediction Nucleosome position prediction operation_0433 beta12orEarlier Identify, predict or analyse splice sites in nucleotide sequences. Splice prediction Methods might require a pre-mRNA or genomic DNA sequence. Splice site prediction operation_0434 beta12orEarlier 1.19 Predict whole gene structure using a combination of multiple methods to achieve better predictions. Integrated gene prediction true operation_0435 beta12orEarlier Find operons (operators, promoters and genes) in bacteria genes. Operon prediction operation_0436 beta12orEarlier Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. ORF finding ORF prediction Coding region prediction operation_0437 beta12orEarlier Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. Selenocysteine insertion sequence (SECIS) prediction SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. SECIS element prediction operation_0438 beta12orEarlier Identify or predict transcriptional regulatory motifs, patterns, elements or regions in DNA sequences. Regulatory element prediction Transcription regulatory element prediction Conserved transcription regulatory sequence identification Translational regulatory element prediction This includes comparative genomics approaches that identify common, conserved (homologous) or synonymous transcriptional regulatory elements. For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. Transcriptional regulatory element prediction operation_0439 beta12orEarlier Predict translation initiation sites, possibly by searching a database of sites. Translation initiation site prediction operation_0440 beta12orEarlier Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. Promoter prediction operation_0441 beta12orEarlier Identify, predict or analyse cis-regulatory elements in DNA sequences (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) or in RNA sequences (e.g. riboswitches). Transcriptional regulatory element prediction (DNA-cis) Transcriptional regulatory element prediction (RNA-cis) Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand from which the element was transcribed. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. They also occur in RNA sequences, e.g. a riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. cis-regulatory element prediction operation_0442 beta12orEarlier 1.19 Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. Transcriptional regulatory element prediction (RNA-cis) true operation_0443 beta12orEarlier Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. Functional RNA identification Transcriptional regulatory element prediction (trans) Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. trans-regulatory element prediction operation_0444 beta12orEarlier Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. MAR/SAR prediction Matrix/scaffold attachment site prediction MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. S/MAR prediction operation_0445 beta12orEarlier Identify or predict transcription factor binding sites in DNA sequences. Transcription factor binding site prediction operation_0446 beta12orEarlier Identify or predict exonic splicing enhancers (ESE) in exons. An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. Exonic splicing enhancer prediction operation_0447 beta12orEarlier Evaluate molecular sequence alignment accuracy. Sequence alignment quality evaluation Evaluation might be purely sequence-based or use structural information. Sequence alignment validation operation_0448 beta12orEarlier Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. Residue conservation analysis Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. Sequence alignment analysis (conservation) operation_0449 beta12orEarlier Analyse correlations between sites in a molecular sequence alignment. This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. Sequence alignment analysis (site correlation) operation_0450 beta12orEarlier Detects chimeric sequences (chimeras) from a sequence alignment. Chimeric sequence detection A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. Chimera detection operation_0451 beta12orEarlier Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. Sequence alignment analysis (recombination detection) Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Recombination detection operation_0452 beta12orEarlier Identify insertion, deletion and duplication events from a sequence alignment. Indel discovery Sequence alignment analysis (indel detection) Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Indel detection operation_0453 beta12orEarlier beta12orEarlier Predict nucleosome formation potential of DNA sequences. Nucleosome formation potential prediction true operation_0455 beta12orEarlier Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. Nucleic acid thermodynamic property calculation operation_0456 beta12orEarlier Calculate and plot a DNA or DNA/RNA melting profile. A melting profile is used to visualise and analyse partly melted DNA conformations. Nucleic acid melting profile plotting operation_0457 beta12orEarlier Calculate and plot a DNA or DNA/RNA stitch profile. A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. Nucleic acid stitch profile plotting operation_0458 beta12orEarlier Calculate and plot a DNA or DNA/RNA melting curve. Nucleic acid melting curve plotting operation_0459 beta12orEarlier Calculate and plot a DNA or DNA/RNA probability profile. Nucleic acid probability profile plotting operation_0460 beta12orEarlier Calculate and plot a DNA or DNA/RNA temperature profile. Nucleic acid temperature profile plotting operation_0461 beta12orEarlier Calculate curvature and flexibility / stiffness of a nucleotide sequence. This includes properties such as. Nucleic acid curvature calculation operation_0463 beta12orEarlier Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. miRNA prediction microRNA detection microRNA target detection miRNA target prediction operation_0464 beta12orEarlier Identify or predict tRNA genes in genomic sequences (tRNA). tRNA gene prediction operation_0465 beta12orEarlier Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. siRNA binding specificity prediction operation_0467 beta12orEarlier 1.18 Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. Protein secondary structure prediction (integrated) true operation_0468 beta12orEarlier Predict helical secondary structure of protein sequences. Protein secondary structure prediction (helices) operation_0469 beta12orEarlier Predict turn structure (for example beta hairpin turns) of protein sequences. Protein secondary structure prediction (turns) operation_0470 beta12orEarlier Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. Protein secondary structure prediction (coils) operation_0471 beta12orEarlier Predict cysteine bonding state and disulfide bond partners in protein sequences. Disulfide bond prediction operation_0472 beta12orEarlier Not sustainable to have protein type-specific concepts. 1.19 Predict G protein-coupled receptors (GPCR). GPCR prediction true operation_0473 beta12orEarlier Not sustainable to have protein type-specific concepts. 1.19 Analyse G-protein coupled receptor proteins (GPCRs). GPCR analysis true operation_0474 beta12orEarlier Predict tertiary structure (backbone and side-chain conformation) of protein sequences. Protein folding pathway prediction This includes methods that predict the folding pathway(s) or non-native structural intermediates of a protein. Protein structure prediction operation_0475 beta12orEarlier Predict structure of DNA or RNA. Methods might identify thermodynamically stable or evolutionarily conserved structures. Nucleic acid structure prediction operation_0476 beta12orEarlier Predict tertiary structure of protein sequence(s) without homologs of known structure. de novo structure prediction Ab initio structure prediction operation_0477 beta12orEarlier Build a three-dimensional protein model based on known (for example homologs) structures. Comparative modelling Homology modelling Homology structure modelling Protein structure comparative modelling The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc. Protein modelling operation_0478 beta12orEarlier Model the structure of a protein in complex with a small molecule or another macromolecule. Docking simulation Macromolecular docking This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. Molecular docking operation_0479 beta12orEarlier Model protein backbone conformation. Protein modelling (backbone) Design optimization Epitope grafting Scaffold search Scaffold selection Methods might require a preliminary C(alpha) trace. Scaffold selection, scaffold search, epitope grafting and design optimization are stages of backbone modelling done during rational vaccine design. Backbone modelling operation_0480 beta12orEarlier Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. Protein modelling (side chains) Antibody optimisation Antigen optimisation Antigen resurfacing Rotamer likelihood prediction Antibody optimisation is to optimize the antibody-interacting surface of the antigen (epitope). Antigen optimisation is to optimize the antigen-interacting surface of the antibody (paratope). Antigen resurfacing is to resurface the antigen by varying the sequence of non-epitope regions. Methods might use a residue rotamer library. This includes rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. Side chain modelling operation_0481 beta12orEarlier Model loop conformation in protein structures. Protein loop modelling Protein modelling (loops) Loop modelling operation_0482 beta12orEarlier Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. Ligand-binding simulation Protein-peptide docking Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. Virtual screening is used in drug discovery to search libraries of small molecules in order to identify those molecules which are most likely to bind to a drug target (typically a protein receptor or enzyme). Protein-ligand docking operation_0483 beta12orEarlier Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. Nucleic acid folding family identification Structured RNA prediction and optimisation RNA inverse folding operation_0484 beta12orEarlier Find single nucleotide polymorphisms (SNPs) - single nucleotide change in base positions - between sequences. Typically done for sequences from a high-throughput sequencing experiment that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. SNP calling SNP discovery Single nucleotide polymorphism detection This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. SNP detection operation_0485 beta12orEarlier Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. Radiation Hybrid Mapping operation_0486 beta12orEarlier beta12orEarlier Map the genetic architecture of dynamic complex traits. This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Functional mapping true operation_0487 beta12orEarlier Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Haplotype inference Haplotype map generation Haplotype reconstruction Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). Haplotype mapping operation_0488 beta12orEarlier Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. Linkage disequilibrium calculation operation_0489 beta12orEarlier Predict genetic code from analysis of codon usage data. Genetic code prediction operation_0490 beta12orEarlier Render a representation of a distribution that consists of group of data points plotted on a simple scale. Categorical plot plotting Dotplot plotting Dot plots are useful when having not too many (e.g. 20) data points for each category. Example: draw a dotplot of sequence similarities identified from word-matching or character comparison. Dot plot plotting operation_0491 beta12orEarlier Align exactly two molecular sequences. Pairwise alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. Pairwise sequence alignment operation_0492 beta12orEarlier Align more than two molecular sequences. Multiple alignment This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. Multiple sequence alignment operation_0493 beta12orEarlier 1.6 Locally align exactly two molecular sequences. Local alignment methods identify regions of local similarity. Pairwise sequence alignment generation (local) true operation_0494 beta12orEarlier 1.6 Globally align exactly two molecular sequences. Global alignment methods identify similarity across the entire length of the sequences. Pairwise sequence alignment generation (global) true operation_0495 beta12orEarlier Locally align two or more molecular sequences. Local sequence alignment Sequence alignment (local) Smith-Waterman Local alignment methods identify regions of local similarity. Local alignment operation_0496 beta12orEarlier Globally align two or more molecular sequences. Global sequence alignment Sequence alignment (global) Global alignment methods identify similarity across the entire length of the sequences. Global alignment operation_0497 beta12orEarlier 1.19 Align two or more molecular sequences with user-defined constraints. Constrained sequence alignment true operation_0498 beta12orEarlier 1.16 Align two or more molecular sequences using multiple methods to achieve higher quality. Consensus-based sequence alignment true operation_0499 beta12orEarlier Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. Multiple sequence alignment (phylogenetic tree-based) Multiple sequence alignment construction (phylogenetic tree-based) Phylogenetic tree-based multiple sequence alignment construction Sequence alignment (phylogenetic tree-based) Sequence alignment generation (phylogenetic tree-based) This is supposed to give a more biologically meaningful alignment than standard alignments. Tree-based sequence alignment operation_0500 beta12orEarlier 1.6 Align molecular secondary structure (represented as a 1D string). Secondary structure alignment generation true operation_0501 beta12orEarlier 1.18 Align protein secondary structures. Protein secondary structure alignment generation true operation_0502 beta12orEarlier Align RNA secondary structures. RNA secondary structure alignment construction RNA secondary structure alignment generation Secondary structure alignment construction (RNA) RNA secondary structure alignment operation_0503 beta12orEarlier Align (superimpose) exactly two molecular tertiary structures. Structure alignment (pairwise) Pairwise protein structure alignment Pairwise structure alignment operation_0504 beta12orEarlier Align (superimpose) more than two molecular tertiary structures. Structure alignment (multiple) Multiple protein structure alignment This includes methods that use an existing alignment. Multiple structure alignment operation_0505 beta12orEarlier beta13 Align protein tertiary structures. Structure alignment (protein) true operation_0506 beta12orEarlier beta13 Align RNA tertiary structures. Structure alignment (RNA) true operation_0507 beta12orEarlier 1.6 Locally align (superimpose) exactly two molecular tertiary structures. Local alignment methods identify regions of local similarity, common substructures etc. Pairwise structure alignment generation (local) true operation_0508 beta12orEarlier 1.6 Globally align (superimpose) exactly two molecular tertiary structures. Global alignment methods identify similarity across the entire structures. Pairwise structure alignment generation (global) true operation_0509 beta12orEarlier Locally align (superimpose) two or more molecular tertiary structures. Structure alignment (local) Local protein structure alignment Local alignment methods identify regions of local similarity, common substructures etc. Local structure alignment operation_0510 beta12orEarlier Globally align (superimpose) two or more molecular tertiary structures. Structure alignment (global) Global protein structure alignment Global alignment methods identify similarity across the entire structures. Global structure alignment operation_0511 beta12orEarlier 1.16 Align exactly two molecular profiles. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Profile-profile alignment (pairwise) true operation_0512 beta12orEarlier 1.6 Align two or more molecular profiles. Sequence alignment generation (multiple profile) true operation_0513 beta12orEarlier 1.16 Align exactly two molecular Structural (3D) profiles. 3D profile-to-3D profile alignment (pairwise) true operation_0514 beta12orEarlier 1.6 Align two or more molecular 3D profiles. Structural profile alignment generation (multiple) true operation_0515 beta12orEarlier 1.6 Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. Data retrieval (tool metadata) true operation_0516 beta12orEarlier 1.6 Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. Data retrieval (database metadata) true operation_0517 beta12orEarlier 1.13 Predict primers for large scale sequencing. PCR primer design (for large scale sequencing) true operation_0518 beta12orEarlier 1.13 Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). PCR primer design (for genotyping polymorphisms) true operation_0519 beta12orEarlier 1.13 Predict primers for gene transcription profiling. PCR primer design (for gene transcription profiling) true operation_0520 beta12orEarlier 1.13 Predict primers that are conserved across multiple genomes or species. PCR primer design (for conserved primers) true operation_0521 beta12orEarlier 1.13 Predict primers based on gene structure. PCR primer design (based on gene structure) true operation_0522 beta12orEarlier 1.13 Predict primers for methylation PCRs. PCR primer design (for methylation PCRs) true operation_0523 beta12orEarlier Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. Sequence assembly (mapping assembly) The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. Mapping assembly operation_0524 beta12orEarlier Sequence assembly by combining fragments without the aid of a reference sequence or genome. De Bruijn graph Sequence assembly (de-novo assembly) De-novo assemblers are much slower and more memory intensive than mapping assemblers. De-novo assembly operation_0525 beta12orEarlier The process of assembling many short DNA sequences together such that they represent the original chromosomes from which the DNA originated. Genomic assembly Sequence assembly (genome assembly) Breakend assembly Genome assembly operation_0526 beta12orEarlier Sequence assembly for EST sequences (transcribed mRNA). Sequence assembly (EST assembly) Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. EST assembly operation_0527 beta12orEarlier Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Tag to gene assignment Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome. Sequence tag mapping operation_0528 beta12orEarlier beta12orEarlier Process (read and / or write) serial analysis of gene expression (SAGE) data. SAGE data processing true operation_0529 beta12orEarlier beta12orEarlier Process (read and / or write) massively parallel signature sequencing (MPSS) data. MPSS data processing true operation_0530 beta12orEarlier beta12orEarlier Process (read and / or write) sequencing by synthesis (SBS) data. SBS data processing true operation_0531 beta12orEarlier Generate a heat map of expression data from e.g. microarray data. Heat map construction Heatmap generation The heat map usually uses a coloring scheme to represent expression values. They can show how quantitative measurements were influenced by experimental conditions. Heat map generation operation_0532 beta12orEarlier 1.6 Analyse one or more gene expression profiles, typically to interpret them in functional terms. Gene expression profile analysis true operation_0533 beta12orEarlier Map an expression profile to known biological pathways, for example, to identify or reconstruct a pathway. Pathway mapping Gene expression profile pathway mapping Gene to pathway mapping Gene-to-pathway mapping Expression profile pathway mapping operation_0534 beta12orEarlier 1.18 Assign secondary structure from protein coordinate data. Protein secondary structure assignment (from coordinate data) true operation_0535 beta12orEarlier 1.18 Assign secondary structure from circular dichroism (CD) spectroscopic data. Protein secondary structure assignment (from CD data) true operation_0536 beta12orEarlier 1.7 Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. Protein structure assignment (from X-ray crystallographic data) true operation_0537 beta12orEarlier 1.7 Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. Protein structure assignment (from NMR data) true operation_0538 beta12orEarlier true Construct a phylogenetic tree from a specific type of data. Phylogenetic tree construction (data centric) Phylogenetic tree generation (data centric) Subconcepts of this concept reflect different types of data used to generate a tree, and provide an alternate axis for curation. Phylogenetic inference (data centric) operation_0539 beta12orEarlier true Construct a phylogenetic tree using a specific method. Phylogenetic tree construction (method centric) Phylogenetic tree generation (method centric) Subconcepts of this concept reflect different computational methods used to generate a tree, and provide an alternate axis for curation. Phylogenetic inference (method centric) operation_0540 beta12orEarlier Phylogenetic tree construction from molecular sequences. Phylogenetic tree construction (from molecular sequences) Phylogenetic tree generation (from molecular sequences) Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. Phylogenetic inference (from molecular sequences) operation_0541 beta12orEarlier Phylogenetic tree construction from continuous quantitative character data. Phylogenetic tree construction (from continuous quantitative characters) Phylogenetic tree generation (from continuous quantitative characters) Phylogenetic inference (from continuous quantitative characters) operation_0542 beta12orEarlier Phylogenetic tree construction from gene frequency data. Phylogenetic tree construction (from gene frequencies) Phylogenetic tree generation (from gene frequencies) Phylogenetic inference (from gene frequencies) operation_0543 beta12orEarlier Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. Phylogenetic tree construction (from polymorphism data) Phylogenetic tree generation (from polymorphism data) Phylogenetic inference (from polymorphism data) operation_0544 beta12orEarlier Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. Phylogenetic species tree construction Phylogenetic species tree generation Species tree construction operation_0545 beta12orEarlier Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. Phylogenetic tree construction (parsimony methods) Phylogenetic tree generation (parsimony methods) This includes evolutionary parsimony (invariants) methods. Phylogenetic inference (parsimony methods) operation_0546 beta12orEarlier Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. Phylogenetic tree construction (minimum distance methods) Phylogenetic tree generation (minimum distance methods) This includes neighbor joining (NJ) clustering method. Phylogenetic inference (minimum distance methods) operation_0547 beta12orEarlier Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. Phylogenetic tree construction (maximum likelihood and Bayesian methods) Phylogenetic tree generation (maximum likelihood and Bayesian methods) Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. Phylogenetic inference (maximum likelihood and Bayesian methods) operation_0548 beta12orEarlier Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. Phylogenetic tree construction (quartet methods) Phylogenetic tree generation (quartet methods) Phylogenetic inference (quartet methods) operation_0549 beta12orEarlier Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. Phylogenetic tree construction (AI methods) Phylogenetic tree generation (AI methods) Phylogenetic inference (AI methods) operation_0550 beta12orEarlier Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. Nucleotide substitution modelling DNA substitution modelling operation_0551 beta12orEarlier Analyse the shape (topology) of a phylogenetic tree. Phylogenetic tree analysis (shape) Phylogenetic tree topology analysis operation_0552 beta12orEarlier Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. Phylogenetic tree bootstrapping operation_0553 beta12orEarlier Construct a "gene tree" which represents the evolutionary history of the genes included in the study. This can be used to predict families of genes and gene function based on their position in a phylogenetic tree. Phylogenetic tree analysis (gene family prediction) Gene trees can provide evidence for gene duplication events, as well as speciation events. Where sequences from different homologs are included in a gene tree, subsequent clustering of the orthologs can demonstrate evolutionary history of the orthologs. Gene tree construction operation_0554 beta12orEarlier Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). Phylogenetic tree analysis (natural selection) Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. Allele frequency distribution analysis operation_0555 beta12orEarlier Compare two or more phylogenetic trees to produce a consensus tree. Phylogenetic tree construction (consensus) Phylogenetic tree generation (consensus) Methods typically test for topological similarity between trees using for example a congruence index. Consensus tree construction operation_0556 beta12orEarlier Compare two or more phylogenetic trees to detect subtrees or supertrees. Phylogenetic sub/super tree detection Subtree construction Supertree construction Phylogenetic sub/super tree construction operation_0557 beta12orEarlier Compare two or more phylogenetic trees to calculate distances between trees. Phylogenetic tree distances calculation operation_0558 beta12orEarlier Annotate a phylogenetic tree with terms from a controlled vocabulary. Phylogenetic tree annotation http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation operation_0559 beta12orEarlier 1.12 Predict and optimise peptide ligands that elicit an immunological response. Immunogenicity prediction true operation_0560 beta12orEarlier Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. DNA vaccine design operation_0561 beta12orEarlier 1.12 Reformat (a file or other report of) molecular sequence(s). Sequence formatting true operation_0562 beta12orEarlier 1.12 Reformat (a file or other report of) molecular sequence alignment(s). Sequence alignment formatting true operation_0563 beta12orEarlier 1.12 Reformat a codon usage table. Codon usage table formatting true operation_0564 beta12orEarlier Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown. Sequence rendering Sequence alignment visualisation Sequence visualisation operation_0565 beta12orEarlier 1.15 Visualise, format or print a molecular sequence alignment. Sequence alignment visualisation true operation_0566 beta12orEarlier Visualise, format or render sequence clusters. Sequence cluster rendering Sequence cluster visualisation operation_0567 beta12orEarlier Render or visualise a phylogenetic tree. Phylogenetic tree rendering Phylogenetic tree visualisation operation_0568 beta12orEarlier 1.15 Visualise RNA secondary structure, knots, pseudoknots etc. RNA secondary structure visualisation true operation_0569 beta12orEarlier 1.15 Render and visualise protein secondary structure. Protein secondary structure visualisation true operation_0570 beta12orEarlier Visualise or render molecular 3D structure, for example a high-quality static picture or animation. Structure rendering Protein secondary structure visualisation RNA secondary structure visualisation This includes visualisation of protein secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure. Structure visualisation operation_0571 beta12orEarlier Visualise microarray or other expression data. Expression data rendering Gene expression data visualisation Microarray data rendering Expression data visualisation operation_0572 beta12orEarlier 1.19 Identify and analyse networks of protein interactions. Protein interaction network visualisation true operation_0573 beta12orEarlier Draw or visualise a DNA map. DNA map drawing Map rendering Map drawing operation_0574 beta12orEarlier beta12orEarlier Render a sequence with motifs. Sequence motif rendering true operation_0575 beta12orEarlier Draw or visualise restriction maps in DNA sequences. Restriction map drawing operation_0577 beta12orEarlier beta12orEarlier Draw a linear maps of DNA. DNA linear map rendering true operation_0578 beta12orEarlier DNA circular map rendering Draw a circular maps of DNA, for example a plasmid map. Plasmid map drawing operation_0579 beta12orEarlier Visualise operon structure etc. Operon rendering Operon drawing operation_1768 beta12orEarlier beta12orEarlier Identify folding families of related RNAs. Nucleic acid folding family identification true operation_1769 beta12orEarlier 1.20 Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. Nucleic acid folding energy calculation true operation_1774 beta12orEarlier beta12orEarlier Retrieve existing annotation (or documentation), typically annotation on a database entity. Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. Annotation retrieval true operation_1777 beta12orEarlier Predict the biological or biochemical role of a protein, or other aspects of a protein function. Protein function analysis Protein functional analysis For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. Protein function prediction operation_1778 beta12orEarlier Compare the functional properties of two or more proteins. Protein function comparison operation_1780 beta12orEarlier 1.6 Submit a molecular sequence to a database. Sequence submission true operation_1781 beta12orEarlier Analyse a known network of gene regulation. Gene regulatory network comparison Gene regulatory network modelling Regulatory network comparison Regulatory network modelling Gene regulatory network analysis operation_1812 beta12orEarlier WHATIF:UploadPDB Parse, prepare or load a user-specified data file so that it is available for use. Data loading Loading Data parsing operation_1813 beta12orEarlier 1.6 Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. Sequence retrieval true operation_1814 beta12orEarlier 1.6 WHATIF:DownloadPDB WHATIF:EchoPDB Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. This includes direct retrieval methods but not those that perform calculations on the sequence or structure. Structure retrieval true operation_1816 beta12orEarlier WHATIF:GetSurfaceDots Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. A dot has three coordinates (x,y,z) and (typically) a color. Surface rendering operation_1817 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible surface') for each atom in a structure. Waters are not considered. Protein atom surface calculation (accessible) true operation_1818 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. Waters are not considered. Protein atom surface calculation (accessible molecular) true operation_1819 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible surface') for each residue in a structure. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Protein residue surface calculation (accessible) true operation_1820 beta12orEarlier 1.12 Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Protein residue surface calculation (vacuum accessible) true operation_1821 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Protein residue surface calculation (accessible molecular) true operation_1822 beta12orEarlier 1.12 Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Protein residue surface calculation (vacuum molecular) true operation_1823 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. Protein surface calculation (accessible molecular) true operation_1824 beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible surface') for a structure as a whole. Protein surface calculation (accessible) true operation_1825 beta12orEarlier 1.12 Calculate for each residue in a protein structure all its backbone torsion angles. Backbone torsion angle calculation true operation_1826 beta12orEarlier 1.12 Calculate for each residue in a protein structure all its torsion angles. Full torsion angle calculation true operation_1827 beta12orEarlier 1.12 Calculate for each cysteine (bridge) all its torsion angles. Cysteine torsion angle calculation true operation_1828 beta12orEarlier 1.12 For each amino acid in a protein structure calculate the backbone angle tau. Tau is the backbone angle N-Calpha-C (angle over the C-alpha). Tau angle calculation true operation_1829 beta12orEarlier WHATIF:ShowCysteineBridge Detect cysteine bridges (from coordinate data) in a protein structure. Cysteine bridge detection operation_1830 beta12orEarlier WHATIF:ShowCysteineFree Detect free cysteines in a protein structure. A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. Free cysteine detection operation_1831 beta12orEarlier WHATIF:ShowCysteineMetal Detect cysteines that are bound to metal in a protein structure. Metal-bound cysteine detection operation_1832 beta12orEarlier 1.12 Calculate protein residue contacts with nucleic acids in a structure. Residue contact calculation (residue-nucleic acid) true operation_1834 beta12orEarlier Calculate protein residue contacts with metal in a structure. Residue-metal contact calculation Protein-metal contact calculation operation_1835 beta12orEarlier 1.12 Calculate ion contacts in a structure (all ions for all side chain atoms). Residue contact calculation (residue-negative ion) true operation_1836 beta12orEarlier WHATIF:ShowBumps Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. Residue bump detection operation_1837 beta12orEarlier 1.12 WHATIF:SymmetryContact Calculate the number of symmetry contacts made by residues in a protein structure. A symmetry contact is a contact between two atoms in different asymmetric unit. Residue symmetry contact calculation true operation_1838 beta12orEarlier 1.12 Calculate contacts between residues and ligands in a protein structure. Residue contact calculation (residue-ligand) true operation_1839 beta12orEarlier WHATIF:HasSaltBridge WHATIF:HasSaltBridgePlus WHATIF:ShowSaltBridges WHATIF:ShowSaltBridgesH Calculate (and possibly score) salt bridges in a protein structure. Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. Salt bridge calculation operation_1841 beta12orEarlier 1.12 WHATIF:ShowLikelyRotamers WHATIF:ShowLikelyRotamers100 WHATIF:ShowLikelyRotamers200 WHATIF:ShowLikelyRotamers300 WHATIF:ShowLikelyRotamers400 WHATIF:ShowLikelyRotamers500 WHATIF:ShowLikelyRotamers600 WHATIF:ShowLikelyRotamers700 WHATIF:ShowLikelyRotamers800 WHATIF:ShowLikelyRotamers900 Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. Rotamer likelihood prediction true operation_1842 beta12orEarlier 1.12 WHATIF:ProlineMutationValue Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. Proline mutation value calculation true operation_1843 beta12orEarlier WHATIF: PackingQuality Identify poorly packed residues in protein structures. Residue packing validation operation_1844 beta12orEarlier WHATIF: ImproperQualityMax WHATIF: ImproperQualitySum Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. An example is validation of a Ramachandran plot of a protein structure. Ramachandran plot validation Protein geometry validation operation_1845 beta12orEarlier beta12orEarlier WHATIF: PDB_sequence Extract a molecular sequence from a PDB file. PDB file sequence retrieval true operation_1846 beta12orEarlier 1.12 Identify HET groups in PDB files. A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. HET group detection true operation_1847 beta12orEarlier beta12orEarlier Determine for residue the DSSP determined secondary structure in three-state (HSC). DSSP secondary structure assignment true operation_1848 beta12orEarlier 1.12 WHATIF: PDBasXML Reformat (a file or other report of) tertiary structure data. Structure formatting true operation_1850 beta12orEarlier Assign cysteine bonding state and disulfide bond partners in protein structures. Protein cysteine and disulfide bond assignment operation_1913 beta12orEarlier 1.12 Identify poor quality amino acid positions in protein structures. Residue validation true operation_1914 beta12orEarlier 1.6 WHATIF:MovedWaterPDB Query a tertiary structure database and retrieve water molecules. Structure retrieval (water) true operation_2008 beta12orEarlier Identify or predict siRNA duplexes in RNA. siRNA duplex prediction operation_2089 beta12orEarlier Refine an existing sequence alignment. Sequence alignment refinement operation_2120 beta12orEarlier 1.6 Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). Listfile processing true operation_2121 beta12orEarlier Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. Sequence file editing operation_2122 beta12orEarlier 1.6 Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. Sequence alignment file processing true operation_2123 beta12orEarlier beta13 Process (read and / or write) physicochemical property data for small molecules. Small molecule data processing true operation_2222 beta12orEarlier beta13 Search and retrieve documentation on a bioinformatics ontology. Data retrieval (ontology annotation) true operation_2224 beta12orEarlier beta13 Query an ontology and retrieve concepts or relations. Data retrieval (ontology concept) true operation_2233 beta12orEarlier Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. Representative sequence identification operation_2234 beta12orEarlier 1.6 Perform basic (non-analytical) operations on a file of molecular tertiary structural data. Structure file processing true operation_2237 beta12orEarlier beta13 Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. Data retrieval (sequence profile) true operation_2238 beta12orEarlier Perform a statistical data operation of some type, e.g. calibration or validation. Significance testing Statistical analysis Statistical test Statistical testing Expectation maximisation Gibbs sampling Hypothesis testing Omnibus test Statistical calculation operation_2239 beta12orEarlier Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. 3D-1D scoring matrix construction A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. 3D-1D scoring matrix generation operation_2241 beta12orEarlier Visualise transmembrane proteins, typically the transmembrane regions within a sequence. Transmembrane protein rendering Transmembrane protein visualisation operation_2246 beta12orEarlier beta13 An operation performing purely illustrative (pedagogical) purposes. Demonstration true operation_2264 beta12orEarlier beta13 Query a biological pathways database and retrieve annotation on one or more pathways. Data retrieval (pathway or network) true operation_2265 beta12orEarlier beta13 Query a database and retrieve one or more data identifiers. Data retrieval (identifier) true operation_2284 beta12orEarlier Calculate a density plot (of base composition) for a nucleotide sequence. Nucleic acid density plotting operation_2403 beta12orEarlier Analyse one or more known molecular sequences. Sequence analysis (general) Sequence analysis operation_2404 beta12orEarlier Analyse molecular sequence motifs. Sequence motif processing Sequence motif analysis operation_2405 beta12orEarlier 1.6 Process (read and / or write) protein interaction data. Protein interaction data processing true operation_2406 beta12orEarlier Analyse protein structural data. Structure analysis (protein) Protein structure analysis operation_2407 beta12orEarlier beta12orEarlier Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. Annotation processing true operation_2408 beta12orEarlier beta12orEarlier Analyse features in molecular sequences. Sequence feature analysis true operation_2409 beta12orEarlier true Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output. File handling File processing Report handling Utility operation Processing Data handling operation_2410 beta12orEarlier beta12orEarlier Analyse gene expression and regulation data. Gene expression analysis true operation_2411 beta12orEarlier 1.6 Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. Structural profile processing true operation_2412 beta12orEarlier 1.6 Process (read and / or write) an index of (typically a file of) biological data. Data index processing true operation_2413 beta12orEarlier 1.6 Process (read and / or write) some type of sequence profile. Sequence profile processing true operation_2414 beta12orEarlier 1.22 Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. Protein function analysis true operation_2415 beta12orEarlier Analyse, simulate or predict protein folding, typically by processing sequence and / or structural data. For example, predict sites of nucleation or stabilisation key to protein folding. Protein folding modelling Protein folding simulation Protein folding site prediction Protein folding analysis operation_2416 beta12orEarlier Analyse protein secondary structure data. Secondary structure analysis (protein) Protein secondary structure analysis operation_2417 beta12orEarlier beta13 Process (read and / or write) data on the physicochemical property of a molecule. Physicochemical property data processing true operation_2419 beta12orEarlier Predict oligonucleotide primers or probes. Primer and probe prediction Primer and probe design operation_2420 beta12orEarlier 1.12 Process (read and / or write) data of a specific type, for example applying analytical methods. Operation (typed) true operation_2421 beta12orEarlier Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. Search Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. Database search operation_2422 beta12orEarlier Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. Data extraction Retrieval Data retrieval (metadata) Metadata retrieval Data retrieval operation_2423 beta12orEarlier true Predict, recognise, detect or identify some properties of a biomolecule. Detection Prediction Recognition Prediction and recognition operation_2424 beta12orEarlier true Compare two or more things to identify similarities. Comparison operation_2425 beta12orEarlier true Refine or optimise some data model. Optimisation and refinement operation_2426 beta12orEarlier true Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. Mathematical modelling Modelling and simulation operation_2427 beta12orEarlier beta12orEarlier Perform basic operations on some data or a database. Data handling true operation_2428 beta12orEarlier true Validate some data. Quality control Validation operation_2429 beta12orEarlier true Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. Cartography Mapping operation_2430 beta12orEarlier true Design a biological entity (typically a molecular sequence or structure) with specific properties. Design operation_2432 beta12orEarlier beta12orEarlier Process (read and / or write) microarray data. Microarray data processing true operation_2433 beta12orEarlier 1.18 Process (read and / or write) a codon usage table. Codon usage table processing true operation_2434 beta12orEarlier beta13 Retrieve a codon usage table and / or associated annotation. Data retrieval (codon usage table) true operation_2435 beta12orEarlier 1.6 Process (read and / or write) a gene expression profile. Gene expression profile processing true operation_2436 beta12orEarlier Gene set testing Identify classes of genes or proteins that are over or under-represented in a large set of genes or proteins. For example analysis of a set of genes corresponding to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed. Functional enrichment analysis GSEA Gene-set over-represenation analysis Gene set analysis GO-term enrichment Gene Ontology concept enrichment Gene Ontology term enrichment "Gene set analysis" (often used interchangeably or in an overlapping sense with "gene-set enrichment analysis") refers to the functional analysis (term enrichment) of a differentially expressed set of genes, rather than all genes analysed. Analyse gene expression patterns to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. Gene sets can be defined beforehand by biological function, chromosome locations and so on. The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value. Gene-set enrichment analysis operation_2437 beta12orEarlier Predict a network of gene regulation. Gene regulatory network prediction operation_2438 beta12orEarlier 1.12 Generate, analyse or handle a biological pathway or network. Pathway or network processing true operation_2439 beta12orEarlier Process (read and / or write) RNA secondary structure data. RNA secondary structure analysis operation_2440 beta12orEarlier beta13 Process (read and / or write) RNA tertiary structure data. Structure processing (RNA) true operation_2441 beta12orEarlier Predict RNA tertiary structure. RNA structure prediction operation_2442 beta12orEarlier Predict DNA tertiary structure. DNA structure prediction operation_2443 beta12orEarlier 1.12 Generate, process or analyse phylogenetic tree or trees. Phylogenetic tree processing true operation_2444 beta12orEarlier 1.6 Process (read and / or write) protein secondary structure data. Protein secondary structure processing true operation_2445 beta12orEarlier 1.6 Process (read and / or write) a network of protein interactions. Protein interaction network processing true operation_2446 beta12orEarlier 1.6 Process (read and / or write) one or more molecular sequences and associated annotation. Sequence processing true operation_2447 beta12orEarlier 1.6 Process (read and / or write) a protein sequence and associated annotation. Sequence processing (protein) true operation_2448 beta12orEarlier 1.6 Process (read and / or write) a nucleotide sequence and associated annotation. Sequence processing (nucleic acid) true operation_2451 beta12orEarlier Compare two or more molecular sequences. Sequence comparison operation_2452 beta12orEarlier 1.6 Process (read and / or write) a sequence cluster. Sequence cluster processing true operation_2453 beta12orEarlier 1.6 Process (read and / or write) a sequence feature table. Feature table processing true operation_2454 beta12orEarlier Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. Gene calling Gene finding Whole gene prediction Includes methods that predict whole gene structure using a combination of multiple methods to achieve better predictions. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene prediction operation_2456 beta12orEarlier 1.16 Classify G-protein coupled receptors (GPCRs) into families and subfamilies. GPCR classification true operation_2457 beta12orEarlier Not sustainable to have protein type-specific concepts. 1.19 Predict G-protein coupled receptor (GPCR) coupling selectivity. GPCR coupling selectivity prediction true operation_2459 beta12orEarlier 1.6 Process (read and / or write) a protein tertiary structure. Structure processing (protein) true operation_2460 beta12orEarlier 1.12 Calculate the solvent accessibility for each atom in a structure. Waters are not considered. Protein atom surface calculation true operation_2461 beta12orEarlier 1.12 Calculate the solvent accessibility for each residue in a structure. Protein residue surface calculation true operation_2462 beta12orEarlier 1.12 Calculate the solvent accessibility of a structure as a whole. Protein surface calculation true operation_2463 beta12orEarlier 1.6 Process (read and / or write) a molecular sequence alignment. Sequence alignment processing true operation_2464 beta12orEarlier Identify or predict protein-protein binding sites. Protein-protein binding site detection Protein-protein binding site prediction operation_2465 beta12orEarlier 1.6 Process (read and / or write) a molecular tertiary structure. Structure processing true operation_2466 beta12orEarlier 1.6 Annotate a DNA map of some type with terms from a controlled vocabulary. Map annotation true operation_2467 beta12orEarlier beta13 Retrieve information on a protein. Data retrieval (protein annotation) true operation_2468 beta12orEarlier beta13 Retrieve a phylogenetic tree from a data resource. Data retrieval (phylogenetic tree) true operation_2469 beta12orEarlier beta13 Retrieve information on a protein interaction. Data retrieval (protein interaction annotation) true operation_2470 beta12orEarlier beta13 Retrieve information on a protein family. Data retrieval (protein family annotation) true operation_2471 beta12orEarlier beta13 Retrieve information on an RNA family. Data retrieval (RNA family annotation) true operation_2472 beta12orEarlier beta13 Retrieve information on a specific gene. Data retrieval (gene annotation) true operation_2473 beta12orEarlier beta13 Retrieve information on a specific genotype or phenotype. Data retrieval (genotype and phenotype annotation) true operation_2474 beta12orEarlier Compare the architecture of two or more protein structures. Protein architecture comparison operation_2475 beta12orEarlier Identify the architecture of a protein structure. Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. Protein architecture recognition operation_2476 beta12orEarlier The simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. Molecular dynamics simulation Protein dynamics Molecular dynamics operation_2478 beta12orEarlier Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). Sequence analysis (nucleic acid) Nucleic acid sequence alignment analysis Sequence alignment analysis (nucleic acid) Nucleic acid sequence analysis operation_2479 beta12orEarlier Analyse a protein sequence (using methods that are only applicable to protein sequences). Sequence analysis (protein) Protein sequence alignment analysis Sequence alignment analysis (protein) Protein sequence analysis operation_2480 beta12orEarlier Analyse known molecular tertiary structures. Structure analysis operation_2481 beta12orEarlier Analyse nucleic acid tertiary structural data. Nucleic acid structure analysis operation_2482 beta12orEarlier 1.6 Process (read and / or write) a molecular secondary structure. Secondary structure processing true operation_2483 beta12orEarlier Compare two or more molecular tertiary structures. Structure comparison operation_2485 beta12orEarlier Render a helical wheel representation of protein secondary structure. Helical wheel rendering Helical wheel drawing operation_2486 beta12orEarlier Render a topology diagram of protein secondary structure. Topology diagram rendering Topology diagram drawing operation_2487 beta12orEarlier Compare protein tertiary structures. Structure comparison (protein) Methods might identify structural neighbors, find structural similarities or define a structural core. Protein structure comparison operation_2488 beta12orEarlier Compare protein secondary structures. Protein secondary structure Secondary structure comparison (protein) Protein secondary structure alignment Protein secondary structure comparison operation_2489 beta12orEarlier Predict the subcellular localisation of a protein sequence. Protein cellular localization prediction Protein subcellular localisation prediction Protein targeting prediction The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. Subcellular localisation prediction operation_2490 beta12orEarlier 1.12 Calculate contacts between residues in a protein structure. Residue contact calculation (residue-residue) true operation_2491 beta12orEarlier 1.12 Identify potential hydrogen bonds between amino acid residues. Hydrogen bond calculation (inter-residue) true operation_2492 beta12orEarlier Predict the interactions of proteins with other proteins. Protein-protein interaction detection Protein-protein binding prediction Protein-protein interaction prediction Protein interaction prediction operation_2493 beta12orEarlier beta13 Process (read and / or write) codon usage data. Codon usage data processing true operation_2495 beta12orEarlier Process (read and/or write) expression data from experiments measuring molecules (e.g. omics data), including analysis of one or more expression profiles, typically to interpret them in functional terms. Expression data analysis Gene expression analysis Gene expression data analysis Gene expression regulation analysis Metagenomic inference Microarray data analysis Protein expression analysis Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function. Expression analysis operation_2496 beta12orEarlier 1.6 Process (read and / or write) a network of gene regulation. Gene regulatory network processing true operation_2497 beta12orEarlier Notions of pathway and network were mixed up, EDAM 1.24 disentangles them. 1.24 Generate, process or analyse a biological pathway or network. Pathway or network analysis true operation_2498 beta12orEarlier beta12orEarlier Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. Sequencing-based expression profile data analysis true operation_2499 beta12orEarlier Predict, analyse, characterize or model splice sites, splicing events and so on, typically by comparing multiple nucleic acid sequences. Splicing model analysis Splicing analysis operation_2500 beta12orEarlier beta12orEarlier Analyse raw microarray data. Microarray raw data analysis true operation_2501 beta12orEarlier 1.19 Process (read and / or write) nucleic acid sequence or structural data. Nucleic acid analysis true operation_2502 beta12orEarlier 1.19 Process (read and / or write) protein sequence or structural data. Protein analysis true operation_2503 beta12orEarlier beta13 Process (read and / or write) molecular sequence data. Sequence data processing true operation_2504 beta12orEarlier beta13 Process (read and / or write) molecular structural data. Structural data processing true operation_2505 beta12orEarlier 1.6 Process (read and / or write) text. Text processing true operation_2506 beta12orEarlier 1.18 Analyse a protein sequence alignment, typically to detect features or make predictions. Protein sequence alignment analysis true operation_2507 beta12orEarlier 1.18 Analyse a protein sequence alignment, typically to detect features or make predictions. Nucleic acid sequence alignment analysis true operation_2508 beta12orEarlier 1.18 Compare two or more nucleic acid sequences. Nucleic acid sequence comparison true operation_2509 beta12orEarlier 1.18 Compare two or more protein sequences. Protein sequence comparison true operation_2510 beta12orEarlier Back-translate a protein sequence into DNA. DNA back-translation operation_2511 beta12orEarlier 1.8 Edit or change a nucleic acid sequence, either randomly or specifically. Sequence editing (nucleic acid) true operation_2512 beta12orEarlier 1.8 Edit or change a protein sequence, either randomly or specifically. Sequence editing (protein) true operation_2513 beta12orEarlier 1.22 Generate a nucleic acid sequence by some means. Sequence generation (nucleic acid) true operation_2514 beta12orEarlier 1.22 Generate a protein sequence by some means. Sequence generation (protein) true operation_2515 beta12orEarlier 1.8 Visualise, format or render a nucleic acid sequence. Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. Nucleic acid sequence visualisation true operation_2516 beta12orEarlier 1.8 Visualise, format or render a protein sequence. Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. Protein sequence visualisation true operation_2518 beta12orEarlier Compare nucleic acid tertiary structures. Structure comparison (nucleic acid) Nucleic acid structure comparison operation_2519 beta12orEarlier 1.6 Process (read and / or write) nucleic acid tertiary structure data. Structure processing (nucleic acid) true operation_2520 beta12orEarlier Generate a map of a DNA sequence annotated with positional or non-positional features of some type. DNA mapping operation_2521 beta12orEarlier 1.6 Process (read and / or write) a DNA map of some type. Map data processing true operation_2574 beta12orEarlier Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). Protein hydropathy calculation operation_2575 beta12orEarlier Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. Protein binding site detection Protein binding site prediction Binding site prediction operation_2844 beta12orEarlier Build clusters of similar structures, typically using scores from structural alignment methods. Structural clustering Structure clustering operation_2871 beta12orEarlier Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). Sequence mapping An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. Sequence tagged site (STS) mapping operation_2928 beta12orEarlier true Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. Alignment construction Alignment generation Alignment operation_2929 beta12orEarlier Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification. PMF Peptide mass fingerprinting Protein fingerprinting Protein fragment weight comparison operation_2930 beta12orEarlier Compare the physicochemical properties of two or more proteins (or reference data). Protein property comparison operation_2931 beta12orEarlier 1.18 Compare two or more molecular secondary structures. Secondary structure comparison true operation_2932 beta12orEarlier 1.12 Generate a Hopp and Woods plot of antigenicity of a protein. Hopp and Woods plotting true operation_2934 beta12orEarlier 1.19 Generate a view of clustered quantitative data, annotated with textual information. Cluster textual view generation true operation_2935 beta12orEarlier Visualise clustered quantitative data as set of different profiles, where each profile is plotted versus different entities or samples on the X-axis. Clustered quantitative data plotting Clustered quantitative data rendering Wave graph plotting Microarray cluster temporal graph rendering Microarray wave graph plotting Microarray wave graph rendering In the case of microarray data, visualise clustered gene expression data as a set of profiles, where each profile shows the gene expression values of a cluster across samples on the X-axis. Clustering profile plotting operation_2936 beta12orEarlier 1.19 Generate a dendrograph of raw, preprocessed or clustered expression (e.g. microarray) data. Dendrograph plotting true operation_2937 beta12orEarlier Generate a plot of distances (distance or correlation matrix) between expression values. Distance map rendering Distance matrix plotting Distance matrix rendering Proximity map rendering Correlation matrix plotting Correlation matrix rendering Microarray distance map rendering Microarray proximity map plotting Microarray proximity map rendering Proximity map plotting operation_2938 beta12orEarlier Visualise clustered expression data using a tree diagram. Dendrogram plotting Dendrograph plotting Dendrograph visualisation Expression data tree or dendrogram rendering Expression data tree visualisation Microarray 2-way dendrogram rendering Microarray checks view rendering Microarray matrix tree plot rendering Microarray tree or dendrogram rendering Dendrogram visualisation operation_2939 beta12orEarlier Visualize the results of a principal component analysis (orthogonal data transformation). For example, visualization of the principal components (essential subspace) coming from a Principal Component Analysis (PCA) on the trajectory atomistic coordinates of a molecular structure. PCA plotting Principal component plotting ED visualization Essential Dynamics visualization Microarray principal component plotting Microarray principal component rendering PCA visualization Principal modes visualization Examples for visualization are the distribution of variance over the components, loading and score plots. The use of Principal Component Analysis (PCA), a multivariate statistical analysis to obtain collective variables on the atomic positional fluctuations, helps to separate the configurational space in two subspaces: an essential subspace containing relevant motions, and another one containing irrelevant local fluctuations. Principal component visualisation operation_2940 beta12orEarlier Render a graph in which the values of two variables are plotted along two axes; the pattern of the points reveals any correlation. Scatter chart plotting Microarray scatter plot plotting Microarray scatter plot rendering Comparison of two sets of quantitative data such as two samples of gene expression values. Scatter plot plotting operation_2941 beta12orEarlier 1.18 Visualise gene expression data where each band (or line graph) corresponds to a sample. Whole microarray graph plotting true operation_2942 beta12orEarlier Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. Expression data tree-map rendering Treemapping Microarray tree-map rendering Treemap visualisation operation_2943 beta12orEarlier Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles. Box plot plotting Microarray Box-Whisker plot plotting In the case of micorarray data, visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. Box-Whisker plot plotting operation_2944 beta12orEarlier Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. Physical cartography Physical mapping operation_2945 beta12orEarlier true Apply analytical methods to existing data of a specific type. This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling'). Data analysis operation_2946 beta12orEarlier 1.8 Process or analyse an alignment of molecular sequences or structures. Alignment analysis true operation_2947 beta12orEarlier 1.16 Analyse a body of scientific text (typically a full text article from a scientific journal). Article analysis true operation_2948 beta12orEarlier beta13 Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. Molecular interaction analysis true operation_2949 beta12orEarlier Analyse the interactions of proteins with other proteins. Protein interaction analysis Protein interaction raw data analysis Protein interaction simulation Includes analysis of raw experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. Protein-protein interaction analysis operation_2950 beta12orEarlier WHATIF: HETGroupNames WHATIF:HasMetalContacts WHATIF:HasMetalContactsPlus WHATIF:HasNegativeIonContacts WHATIF:HasNegativeIonContactsPlus WHATIF:HasNucleicContacts WHATIF:ShowDrugContacts WHATIF:ShowDrugContactsShort WHATIF:ShowLigandContacts WHATIF:ShowProteiNucleicContacts Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations. HET group detection Residue contact calculation (residue-ligand) Residue contact calculation (residue-metal) Residue contact calculation (residue-negative ion) Residue contact calculation (residue-nucleic acid) WHATIF:SymmetryContact This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit. Residue distance calculation operation_2951 beta12orEarlier 1.6 Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. Alignment processing true operation_2952 beta12orEarlier 1.6 Process (read and / or write) a molecular tertiary (3D) structure alignment. Structure alignment processing true operation_2962 beta12orEarlier Calculate codon usage bias, e.g. generate a codon usage bias plot. Codon usage bias plotting Codon usage bias calculation operation_2963 beta12orEarlier 1.22 Generate a codon usage bias plot. Codon usage bias plotting true operation_2964 beta12orEarlier Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. Codon usage fraction calculation operation_2990 beta12orEarlier true Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. Classification operation_2993 beta12orEarlier beta13 Process (read and / or write) molecular interaction data. Molecular interaction data processing true operation_2995 beta12orEarlier Assign molecular sequence(s) to a group or category. Sequence classification operation_2996 beta12orEarlier Assign molecular structure(s) to a group or category. Structure classification operation_2997 beta12orEarlier Compare two or more proteins (or some aspect) to identify similarities. Protein comparison operation_2998 beta12orEarlier Compare two or more nucleic acids to identify similarities. Nucleic acid comparison operation_3023 beta12orEarlier 1.19 Predict, recognise, detect or identify some properties of proteins. Prediction and recognition (protein) true operation_3024 beta12orEarlier 1.19 Predict, recognise, detect or identify some properties of nucleic acids. Prediction and recognition (nucleic acid) true operation_3080 beta13 Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. Structure editing operation_3081 beta13 Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. Sequence alignment editing operation_3083 beta13 Notions of pathway and network were mixed up, EDAM 1.24 disentangles them. 1.24 Render (visualise) a biological pathway or network. Pathway or network visualisation true operation_3084 beta13 1.6 Predict general (non-positional) functional properties of a protein from analysing its sequence. For functional properties that are positional, use 'Protein site detection' instead. Protein function prediction (from sequence) true operation_3087 beta13 (jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed (consolidate with "Protein feature detection"). 1.17 Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. Protein sequence feature detection true operation_3088 beta13 1.18 Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. Protein property calculation (from sequence) true operation_3090 beta13 1.6 Predict, recognise and identify positional features in proteins from analysing protein structure. Protein feature prediction (from structure) true operation_3092 beta13 Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. Protein feature prediction Protein feature recognition Protein secondary database search Protein site detection Protein site prediction Protein site recognition Sequence feature detection (protein) Sequence profile database search Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. Protein feature detection operation_3093 beta13 1.6 Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. Database search (by sequence) true operation_3094 beta13 Predict a network of protein interactions. Protein interaction network prediction operation_3095 beta13 Design (or predict) nucleic acid sequences with specific chemical or physical properties. Gene design Nucleic acid design operation_3096 beta13 Edit a data entity, either randomly or specifically. Data editing operation_3180 1.1 Evaluate a DNA sequence assembly, typically for purposes of quality control. Assembly QC Assembly quality evaluation Sequence assembly QC Sequence assembly quality evaluation Sequence assembly validation operation_3182 1.1 Align two or more (tpyically huge) molecular sequences that represent genomes. Genome alignment construction Whole genome alignment Genome alignment operation_3183 1.1 Reconstruction of a sequence assembly in a localised area. Localised reassembly operation_3184 1.1 Render and visualise a DNA sequence assembly. Assembly rendering Assembly visualisation Sequence assembly rendering Sequence assembly visualisation operation_3185 1.1 Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. Base calling Phred base calling Phred base-calling Base-calling operation_3186 1.1 The mapping of methylation sites in a DNA (genome) sequence. Typically, the mapping of high-throughput bisulfite reads to the reference genome. Bisulfite read mapping Bisulfite sequence alignment Bisulfite sequence mapping Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. Bisulfite mapping operation_3187 1.1 Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. Sequence contamination filtering operation_3189 1.1 1.12 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. Trim ends true operation_3190 1.1 1.12 Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. Trim vector true operation_3191 1.1 1.12 Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. Trim to reference true operation_3192 1.1 Cut (remove) the end from a molecular sequence. Trimming Barcode sequence removal Trim ends Trim to reference Trim vector This includes end trimming, -- Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.-- trimming to a reference sequence, --Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. -- vector trimming -- Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. Sequence trimming operation_3194 1.1 Compare the features of two genome sequences. Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. Genome feature comparison operation_3195 1.1 Detect errors in DNA sequences generated from sequencing projects). Short read error correction Short-read error correction Sequencing error detection operation_3196 1.1 Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. Genotyping operation_3197 1.1 Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. Genetic variation annotation Sequence variation analysis Variant analysis Transcript variant analysis Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. Genetic variation analysis operation_3198 1.1 Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. Oligonucleotide alignment Oligonucleotide alignment construction Oligonucleotide alignment generation Oligonucleotide mapping Read alignment Short oligonucleotide alignment Short read alignment Short read mapping Short sequence read mapping The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Read mapping operation_3199 1.1 A variant of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. Split-read mapping Split read mapping operation_3200 1.1 Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. Community profiling Sample barcoding DNA barcoding operation_3201 1.1 1.19 Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. SNP calling true operation_3202 1.1 "Polymorphism detection" and "Variant calling" are essentially the same thing - keeping the later as a more prevalent term nowadays. 1.24 Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. Polymorphism detection true operation_3203 1.1 Visualise, format or render an image of a Chromatogram. Chromatogram viewing Chromatogram visualisation operation_3204 1.1 Analyse cytosine methylation states in nucleic acid sequences. Methylation profile analysis Methylation analysis operation_3205 1.1 1.19 Determine cytosine methylation status of specific positions in a nucleic acid sequences. Methylation calling true operation_3206 1.1 Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. Genome methylation analysis Global methylation analysis Methylation level analysis (global) Whole genome methylation analysis operation_3207 1.1 Analysing the DNA methylation of specific genes or regions of interest. Gene-specific methylation analysis Methylation level analysis (gene-specific) Gene methylation analysis operation_3208 1.1 Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. Genome browser Genome browsing Genome rendering Genome viewing Genome visualisation operation_3209 1.1 Compare the sequence or features of two or more genomes, for example, to find matching regions. Genomic region matching Genome comparison operation_3211 1.1 Generate an index of a genome sequence. Burrows-Wheeler Genome indexing (Burrows-Wheeler) Genome indexing (suffix arrays) Suffix arrays Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. Genome indexing operation_3212 1.1 1.12 Generate an index of a genome sequence using the Burrows-Wheeler algorithm. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. Genome indexing (Burrows-Wheeler) true operation_3213 1.1 1.12 Generate an index of a genome sequence using a suffix arrays algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. Genome indexing (suffix arrays) true operation_3214 1.1 Analyse one or more spectra from mass spectrometry (or other) experiments. Mass spectrum analysis Spectrum analysis Spectral analysis operation_3215 1.1 Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. Peak assignment Peak finding Peak detection operation_3216 1.1 Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. Scaffold construction Scaffold generation Scaffold may be positioned along a chromosome physical map to create a "golden path". Scaffolding operation_3217 1.1 Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. Scaffold gap completion operation_3218 1.1 Raw sequence data quality control. Sequencing QC Sequencing quality assessment Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems. Sequencing quality control operation_3219 1.1 Pre-process sequence reads to ensure (or improve) quality and reliability. Sequence read pre-processing For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequences including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. Read pre-processing operation_3221 1.1 Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. Species frequency estimation operation_3222 1.1 Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. Protein binding peak detection Peak-pair calling Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo. Peak calling operation_3223 1.1 Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. Differential expression analysis Differential gene analysis Differential gene expression analysis Differentially expressed gene identification Differential gene expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. Differential gene expression profiling operation_3224 1.1 1.21 Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. Gene set testing true operation_3225 1.1 Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) Variant classification operation_3226 1.1 Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. Variant prioritisation operation_3227 1.1 Detect, identify and map mutations, such as single nucleotide polymorphisms, short indels and structural variants, in multiple DNA sequences. Typically the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware, to study genomic alterations. Variant mapping Allele calling Exome variant detection Genome variant detection Germ line variant calling Mutation detection Somatic variant calling de novo mutation detection Methods often utilise a database of aligned reads. Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant. Variant detection Variant calling operation_3228 1.1 Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). Structural variation discovery Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. Structural variation detection operation_3229 1.1 Analyse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. Exome sequence analysis Exome assembly operation_3230 1.1 Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. Read depth analysis operation_3232 1.1 Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. Gene expression QTL profiling Gene expression quantitative trait loci profiling eQTL profiling Gene expression QTL analysis operation_3233 1.1 Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. Transcript copy number estimation Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). Copy number estimation operation_3237 1.2 Adapter removal Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). Primer removal operation_3258 1.2 Infer a transcriptome sequence by analysis of short sequence reads. Transcriptome assembly operation_3259 1.2 1.6 Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. Transcriptome assembly (de novo) true operation_3260 1.2 1.6 Infer a transcriptome sequence by mapping short reads to a reference genome. Transcriptome assembly (mapping) true operation_3267 1.3 Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. Sequence coordinate conversion operation_3278 1.3 Calculate similarity between 2 or more documents. Document similarity calculation operation_3279 1.3 Cluster (group) documents on the basis of their calculated similarity. Document clustering operation_3280 1.3 Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents. Concept mining Entity chunking Entity extraction Entity identification Event extraction NER Named-entity recognition Named-entity and concept recognition operation_3282 1.3 Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. Accession mapping Identifier mapping The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. ID mapping operation_3283 1.3 Process data in such a way that makes it hard to trace to the person which the data concerns. Data anonymisation Anonymisation operation_3289 1.3 (jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved. 1.17 Search for and retrieve a data identifier of some kind, e.g. a database entry accession. ID retrieval true operation_3348 1.4 Generate a checksum of a molecular sequence. Sequence checksum generation operation_3349 1.4 Construct a bibliography from the scientific literature. Bibliography construction Bibliography generation operation_3350 1.4 Predict the structure of a multi-subunit protein and particularly how the subunits fit together. Protein quaternary structure prediction operation_3351 1.4 Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc. Molecular surface analysis operation_3352 1.4 Compare two or more ontologies, e.g. identify differences. Ontology comparison operation_3353 1.4 1.9 Compare two or more ontologies, e.g. identify differences. Ontology comparison true operation_3357 1.4 Recognition of which format the given data is in. Format identification Format inference Format recognition 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. Format detection The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. operation_3359 1.4 Split a file containing multiple data items into many files, each containing one item. File splitting Splitting operation_3429 1.6 true Construct some data entity. Construction For non-analytical operations, see the 'Processing' branch. Generation operation_3430 1.6 (jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed. 1.17 Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. Nucleic acid sequence feature detection true operation_3431 1.6 Data publication Data deposition is the submission and upload of data to a dedicated repository, archive, or deposition database, usually with accompanying metadata. Data submission Database deposition Database submission Data brokering Data deposition brokering Data publishing Data deposition operation_3432 1.6 true Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). Clustering operation_3433 1.6 1.19 Construct some entity (typically a molecule sequence) from component pieces. Assembly true operation_3434 1.6 true Convert a data set from one form to another. Conversion operation_3435 1.6 Standardize or normalize data by some statistical method. Normalisation Standardisation In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean. Standardisation and normalisation operation_3436 1.6 Combine multiple files or data items into a single file or object. Aggregation operation_3437 1.6 Compare two or more scientific articles. Article comparison operation_3438 1.6 true Mathematical determination of the value of something, typically a properly of a molecule. Calculation operation_3439 1.6 Notions of pathway and network were mixed up, EDAM 1.24 disentangles them. 1.24 Predict a molecular pathway or network. Pathway or network prediction true operation_3440 1.6 1.12 The process of assembling many short DNA sequences together such that they represent the original chromosomes from which the DNA originated. Genome assembly true operation_3441 1.6 1.19 Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. Plotting true operation_3443 1.7 Image processing The analysis of a image (typically a digital image) of some type in order to extract information from it. Image analysis operation_3445 1.7 Analysis of data from a diffraction experiment. Diffraction data analysis operation_3446 1.7 Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. Cell migration analysis operation_3447 1.7 Processing of diffraction data into a corrected, ordered, and simplified form. Diffraction data reduction operation_3450 1.7 Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. Neurite measurement operation_3453 1.7 The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. Diffraction profile fitting Diffraction summation integration Diffraction data integration operation_3454 1.7 Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. Phasing operation_3455 1.7 A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. The technique solves the phase problem, i.e. retrieve information concern phases of the structure. Molecular replacement operation_3456 1.7 A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. Rigid body refinement operation_3457 1.7 An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted. Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). Single particle analysis operation_3458 1.7 true This is two related concepts. Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final 3D EM map. Single particle alignment and classification operation_3459 1.7 Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. Functional sequence clustering Functional clustering operation_3460 1.7 Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy. Taxonomy assignment Taxonomic profiling Taxonomic classification operation_3461 1.7 The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. Pathogenicity prediction Virulence prediction operation_3463 1.7 Analyse the correlation patterns among features/molecules across across a variety of experiments, samples etc. Co-expression analysis Gene co-expression network analysis Gene expression correlation Gene expression correlation analysis Expression correlation analysis operation_3465 1.7 true Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. Correlation operation_3469 1.7 Compute the covariance model for (a family of) RNA secondary structures. RNA structure covariance model generation operation_3470 1.7 1.18 Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. RNA secondary structure prediction (shape-based) true operation_3471 1.7 1.18 Prediction of nucleic-acid folding using sequence alignments as a source of data. Nucleic acid folding prediction (alignment-based) true operation_3472 1.7 Count k-mers (substrings of length k) in DNA sequence data. k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. k-mer counting operation_3478 1.7 Reconstructing the inner node labels of a phylogenetic tree from its leafes. Phylogenetic tree reconstruction Gene tree reconstruction Species tree reconstruction Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. Phylogenetic reconstruction operation_3480 1.7 Generate some data from a chosen probibalistic model, possibly to evaluate algorithms. Probabilistic data generation operation_3481 1.7 Generate sequences from some probabilistic model, e.g. a model that simulates evolution. Probabilistic sequence generation operation_3482 1.7 Identify or predict causes for antibiotic resistance from molecular sequence analysis. Antimicrobial resistance prediction operation_3501 1.8 Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed. Enrichment Over-representation analysis Functional enrichment Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data. Enrichment analysis operation_3502 1.8 Analyse a dataset with respect to concepts from an ontology of chemical structure, leveraging chemical similarity information. Chemical class enrichment Chemical similarity enrichment operation_3503 1.8 Plot an incident curve such as a survival curve, death curve, mortality curve. Incident curve plotting operation_3504 1.8 Identify and map patterns of genomic variations. Methods often utilise a database of aligned reads. Variant pattern analysis operation_3545 1.8 1.12 Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. Mathematical modelling true operation_3552 1.9 Visualise images resulting from various types of microscopy. Microscope image visualisation operation_3553 1.9 Annotate an image of some sort, typically with terms from a controlled vocabulary. Image annotation operation_3557 1.9 Replace missing data with substituted values, usually by using some statistical or other mathematical approach. Data imputation Imputation operation_3559 1.9 Visualise, format or render data from an ontology, typically a tree of terms. Ontology browsing Ontology visualisation operation_3560 1.9 A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. Maximum occurrence analysis operation_3561 1.9 Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves. Data model comparison Schema comparison Database comparison operation_3562 1.9 1.24 Simulate the bevaviour of a biological pathway or network. Notions of pathway and network were mixed up, EDAM 1.24 disentangles them. Network simulation true operation_3563 1.9 Analyze read counts from RNA-seq experiments. RNA-seq read count analysis operation_3564 1.9 Identify and remove redundancy from a set of small molecule structures. Chemical redundancy removal operation_3565 1.9 Analyze time series data from an RNA-seq experiment. RNA-seq time series data analysis operation_3566 1.9 Simulate gene expression data, e.g. for purposes of benchmarking. Simulated gene expression data generation operation_3625 1.12 Identify semantic relations among entities and concepts within a text, using text mining techniques. Relation discovery Relation inference Relationship discovery Relationship extraction Relationship inference Relation extraction operation_3627 1.12 Re-adjust the output of mass spectrometry experiments with shifted ppm values. Mass spectra calibration operation_3628 1.12 Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments. Chromatographic alignment operation_3629 1.12 The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point. Deconvolution Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution. Deisotoping operation_3630 1.12 Technique for determining the amount of proteins in a sample. Protein quantitation Protein quantification operation_3631 1.12 Determination of peptide sequence from mass spectrum. Peptide-spectrum-matching Peptide identification operation_3632 1.12 Calculate the isotope distribution of a given chemical species. Isotopic distributions calculation operation_3633 1.12 Prediction of retention time in a mass spectrometry experiment based on compositional and structural properties of the separated species. Retention time calculation Retention time prediction operation_3634 1.12 Quantification without the use of chemical tags. Label-free quantification operation_3635 1.12 Quantification based on the use of chemical tags. Labeled quantification operation_3636 1.12 Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). MRM/SRM operation_3637 1.12 Calculate number of identified MS2 spectra as approximation of peptide / protein quantity. Spectral counting operation_3638 1.12 Quantification analysis using stable isotope labeling by amino acids in cell culture. SILAC operation_3639 1.12 Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z. iTRAQ operation_3640 1.12 Quantification analysis using labeling based on 18O-enriched H2O. 18O labeling operation_3641 1.12 Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow. TMT-tag operation_3642 1.12 Quantification analysis using chemical labeling by stable isotope dimethylation. Stable isotope dimethyl labelling operation_3643 1.12 Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry. Tag-based peptide identification operation_3644 1.12 Analytical process that derives a peptide's amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database. de Novo sequencing operation_3645 1.12 Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum. PTM identification operation_3646 1.12 Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences. Peptide database search operation_3647 1.12 Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches. Modification-tolerant peptide database search Unrestricted peptide database search Blind peptide database search operation_3648 1.12 1.19 Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search. Validation of peptide-spectrum matches true operation_3649 1.12 Validation of peptide-spectrum matches Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search, and by comparison to search results with a database containing incorrect information. Target-Decoy operation_3658 1.12 Analyse data in order to deduce properties of an underlying distribution or population. Empirical Bayes Statistical inference operation_3659 1.12 A statistical calculation to estimate the relationships among variables. Regression Regression analysis operation_3660 1.12 Model a metabolic network. This can include 1) reconstruction to break down a metabolic pathways into reactions, enzymes, and other relevant information, and compilation of this into a mathematical model and 2) simulations of metabolism based on the model. Metabolic pathway modelling Metabolic network reconstruction Metabolic network simulation Metabolic pathway reconstruction Metabolic pathway simulation Metabolic reconstruction The terms and synyonyms here reflect that for practical intents and purposes, "pathway" and "network" can be treated the same. Metabolic network modelling operation_3661 1.12 Predict the effect or function of an individual single nucleotide polymorphism (SNP). SNP annotation operation_3662 1.12 Prediction of genes or gene components from first principles, i.e. without reference to existing genes. Gene prediction (ab-initio) Ab-initio gene prediction operation_3663 1.12 Prediction of genes or gene components by reference to homologous genes. Empirical gene finding Empirical gene prediction Evidence-based gene prediction Gene prediction (homology-based) Similarity-based gene prediction Homology prediction Orthology prediction Homology-based gene prediction operation_3664 1.12 Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data. Statistical modelling operation_3666 1.12 Compare two or more molecular surfaces. Molecular surface comparison operation_3672 1.12 Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO). Sequence functional annotation Gene functional annotation operation_3675 1.12 Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info. Variant filtering operation_3677 1.12 Identify binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups. Differential binding analysis operation_3680 1.13 Analyze data from RNA-seq experiments. RNA-Seq analysis operation_3694 1.13 Visualise, format or render a mass spectrum. Mass spectrum visualisation operation_3695 1.13 Filter a set of files or data items according to some property. Sequence filtering rRNA filtering Data filtering operation_3703 1.14 Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis. Reference identification operation_3704 1.14 Label-free quantification by integration of ion current (ion counting). Ion current integration Ion counting operation_3705 1.14 Chemical tagging free amino groups of intact proteins with stable isotopes. ICPL Isotope-coded protein label operation_3715 1.14 Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed. C-13 metabolic labeling N-15 metabolic labeling This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed). Metabolic labeling operation_3730 1.15 Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis. Sequence assembly (cross-assembly) Cross-assembly operation_3731 1.15 The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method. Sample comparison operation_3741 1.15 Differential protein analysis The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup. Differential protein expression analysis Differential protein expression profiling operation_3742 1.15 1.17 The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup. Differential gene expression analysis true operation_3744 1.15 Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment. Multiple sample visualisation operation_3745 1.15 The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors. Ancestral sequence reconstruction Character mapping Character optimisation Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms. Ancestral reconstruction operation_3755 1.16 Site localisation of post-translational modifications in peptide or protein mass spectra. PTM scoring Site localisation PTM localisation operation_3760 1.16 Operations concerning the handling and use of other tools. Endpoint management Service management operation_3761 1.16 An operation supporting the browsing or discovery of other tools and services. Service discovery operation_3762 1.16 An operation supporting the aggregation of other services (at least two) into a functional unit, for the automation of some task. Service composition operation_3763 1.16 An operation supporting the calling (invocation) of other tools and services. Service invocation operation_3766 1.16 A data mining method typically used for studying biological networks based on pairwise correlations between variables. WGCNA Weighted gene co-expression network analysis Weighted correlation network analysis operation_3767 1.16 Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry. Protein inference Protein identification operation_3778 1.16 Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article). Article annotation Literature annotation Text annotation operation_3791 1.17 A method whereby data on several variants are "collapsed" into a single covariate based on regions such as genes. Genome-wide association studies (GWAS) analyse a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Traditional association techniques can lack the power to detect the significance of rare variants individually, or measure their compound effect (rare variant burden). "Collapsing methods" were developed to overcome these problems. Collapsing methods operation_3792 1.17 miRNA analysis The analysis of microRNAs (miRNAs) : short, highly conserved small noncoding RNA molecules that are naturally occurring plant and animal genomes. miRNA expression profiling miRNA expression analysis operation_3793 1.17 Counting and summarising the number of short sequence reads that map to genomic features. Read summarisation operation_3795 1.17 A technique whereby molecules with desired properties and function are isolated from libraries of random molecules, through iterative cycles of selection, amplification, and mutagenesis. In vitro selection operation_3797 1.17 The calculation of species richness for a number of individual samples, based on plots of the number of species as a function of the number of samples (rarefaction curves). Species richness assessment Rarefaction operation_3798 1.17 An operation which groups reads or contigs and assigns them to operational taxonomic units. Binning Binning shotgun reads Binning methods use one or a combination of compositional features or sequence similarity. Read binning operation_3799 1.17 true Counting and measuring experimentally determined observations into quantities. Quantitation Quantification operation_3800 1.17 Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study. RNA-Seq quantitation RNA-Seq quantification operation_3801 1.17 Match experimentally measured mass spectrum to a spectrum in a spectral library or database. Spectral library search operation_3802 1.17 Sort a set of files or data items according to some property. Data sorting operation_3803 1.17 Mass spectra identification of compounds that are produced by living systems. Including polyketides, terpenoids, phenylpropanoids, alkaloids and antibiotics. De novo metabolite identification Fragmenation tree generation Metabolite identification Natural product identification operation_3809 1.19 Identify and assess specific genes or regulatory regions of interest that are differentially methylated. Differentially-methylated region identification DMR identification operation_3840 1.21 Genotyping of multiple loci, typically characterizing microbial species isolates using internal fragments of multiple housekeeping genes. MLST Multilocus sequence typing operation_3860 1.21 Calculate a theoretical mass spectrometry spectra for given sequences. Spectrum prediction Spectrum calculation operation_3890 1.22 3D visualization of a molecular trajectory. Trajectory visualization operation_3891 1.22 Compute Essential Dynamics (ED) on a simulation trajectory: an analysis of molecule dynamics using PCA (Principal Component Analysis) applied to the atomic positional fluctuations. ED PCA Principal modes Principal Component Analysis (PCA) is a multivariate statistical analysis to obtain collective variables and reduce the dimensionality of the system. Essential dynamics operation_3893 1.22 Obtain force field parameters (charge, bonds, dihedrals, etc.) from a molecule, to be used in molecular simulations. Ligand parameterization Molecule parameterization Forcefield parameterisation operation_3894 1.22 Analyse DNA sequences in order to determine an individual's DNA characteristics, for example in criminal forensics, parentage testing and so on. DNA fingerprinting DNA profiling operation_3896 1.22 Predict or detect active sites in proteins; the region of an enzyme which binds a substrate bind and catalyses a reaction. Active site detection Active site prediction operation_3897 1.22 Predict or detect ligand-binding sites in proteins; a region of a protein which reversibly binds a ligand for some biochemical purpose, such as transport or regulation of protein function. Ligand-binding site detection Peptide-protein binding prediction Ligand-binding site prediction operation_3898 1.22 Predict or detect metal ion-binding sites in proteins. Metal-binding site detection Protein metal-binding site prediction Metal-binding site prediction operation_3899 1.22 Model or simulate protein-protein binding using comparative modelling or other techniques. Protein docking Protein-protein docking operation_3900 1.22 Predict DNA-binding proteins. DNA-binding protein detection DNA-protein interaction prediction Protein-DNA interaction prediction DNA-binding protein prediction operation_3901 1.22 Predict RNA-binding proteins. Protein-RNA interaction prediction RNA-binding protein detection RNA-protein interaction prediction RNA-binding protein prediction operation_3902 1.22 Predict or detect RNA-binding sites in protein sequences. Protein-RNA binding site detection Protein-RNA binding site prediction RNA binding site detection RNA binding site prediction operation_3903 1.22 Predict or detect DNA-binding sites in protein sequences. Protein-DNA binding site detection Protein-DNA binding site prediction DNA binding site detection DNA binding site prediction operation_3904 1.22 Identify or predict intrinsically disordered regions in proteins. Protein disorder prediction operation_3907 1.22 Extract structured information from unstructured ("free") or semi-structured textual documents. IE Information extraction operation_3908 1.22 Retrieve resources from information systems matching a specific information need. Information retrieval operation_3918 1.24 Study of genomic feature structure, variation, function and evolution at a genomic scale. Genomic analysis Genome analysis operation_3919 1.24 The determination of cytosine methylation status of specific positions in a nucleic acid sequences (usually reads from a bisulfite sequencing experiment). Methylation calling operation_3920 1.24 The identification of changes in DNA sequence or chromosome structure, usually in the context of diagnostic tests for disease, or to study ancestry or phylogeny. Genetic testing This can include indirect methods which reveal the results of genetic changes, such as RNA analysis to indicate gene expression, or biochemical analysis to identify expressed proteins. DNA testing operation_3921 1.24 The processing of reads from high-throughput sequencing machines. Sequence read processing operation_3925 1.24 Render (visualise) a network - typically a biological network of some sort. Network rendering Protein interaction network rendering Protein interaction network visualisation Network visualisation operation_3926 1.24 Render (visualise) a biological pathway. Pathway rendering Pathway visualisation operation_3927 1.24 Generate, process or analyse a biological network. Biological network analysis Biological network modelling Biological network prediction Network comparison Network modelling Network prediction Network simulation Network topology simulation Network analysis operation_3928 1.24 Generate, process or analyse a biological pathway. Biological pathway analysis Biological pathway modelling Biological pathway prediction Functional pathway analysis Pathway comparison Pathway modelling Pathway prediction Pathway simulation Pathway analysis operation_3929 1.24 Predict a metabolic pathway. Metabolic pathway prediction operation_3933 1.24 Assigning sequence reads to separate groups / files based on their index tag (sample origin). Sequence demultiplexing NGS sequence runs are often performed with multiple samples pooled together. In such cases, an index tag (or "barcode") - a unique sequence of between 6 and 12bp - is ligated to each sample's genetic material so that the sequence reads from different samples can be identified. The process of demultiplexing (dividing sequence reads into separate files for each index tag/sample) may be performed automatically by the sequencing hardware. Alternatively the reads may be lumped together in one file with barcodes still attached, requiring you to do the splitting using software. In such cases, a "mapping" file is used which indicates which barcodes correspond to which samples. Demultiplexing operation_3935 1.24 A process used in statistics, machine learning, and information theory that reduces the number of random variables by obtaining a set of principal variables. Dimension reduction Dimensionality reduction operation_3936 1.24 A dimensionality reduction process that selects a subset of relevant features (variables, predictors) for use in model construction. Attribute selection Variable selection Variable subset selection Feature selection operation_3937 1.24 A dimensionality reduction process which builds (ideally) informative and non-redundant values (features) from an initial set of measured data, to aid subsequent generalization, learning or interpretation. Feature projection Feature extraction operation_3938 1.24 Virtual screening is used in drug discovery to identify potential drug compounds. It involves searching libraries of small molecules in order to identify those molecules which are most likely to bind to a drug target (typically a protein receptor or enzyme). Ligand-based screening Ligand-based virtual screening Structure-based screening Structured-based virtual screening Virtual ligand screening Virtual screening is widely used for lead identification, lead optimization, and scaffold hopping during drug design and discovery. Virtual screening operation_3942 1.24 The application of phylogenetic and other methods to estimate paleogeographical events such as speciation. Biogeographic dating Speciation dating Species tree dating Tree-dating Tree dating operation_3946 1.24 The development and use of mathematical models and systems analysis for the description of ecological processes, and applications such as the sustainable management of resources. Ecological modelling operation_3947 1.24 Mapping between gene tree nodes and species tree nodes or branches, to analyse and account for possible differences between gene histories and species histories, explaining this in terms of gene-scale events such as duplication, loss, transfer etc. Gene tree / species tree reconciliation Methods typically test for topological similarity between trees using for example a congruence index. Phylogenetic tree reconciliation operation_3950 1.24 The detection of genetic selection, or (the end result of) the process by which certain traits become more prevalent in a species than other traits. Selection detection operation_3960 1.25 A statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. Principal component analysis operation_3961 1.25 Identify where sections of the genome are repeated and the number of repeats in the genome varies between individuals. CNV detection Copy number variation detection operation_3962 1.25 Identify deletion events causing the number of repeats in the genome to vary between individuals. Deletion detection operation_3963 1.25 Identify duplication events causing the number of repeats in the genome to vary between individuals. Duplication detection operation_3964 1.25 Identify copy number variations which are complex, e.g. multi-allelic variations that have many structural alleles and have rearranged multiple times in the ancestral genomes. Complex CNV detection operation_3965 1.25 Identify amplification events causing the number of repeats in the genome to vary between individuals. Amplification detection operation_3968 1.25 Predict adhesins in protein sequences. An adhesin is a cell-surface component that facilitate the adherence of a microorganism to a cell or surface. They are important virulence factors during establishment of infection and thus are targeted during vaccine development approaches that seek to block adhesin function and prevent adherence to host cell. Adhesin prediction operation_4008 1.25 Design new protein molecules with specific structural or functional properties. Protein redesign Rational protein design de novo protein design Protein design operation_4009 1.25 The design of small molecules with specific biological activity, such as inhibitors or modulators for proteins that are of therapeutic interest. This can involve the modification of individual atoms, the addition or removal of molecular fragments, and the use reaction-based design to explore tractable synthesis options for the small molecule. Drug design Ligand-based drug design Structure-based drug design Structure-based small molecule design Small molecule design can involve assessment of target druggability and flexibility, molecular docking, in silico fragment screening, molecular dynamics, and homology modeling. There are two broad categories of small molecule design techniques when applied to the design of drugs: ligand-based drug design (e.g. ligand similarity) and structure-based drug design (ligand docking) methods. Ligand similarity methods exploit structural similarities to known active ligands, whereas ligand docking methods use the 3D structure of a target protein to predict the binding modes and affinities of ligands to it. Small molecule design operation_4031 1.26 The estimation of the power of a test; that is the probability of correctly rejecting the null hypothesis when it is false. Estimation of statistical power Power analysis Power test operation_4032 1.26 The prediction of DNA modifications (e.g. N4-methylcytosine and N6-Methyladenine) using, for example, statistical models. DNA modification prediction operation_4033 1.26 The analysis and simulation of disease transmission using, for example, statistical methods such as the SIR-model. Disease transmission analysis operation_4034 1.26 The correction of p-values from multiple statistical tests to correct for false positives. FDR estimation False discovery rate estimation Multiple testing correction operation_4042 1.26 Data management planning is the process of creating and updating a data management plan (DMP) for a project or an organisation. Good data management planning prevents unexpected legal issues or extra costs related to usage, sharing, storage, or archival of data. Policies often require the submission of a data management plan (DMP) together with a project proposal. A detailed, revised version of the DMP may be required as part of the project's final report. Data management planning operation_4043 1.26 Digital preservation Data digitisation is the process of converting analog data, text, or information into a digital format, appropriate for computational analysis and preservation. Data digitalisation Data digitalization Digital reformatting Data digitisation Data digitization topic_0003 beta12orEarlier true A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. sumo:FieldOfStudy Topic topic_0077 beta12orEarlier true The processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid bioinformatics Nucleic acid informatics Nucleic_acids Nucleic acid physicochemistry Nucleic acid properties Nucleic acids http://purl.bioontology.org/ontology/MSH/D017422 http://purl.bioontology.org/ontology/MSH/D017423 topic_0078 beta12orEarlier true Archival, processing and analysis of protein data, typically molecular sequence and structural data. Protein bioinformatics Protein informatics Proteins Protein databases Proteins http://purl.bioontology.org/ontology/MSH/D020539 topic_0079 beta12orEarlier 1.13 The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Metabolites true topic_0080 beta12orEarlier true The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. Sequence_analysis Biological sequences Sequence databases Sequence analysis http://purl.bioontology.org/ontology/MSH/D017421 topic_0081 beta12orEarlier true The curation, processing, analysis and prediction of data about the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. Biomolecular structure Structural bioinformatics Structure_analysis Computational structural biology Molecular structure Structure data resources Structure databases Structures This includes related concepts such as structural properties, alignments and structural motifs. Structure analysis http://purl.bioontology.org/ontology/MSH/D015394 topic_0082 beta12orEarlier true The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. Structure_prediction DNA structure prediction Nucleic acid design Nucleic acid folding Nucleic acid structure prediction Protein fold recognition Protein structure prediction RNA structure prediction This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). Structure prediction topic_0083 beta12orEarlier beta12orEarlier The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). Alignment true topic_0084 beta12orEarlier true The study of evolutionary relationships amongst organisms. Phylogeny Phylogenetic clocks Phylogenetic dating Phylogenetic simulation Phylogenetic stratigraphy Phylogeny reconstruction This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. Phylogeny http://purl.bioontology.org/ontology/MSH/D010802 topic_0085 beta12orEarlier true The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. Functional_genomics Functional genomics topic_0089 beta12orEarlier true The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. Ontology_and_terminology Applied ontology Ontologies Ontology Ontology relations Terminology Upper ontology Ontology and terminology http://purl.bioontology.org/ontology/MSH/D002965 topic_0090 beta12orEarlier 1.13 The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. Information retrieval true topic_0091 beta12orEarlier true VT 1.5.6 Bioinformatics The archival, curation, processing and analysis of complex biological data. Bioinformatics This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. Bioinformatics http://purl.bioontology.org/ontology/MSH/D016247 topic_0092 beta12orEarlier true Computer graphics VT 1.2.5 Computer graphics Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. Data rendering Data_visualisation Data visualisation topic_0094 beta12orEarlier 1.3 The study of the thermodynamic properties of a nucleic acid. Nucleic acid thermodynamics true topic_0097 beta12orEarlier The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. Nucleic acid structure Nucleic_acid_structure_analysis DNA melting DNA structure Nucleic acid denaturation Nucleic acid thermodynamics RNA alignment RNA structure RNA structure alignment Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. Nucleic acid structure analysis topic_0099 beta12orEarlier RNA sequences and structures. RNA Small RNA RNA topic_0100 beta12orEarlier 1.3 Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. Nucleic acid restriction true topic_0102 beta12orEarlier true The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). Mapping Genetic linkage Linkage Linkage mapping Synteny This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. Mapping topic_0107 beta12orEarlier 1.3 The study of codon usage in nucleotide sequence(s), genetic codes and so on. Genetic codes and codon usage true topic_0108 beta12orEarlier The translation of mRNA into protein and subsequent protein processing in the cell. Protein_expression Translation Protein expression topic_0109 beta12orEarlier 1.3 Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene finding true topic_0110 beta12orEarlier 1.3 The transcription of DNA into mRNA. Transcription true topic_0111 beta12orEarlier beta13 Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). Promoters true topic_0112 beta12orEarlier beta12orEarlier The folding (in 3D space) of nucleic acid molecules. Nucleic acid folding true topic_0114 beta12orEarlier true Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. Gene features Gene_structure Fusion genes This includes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information. This includes the study of promoters, coding regions etc. Gene structure topic_0121 beta12orEarlier true Protein and peptide identification, especially in the study of whole proteomes of organisms. Proteomics Bottom-up proteomics Discovery proteomics MS-based targeted proteomics MS-based untargeted proteomics Metaproteomics Peptide identification Protein and peptide identification Quantitative proteomics Targeted proteomics Top-down proteomics Includes metaproteomics: proteomics analysis of an environmental sample. Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues. Proteomics http://purl.bioontology.org/ontology/MSH/D040901 topic_0122 beta12orEarlier true The elucidation of the three dimensional structure for all (available) proteins in a given organism. Structural_genomics Structural genomics topic_0123 beta12orEarlier true The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. Protein physicochemistry Protein_properties Protein hydropathy Protein properties topic_0128 beta12orEarlier true Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. Protein_interactions Protein interaction map Protein interaction networks Protein interactome Protein-DNA interaction Protein-DNA interactions Protein-RNA interaction Protein-RNA interactions Protein-ligand interactions Protein-nucleic acid interactions Protein-protein interactions This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. Protein interactions topic_0130 beta12orEarlier true Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein_folding_stability_and_design Protein design Protein folding Protein residue interactions Protein stability Rational protein design Protein folding, stability and design topic_0133 beta12orEarlier beta13 Two-dimensional gel electrophoresis image and related data. Two-dimensional gel electrophoresis true topic_0134 beta12orEarlier 1.13 An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. Mass spectrometry true topic_0135 beta12orEarlier beta13 Protein microarray data. Protein microarrays true topic_0137 beta12orEarlier 1.3 The study of the hydrophobic, hydrophilic and charge properties of a protein. Protein hydropathy true topic_0140 beta12orEarlier The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export. Protein_targeting_and_localisation Protein localisation Protein sorting Protein targeting Protein targeting and localisation topic_0141 beta12orEarlier 1.3 Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. Protein cleavage sites and proteolysis true topic_0143 beta12orEarlier beta12orEarlier The comparison of two or more protein structures. Use this concept for methods that are exclusively for protein structure. Protein structure comparison true topic_0144 beta12orEarlier 1.3 The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. Protein residue interactions true topic_0147 beta12orEarlier 1.3 Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. Protein-protein interactions true topic_0148 beta12orEarlier 1.3 Protein-ligand (small molecule) interactions. Protein-ligand interactions true topic_0149 beta12orEarlier 1.3 Protein-DNA/RNA interactions. Protein-nucleic acid interactions true topic_0150 beta12orEarlier 1.3 The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein design true topic_0151 beta12orEarlier beta12orEarlier G-protein coupled receptors (GPCRs). G protein-coupled receptors (GPCR) true topic_0152 beta12orEarlier true Carbohydrates, typically including structural information. Carbohydrates Carbohydrates topic_0153 beta12orEarlier true Lipidome Lipids Lipids and their structures. Lipids Lipidomics topic_0154 beta12orEarlier true Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. Small_molecules Amino acids Chemical structures Drug structures Drug targets Drugs and target structures Metabolite structures Peptides Peptides and amino acids Target structures Targets Toxins Toxins and targets CHEBI:23367 Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. This concept excludes macromolecules such as proteins and nucleic acids. This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances. Small molecules topic_0156 beta12orEarlier beta12orEarlier Edit, convert or otherwise change a molecular sequence, either randomly or specifically. Sequence editing true topic_0157 beta12orEarlier true The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. Sequence_composition_complexity_and_repeats Low complexity sequences Nucleic acid repeats Protein repeats Protein sequence repeats Repeat sequences Sequence complexity Sequence composition Sequence repeats This includes repetitive elements within a nucleic acid sequence, e.g. long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit. This includes short repetitive subsequences (repeat sequences) in a protein sequence. Sequence composition, complexity and repeats topic_0158 beta12orEarlier 1.3 Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. Sequence motifs true topic_0159 beta12orEarlier 1.12 The comparison of two or more molecular sequences, for example sequence alignment and clustering. The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. Sequence comparison true topic_0160 beta12orEarlier true The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Sequence_sites_features_and_motifs Functional sites HMMs Sequence features Sequence motifs Sequence profiles Sequence sites Sequence sites, features and motifs topic_0163 beta12orEarlier beta12orEarlier Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). The query is a sequence-based entity such as another sequence, a motif or profile. Sequence database search true topic_0164 beta12orEarlier 1.7 The comparison and grouping together of molecular sequences on the basis of their similarities. This includes systems that generate, process and analyse sequence clusters. Sequence clustering true topic_0166 beta12orEarlier true Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. Protein 3D motifs Protein_structural_motifs_and_surfaces Protein structural features Protein structural motifs Protein surfaces Structural motifs This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. Protein structural motifs and surfaces topic_0167 beta12orEarlier 1.3 The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. Structural (3D) profiles true topic_0172 beta12orEarlier 1.12 The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. Protein structure prediction true topic_0173 beta12orEarlier 1.12 The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. Nucleic acid structure prediction true topic_0174 beta12orEarlier 1.7 The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. Ab initio structure prediction true topic_0175 beta12orEarlier 1.4 The modelling of the three-dimensional structure of a protein using known sequence and structural data. Homology modelling true topic_0176 beta12orEarlier true Molecular flexibility Molecular motions The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. Molecular_dynamics Protein dynamics This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc. This includes resources concerning flexibility and motion in protein and other molecular structures. Molecular dynamics topic_0177 beta12orEarlier true 1.12 The modelling the structure of proteins in complex with small molecules or other macromolecules. Molecular docking true topic_0178 beta12orEarlier 1.3 The prediction of secondary or supersecondary structure of protein sequences. Protein secondary structure prediction true topic_0179 beta12orEarlier 1.3 The prediction of tertiary structure of protein sequences. Protein tertiary structure prediction true topic_0180 beta12orEarlier 1.12 The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). Protein fold recognition true topic_0182 beta12orEarlier 1.7 The alignment of molecular sequences or sequence profiles (representing sequence alignments). This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. Sequence alignment true topic_0183 beta12orEarlier 1.7 The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). This includes the generation, storage, analysis, rendering etc. of structure alignments. Structure alignment true topic_0184 beta12orEarlier 1.3 The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). Threading true topic_0188 beta12orEarlier 1.3 Sequence profiles; typically a positional, numerical matrix representing a sequence alignment. Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. Sequence profiles and HMMs true topic_0191 beta12orEarlier 1.3 The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. Currently too specific for the topic sub-ontology (but might be unobsoleted). Phylogeny reconstruction true topic_0194 beta12orEarlier true The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. Phylogenomics Phylogenomics topic_0195 beta12orEarlier beta13 Simulated polymerase chain reaction (PCR). Virtual PCR true topic_0196 beta12orEarlier true The assembly of fragments of a DNA sequence to reconstruct the original sequence. Sequence_assembly Assembly Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. Sequence assembly topic_0199 beta12orEarlier true 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 Genetic_variation Genomic variation Mutation Polymorphism Somatic mutations Genetic variation http://purl.bioontology.org/ontology/MSH/D014644 topic_0200 beta12orEarlier 1.3 Microarrays, for example, to process microarray data or design probes and experiments. Microarrays http://purl.bioontology.org/ontology/MSH/D046228 true topic_0202 beta12orEarlier true VT 3.1.7 Pharmacology and pharmacy The study of drugs and their effects or responses in living systems. Pharmacology Computational pharmacology Pharmacoinformatics Pharmacology topic_0203 beta12orEarlier true http://edamontology.org/topic_0197 The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Expression Gene_expression Codon usage DNA chips DNA microarrays Gene expression profiling Gene transcription Gene translation Transcription Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. Gene expression http://purl.bioontology.org/ontology/MSH/D015870 topic_0204 beta12orEarlier true The regulation of gene expression. Regulatory genomics Gene regulation topic_0208 beta12orEarlier true The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. Pharmacogenomics Pharmacogenetics Pharmacogenomics topic_0209 beta12orEarlier true VT 3.1.4 Medicinal chemistry The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. Drug design Medicinal_chemistry This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Medicinal chemistry topic_0210 beta12orEarlier 1.3 Information on a specific fish genome including molecular sequences, genes and annotation. Fish true topic_0211 beta12orEarlier 1.3 Information on a specific fly genome including molecular sequences, genes and annotation. Flies true topic_0213 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Information on a specific mouse or rat genome including molecular sequences, genes and annotation. The resource may be specific to a group of mice / rats or all mice / rats. Mice or rats true topic_0215 beta12orEarlier 1.3 Information on a specific worm genome including molecular sequences, genes and annotation. Worms true topic_0217 beta12orEarlier 1.3 The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. Literature analysis true topic_0218 beta12orEarlier The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction. NLP Natural_language_processing BioNLP Literature mining Text analytics Text data mining Text mining Natural language processing topic_0219 beta12orEarlier Data archive Data library Data provenance Data registry Data repository Data storage Deposition database Research data archive Research data repository Data curation and archival includes the preservation of data in a repository, archive, or a deposition database; and curation of data and metadata, database accessions, annotation, and data provenance. Data archival Data archiving Data curation Data preservation Database curation Research data archiving Note that biocuration is a more specific concept than simply curation and archival of bioscientific data. The purpose of data curation and preservation is ensuring permanent access to the data and enabling its future analysis. Enabling reanalysis of the data in unexpected future contexts requires that the data is findable and reusable (see also FAIR data, topic_4012). Data curation and archival topic_0220 beta12orEarlier 1.13 The management and manipulation of digital documents, including database records, files and reports. Document, record and content management true topic_0221 beta12orEarlier beta12orEarlier Annotation of a molecular sequence. Sequence annotation true topic_0222 beta12orEarlier beta12orEarlier Annotation of a genome. Genome annotation true topic_0593 beta12orEarlier Spectroscopy An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. NMR spectroscopy Nuclear magnetic resonance spectroscopy NMR HOESY Heteronuclear Overhauser Effect Spectroscopy NOESY Nuclear Overhauser Effect Spectroscopy ROESY Rotational Frame Nuclear Overhauser Effect Spectroscopy NMR topic_0594 beta12orEarlier 1.12 The classification of molecular sequences based on some measure of their similarity. Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. Sequence classification true topic_0595 beta12orEarlier 1.3 primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. Protein classification true topic_0598 beta12orEarlier beta12orEarlier Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. This includes comparison, discovery, recognition etc. of sequence motifs. Sequence motif or profile true topic_0601 beta12orEarlier true Protein chemical modifications, e.g. post-translational modifications. PTMs Post-translational modifications Protein post-translational modification Protein_modifications Post-translation modifications Protein chemical modifications Protein post-translational modifications GO:0006464 MOD:00000 EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) Protein modifications topic_0602 beta12orEarlier true http://edamontology.org/topic_3076 Molecular interactions, biological pathways, networks and other models. Molecular_interactions_pathways_and_networks Biological models Biological networks Biological pathways Cellular process pathways Disease pathways Environmental information processing pathways Gene regulatory networks Genetic information processing pathways Interactions Interactome Metabolic pathways Molecular interactions Networks Pathways Signal transduction pathways Signaling pathways Molecular interactions, pathways and networks topic_0605 beta12orEarlier true VT 1.3 Information sciences VT 1.3.3 Information retrieval VT 1.3.4 Information management VT 1.3.5 Knowledge management VT 1.3.99 Other The study and practice of information processing and use of computer information systems. Information management Information science Knowledge management Informatics Informatics topic_0606 beta12orEarlier 1.3 Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. Literature data resources true topic_0607 beta12orEarlier true Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. Laboratory_Information_management Laboratory resources Laboratory information management topic_0608 beta12orEarlier 1.3 General cell culture or data on a specific cell lines. Cell and tissue culture true topic_0610 beta12orEarlier true VT 1.5.15 Ecology The ecological and environmental sciences and especially the application of information technology (ecoinformatics). Ecology Computational ecology Ecoinformatics Ecological informatics Ecosystem science Ecology http://purl.bioontology.org/ontology/MSH/D004777 topic_0611 beta12orEarlier Electron diffraction experiment The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. Electron_microscopy Electron crystallography SEM Scanning electron microscopy Single particle electron microscopy TEM Transmission electron microscopy Electron microscopy topic_0612 beta12orEarlier beta13 The cell cycle including key genes and proteins. Cell cycle true topic_0613 beta12orEarlier 1.13 The physicochemical, biochemical or structural properties of amino acids or peptides. Peptides and amino acids true topic_0616 beta12orEarlier 1.3 A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). Organelles true topic_0617 beta12orEarlier 1.3 Ribosomes, typically of ribosome-related genes and proteins. Ribosomes true topic_0618 beta12orEarlier beta13 A database about scents. Scents true topic_0620 beta12orEarlier 1.13 The structures of drugs, drug target, their interactions and binding affinities. Drugs and target structures true topic_0621 beta12orEarlier true A specific organism, or group of organisms, used to study a particular aspect of biology. Organisms Model_organisms This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. Model organisms topic_0622 beta12orEarlier true Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. Genomics Exomes Genome annotation Genomes Personal genomics Synthetic genomics Viral genomics Whole genomes Genomics http://purl.bioontology.org/ontology/MSH/D023281 topic_0623 beta12orEarlier true Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. Genes, gene family or system Gene_and protein_families Gene families Gene family Gene system Protein families Protein sequence classification A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. Gene and protein families topic_0624 beta12orEarlier 1.13 Study of chromosomes. Chromosomes true topic_0625 beta12orEarlier true The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotype and phenotype resources Genotype-phenotype Genotype-phenotype analysis Genotype_and_phenotype Genotype Genotyping Phenotype Phenotyping Genotype and phenotype topic_0629 beta12orEarlier beta12orEarlier Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. Gene expression and microarray true topic_0632 beta12orEarlier true Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. Probes_and_primers Primer quality Primers Probes This includes the design of primers for PCR and DNA amplification or the design of molecular probes. Probes and primers http://purl.bioontology.org/ontology/MSH/D015335 topic_0634 beta12orEarlier true VT 3.1.6 Pathology Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. Disease Pathology Pathology topic_0635 beta12orEarlier 1.3 A particular protein, protein family or other group of proteins. Specific protein resources true topic_0637 beta12orEarlier true VT 1.5.25 Taxonomy Organism classification, identification and naming. Taxonomy Taxonomy topic_0639 beta12orEarlier 1.8 Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. Protein sequence analysis true topic_0640 beta12orEarlier 1.8 The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. Nucleic acid sequence analysis true topic_0641 beta12orEarlier 1.3 The repetitive nature of molecular sequences. Repeat sequences true topic_0642 beta12orEarlier 1.3 The (character) complexity of molecular sequences, particularly regions of low complexity. Low complexity sequences true topic_0644 beta12orEarlier beta13 A specific proteome including protein sequences and annotation. Proteome true topic_0654 beta12orEarlier DNA sequences and structure, including processes such as methylation and replication. DNA analysis DNA Ancient DNA Chromosomes The DNA sequences might be coding or non-coding sequences. DNA topic_0655 beta12orEarlier 1.13 Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Coding RNA true topic_0659 beta12orEarlier true Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). Functional_regulatory_and_non-coding_RNA Functional RNA Long ncRNA Long non-coding RNA Non-coding RNA Regulatory RNA Small and long non-coding RNAs Small interfering RNA Small ncRNA Small non-coding RNA Small nuclear RNA Small nucleolar RNA lncRNA miRNA microRNA ncRNA piRNA piwi-interacting RNA siRNA snRNA snoRNA Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). Functional, regulatory and non-coding RNA topic_0660 beta12orEarlier 1.3 One or more ribosomal RNA (rRNA) sequences. rRNA true topic_0663 beta12orEarlier 1.3 One or more transfer RNA (tRNA) sequences. tRNA true topic_0694 beta12orEarlier 1.8 Protein secondary structure or secondary structure alignments. This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. Protein secondary structure true topic_0697 beta12orEarlier 1.3 RNA secondary or tertiary structure and alignments. RNA structure true topic_0698 beta12orEarlier 1.8 Protein tertiary structures. Protein tertiary structure true topic_0722 beta12orEarlier 1.3 Classification of nucleic acid sequences and structures. Nucleic acid classification true topic_0724 beta12orEarlier 1.14 Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. Protein families true topic_0736 beta12orEarlier true Protein tertiary structural domains and folds in a protein or polypeptide chain. Protein_folds_and_structural_domains Intramembrane regions Protein domains Protein folds Protein membrane regions Protein structural domains Protein topological domains Protein transmembrane regions Transmembrane regions This includes topological domains such as cytoplasmic regions in a protein. This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. Protein folds and structural domains topic_0740 beta12orEarlier 1.3 Nucleotide sequence alignments. Nucleic acid sequence alignment true topic_0741 beta12orEarlier 1.3 Protein sequence alignments. A sequence profile typically represents a sequence alignment. Protein sequence alignment true topic_0747 beta12orEarlier 1.3 The archival, detection, prediction and analysis ofpositional features such as functional sites in nucleotide sequences. Nucleic acid sites and features true topic_0748 beta12orEarlier 1.3 The detection, identification and analysis of positional features in proteins, such as functional sites. Protein sites and features true topic_0749 beta12orEarlier Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. Transcription_factors_and_regulatory_sites -10 signals -35 signals Attenuators CAAT signals CAT box CCAAT box CpG islands Enhancers GC signals Isochores Promoters TATA signals TFBS Terminators Transcription factor binding sites Transcription factors Transcriptional regulatory sites This includes CpG rich regions (isochores) in a nucleotide sequence. This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. Transcription factors and regulatory sites topic_0751 beta12orEarlier 1.0 Protein phosphorylation and phosphorylation sites in protein sequences. Phosphorylation sites true topic_0753 beta12orEarlier 1.13 Metabolic pathways. Metabolic pathways true topic_0754 beta12orEarlier 1.13 Signaling pathways. Signaling pathways true topic_0767 beta12orEarlier 1.3 Protein and peptide identification. Protein and peptide identification true topic_0769 beta12orEarlier Biological or biomedical analytical workflows or pipelines. Pipelines Workflows Software integration Tool integration Tool interoperability Workflows topic_0770 beta12orEarlier 1.0 Structuring data into basic types and (computational) objects. Data types and objects true topic_0771 beta12orEarlier 1.3 Theoretical biology. Theoretical biology true topic_0779 beta12orEarlier 1.3 Mitochondria, typically of mitochondrial genes and proteins. Mitochondria true topic_0780 beta12orEarlier VT 1.5.10 Botany VT 1.5.22 Plant science Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Botany Plant Plant science Plants Plant_biology Plant anatomy Plant cell biology Plant ecology Plant genetics Plant physiology The resource may be specific to a plant, a group of plants or all plants. Plant biology topic_0781 beta12orEarlier VT 1.5.28 Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. Virology Virology topic_0782 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. The resource may be specific to a fungus, a group of fungi or all fungi. Fungi true topic_0783 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). Definition is wrong anyway. 1.17 Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a pathogen, a group of pathogens or all pathogens. Pathogens true topic_0786 beta12orEarlier 1.3 Arabidopsis-specific data. Arabidopsis true topic_0787 beta12orEarlier 1.3 Rice-specific data. Rice true topic_0796 beta12orEarlier 1.3 Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. Genetic mapping and linkage true topic_0797 beta12orEarlier true The study (typically comparison) of the sequence, structure or function of multiple genomes. Comparative_genomics Comparative genomics topic_0798 beta12orEarlier Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. Mobile_genetic_elements Transposons Mobile genetic elements topic_0803 beta12orEarlier beta13 Human diseases, typically describing the genes, mutations and proteins implicated in disease. Human disease true topic_0804 beta12orEarlier true VT 3.1.3 Immunology The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. Immunology Immunology http://purl.bioontology.org/ontology/MSH/D007120 http://purl.bioontology.org/ontology/MSH/D007125 topic_0820 beta12orEarlier true Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. Membrane_and_lipoproteins Lipoproteins Membrane proteins Transmembrane proteins Membrane and lipoproteins topic_0821 beta12orEarlier true Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. Enzymology Enzymes Enzymes topic_0922 beta12orEarlier 1.13 PCR primers and hybridisation oligos in a nucleic acid sequence. Primers true topic_1302 beta12orEarlier 1.13 Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. PolyA signal or sites true topic_1304 beta12orEarlier 1.13 CpG rich regions (isochores) in a nucleotide sequence. CpG island and isochores true topic_1305 beta12orEarlier 1.13 Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. Restriction sites true topic_1307 beta12orEarlier 1.13 Splice sites in a nucleotide sequence or alternative RNA splicing events. Splice sites true topic_1308 beta12orEarlier 1.13 Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. Matrix/scaffold attachment sites true topic_1311 beta12orEarlier 1.13 Operons (operators, promoters and genes) from a bacterial genome. Operon true topic_1312 beta12orEarlier 1.13 Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. Promoters true topic_1317 beta12orEarlier true VT 1.5.24 Structural biology The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. Structural_biology Structural assignment Structural determination Structure determination This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. Structural biology topic_1456 beta12orEarlier 1.13 Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. Protein membrane regions true topic_1770 beta12orEarlier 1.13 The comparison of two or more molecular structures, for example structure alignment and clustering. This might involve comparison of secondary or tertiary (3D) structural information. Structure comparison true topic_1775 beta12orEarlier true The study of gene and protein function including the prediction of functional properties of a protein. Functional analysis Function_analysis Protein function analysis Protein function prediction Function analysis topic_1811 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. Prokaryotes and Archaea true topic_2225 beta12orEarlier 1.3 Protein data resources. Protein databases true topic_2226 beta12orEarlier 1.3 Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. Structure determination true topic_2229 beta12orEarlier true VT 1.5.11 Cell biology Cells, such as key genes and proteins involved in the cell cycle. Cell_biology Cells Cellular processes Protein subcellular localization Cell biology topic_2230 beta12orEarlier beta13 Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. Classification true topic_2232 beta12orEarlier 1.3 Lipoproteins (protein-lipid assemblies). Lipoproteins true topic_2257 beta12orEarlier beta12orEarlier Visualise a phylogeny, for example, render a phylogenetic tree. Phylogeny visualisation true topic_2258 beta12orEarlier true The application of information technology to chemistry in biological research environment. Chemical informatics Chemoinformatics Cheminformatics Cheminformatics topic_2259 beta12orEarlier true The holistic modelling and analysis of complex biological systems and the interactions therein. Systems_biology Biological modelling Biological system modelling Systems modelling This includes databases of models and methods to construct or analyse a model. Systems biology http://purl.bioontology.org/ontology/MSH/D049490 topic_2269 beta12orEarlier The application of statistical methods to biological problems. Statistics_and_probability Bayesian methods Biostatistics Descriptive statistics Gaussian processes Inferential statistics Markov processes Multivariate statistics Probabilistic graphical model Probability Statistics Statistics and probability http://purl.bioontology.org/ontology/MSH/D056808 topic_2271 beta12orEarlier beta12orEarlier Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. Structure database search true topic_2275 beta12orEarlier true The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). Molecular_modelling Comparative modelling Docking Homology modeling Homology modelling Molecular docking Molecular modelling topic_2276 beta12orEarlier 1.2 The prediction of functional properties of a protein. Protein function prediction true topic_2277 beta12orEarlier 1.13 Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. SNP true topic_2278 beta12orEarlier beta12orEarlier Predict transmembrane domains and topology in protein sequences. Transmembrane protein prediction true topic_2280 beta12orEarlier beta12orEarlier The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. Use this concept for methods that are exclusively for nucleic acid structures. Nucleic acid structure comparison true topic_2397 beta12orEarlier 1.13 Exons in a nucleotide sequences. Exons true topic_2399 beta12orEarlier 1.13 Transcription of DNA into RNA including the regulation of transcription. Gene transcription true topic_2533 beta12orEarlier DNA mutation. DNA_mutation DNA mutation topic_2640 beta12orEarlier true VT 3.2.16 Oncology The study of cancer, for example, genes and proteins implicated in cancer. Cancer biology Oncology Cancer Neoplasm Neoplasms Oncology topic_2661 beta12orEarlier 1.13 Structural and associated data for toxic chemical substances. Toxins and targets true topic_2754 beta12orEarlier 1.13 Introns in a nucleotide sequences. Introns true topic_2807 beta12orEarlier beta12orEarlier A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. Tool topic true topic_2809 beta12orEarlier beta12orEarlier A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. Study topic true topic_2811 beta12orEarlier 1.3 Biological nomenclature (naming), symbols and terminology. Nomenclature true topic_2813 beta12orEarlier 1.3 The genes, gene variations and proteins involved in one or more specific diseases. Disease genes and proteins true topic_2814 beta12orEarlier true http://edamontology.org/topic_3040 Protein secondary or tertiary structural data and/or associated annotation. Protein structure Protein_structure_analysis Protein tertiary structure Protein structure analysis topic_2815 beta12orEarlier The study of human beings in general, including the human genome and proteome. Humans Human_biology Human biology topic_2816 beta12orEarlier 1.3 Informatics resource (typically a database) primarily focused on genes. Gene resources true topic_2817 beta12orEarlier 1.3 Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. Yeast true topic_2818 beta12orEarlier (jison) Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. Eukaryotes true topic_2819 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. Invertebrates true topic_2820 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. Vertebrates true topic_2821 beta12orEarlier (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). 1.17 Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. Unicellular eukaryotes true topic_2826 beta12orEarlier 1.3 Protein secondary or tertiary structure alignments. Protein structure alignment true topic_2828 beta12orEarlier The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. Crystallography X-ray_diffraction X-ray crystallography X-ray microscopy X-ray diffraction topic_2829 beta12orEarlier 1.3 Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. Ontologies, nomenclature and classification http://purl.bioontology.org/ontology/MSH/D002965 true topic_2830 beta12orEarlier Immunity-related proteins and their ligands. Immunoproteins_and_antigens Antigens Immunopeptides Immunoproteins Therapeutic antibodies This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." Immunoproteins and antigens topic_2839 beta12orEarlier beta12orEarlier Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. CHEBI:23367 Molecules true topic_2840 beta12orEarlier true VT 3.1.9 Toxicology Toxins and the adverse effects of these chemical substances on living organisms. Toxicology Computational toxicology Toxicoinformatics Toxicology topic_2842 beta12orEarlier beta13 Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. High-throughput sequencing true topic_2846 beta12orEarlier 1.13 Gene regulatory networks. Gene regulatory networks true topic_2847 beta12orEarlier beta12orEarlier Informatics resources dedicated to one or more specific diseases (not diseases in general). Disease (specific) true topic_2867 beta12orEarlier 1.13 Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTR true topic_2868 beta12orEarlier 1.13 Microsatellite polymorphism in a DNA sequence. Microsatellites true topic_2869 beta12orEarlier 1.13 Restriction fragment length polymorphisms (RFLP) in a DNA sequence. RFLP true topic_2885 beta12orEarlier true DNA polymorphism. DNA_polymorphism Microsatellites RFLP SNP Single nucleotide polymorphism VNTR Variable number of tandem repeat polymorphism snps Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. Includes restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. Includes variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. DNA polymorphism topic_2953 beta12orEarlier 1.3 Topic for the design of nucleic acid sequences with specific conformations. Nucleic acid design true topic_3032 beta13 1.3 The design of primers for PCR and DNA amplification or the design of molecular probes. Primer or probe design true topic_3038 beta13 1.2 Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. Structure databases true topic_3039 beta13 1.2 Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. Nucleic acid structure true topic_3041 beta13 1.3 Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. Sequence databases true topic_3042 beta13 1.3 Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. Nucleic acid sequences true topic_3043 beta13 1.3 Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. Protein sequences true topic_3044 beta13 1.3 Protein interaction networks. Protein interaction networks true topic_3047 beta13 true VT 1.5.4 Biochemistry and molecular biology The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. Molecular_biology Biological processes Molecular biology topic_3048 beta13 1.3 Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. Mammals true topic_3050 beta13 true VT 1.5.5 Biodiversity conservation The degree of variation of life forms within a given ecosystem, biome or an entire planet. Biodiversity Biodiversity http://purl.bioontology.org/ontology/MSH/D044822 topic_3052 beta13 1.3 The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. Sequence clusters and classification true topic_3053 beta13 true The study of genes, genetic variation and heredity in living organisms. Genetics Genes Heredity Genetics http://purl.bioontology.org/ontology/MSH/D005823 topic_3055 beta13 true The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). Quantitative_genetics Quantitative genetics topic_3056 beta13 true The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. Population_genetics Population genetics topic_3060 beta13 1.3 Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). Regulatory RNA true topic_3061 beta13 1.13 The documentation of resources such as tools, services and databases and how to get help. Documentation and help true topic_3062 beta13 1.3 The structural and functional organisation of genes and other genetic elements. Genetic organisation true topic_3063 beta13 true The application of information technology to health, disease and biomedicine. Biomedical informatics Clinical informatics Health and disease Health informatics Healthcare informatics Medical_informatics Medical informatics topic_3064 beta13 true VT 1.5.14 Developmental biology How organisms grow and develop. Developmental_biology Development Developmental biology topic_3065 beta13 true The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. Embryology Embryology topic_3067 beta13 true VT 3.1.1 Anatomy and morphology The form and function of the structures of living organisms. Anatomy Anatomy topic_3068 beta13 true The scientific literature, language processing, reference information, and documentation. Language Literature Literature_and_language Bibliography Citations Documentation References Scientific literature This includes the documentation of resources such as tools, services and databases, user support, how to get help etc. Literature and language http://purl.bioontology.org/ontology/MSH/D011642 topic_3070 beta13 true VT 1.5 Biological sciences VT 1.5.1 Aerobiology VT 1.5.13 Cryobiology VT 1.5.23 Reproductive biology VT 1.5.3 Behavioural biology VT 1.5.7 Biological rhythm VT 1.5.8 Biology VT 1.5.99 Other The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on. Biological science Biology Aerobiology Behavioural biology Biological rhythms Chronobiology Cryobiology Reproductive biology Biology topic_3071 beta13 true Data life cycle Data lifecycle VT 1.3.1 Data management Data management comprises the practices and principles of taking care of data, other than analysing them. This includes for example taking care of the associated metadata, data formats, storage, preservation/archiving, access, and legal aspects related to using and sharing data. Metadata management Research data management (RDM) The purpose of data management is keeping data consistent, easy to access and use, while ensuring a required level of data protection. Good data management improves the visibility, impact, and lifetime of data. Data management topic_3072 beta13 1.3 The detection of the positional features, such as functional and other key sites, in molecular sequences. Sequence feature detection http://purl.bioontology.org/ontology/MSH/D058977 true topic_3073 beta13 1.3 The detection of positional features such as functional sites in nucleotide sequences. Nucleic acid feature detection true topic_3074 beta13 1.3 The detection, identification and analysis of positional protein sequence features, such as functional sites. Protein feature detection true topic_3075 beta13 1.2 Topic for modelling biological systems in mathematical terms. Biological system modelling true topic_3077 beta13 The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means. Data collecting Data collection Data gathering Experimental techniques Experiments Lab method Lab techniques Laboratory experiments Laboratory method Laboratory techniques Data acquisition topic_3078 beta13 1.3 Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. Genes and proteins resources true topic_3118 beta13 1.13 Topological domains such as cytoplasmic regions in a protein. Protein topological domains true topic_3120 beta13 true Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. Protein_variants Protein variants topic_3123 beta13 1.12 Regions within a nucleic acid sequence containing a signal that alters a biological function. Expression signals true topic_3125 beta13 Nucleic acids binding to some other molecule. DNA_binding_sites Matrix-attachment region Matrix/scaffold attachment region Nucleosome exclusion sequences Restriction sites Ribosome binding sites Scaffold-attachment region This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc. This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). DNA binding sites topic_3126 beta13 1.13 Repetitive elements within a nucleic acid sequence. This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. Nucleic acid repeats true topic_3127 beta13 true DNA replication or recombination. DNA_replication_and_recombination DNA replication and recombination topic_3135 beta13 1.13 Coding sequences for a signal or transit peptide. Signal or transit peptide true topic_3139 beta13 1.13 Sequence tagged sites (STS) in nucleic acid sequences. Sequence tagged sites true topic_3168 1.1 true The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. DNA-Seq Sequencing Chromosome walking Clone verification DNase-Seq High throughput sequencing High-throughput sequencing NGS NGS data analysis Next gen sequencing Next generation sequencing Panels Primer walking Sanger sequencing Targeted next-generation sequencing panels Sequencing http://purl.bioontology.org/ontology/MSH/D059014 topic_3169 1.1 The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. ChIP-sequencing Chip Seq Chip sequencing Chip-sequencing ChIP-seq ChIP-exo ChIP-seq topic_3170 1.1 A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. RNA sequencing RNA-Seq analysis Small RNA sequencing Small RNA-Seq Small-Seq Transcriptome profiling WTSS Whole transcriptome shotgun sequencing RNA-Seq MicroRNA sequencing miRNA-seq This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. RNA-Seq topic_3171 1.1 1.3 DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. DNA methylation true topic_3172 1.1 true The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. Metabolomics Exometabolomics LC-MS-based metabolomics MS-based metabolomics MS-based targeted metabolomics MS-based untargeted metabolomics Mass spectrometry-based metabolomics Metabolites Metabolome Metabonomics NMR-based metabolomics Metabolomics http://purl.bioontology.org/ontology/MSH/D055432 topic_3173 1.1 true The study of the epigenetic modifications of a whole cell, tissue, organism etc. Epigenomics Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. Epigenomics http://purl.bioontology.org/ontology/MSH/D057890 topic_3174 1.1 true Environmental DNA (eDNA) Environmental sequencing Biome sequencing Community genomics Ecogenomics Environmental genomics Environmental omics The study of genetic material recovered from environmental samples, and associated environmental data. Metagenomics Shotgun metagenomics Metagenomics topic_3175 1.1 Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. DNA structural variation Genomic structural variation DNA_structural_variation Deletion Duplication Insertion Inversion Translocation Structural variation topic_3176 1.1 DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. DNA_packaging Nucleosome positioning DNA packaging http://purl.bioontology.org/ontology/MSH/D042003 topic_3177 1.1 1.3 A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. DNA-Seq true topic_3178 1.1 1.3 The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. RNA-Seq alignment true topic_3179 1.1 Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. ChIP-chip ChIP-on-chip ChiP ChIP-on-chip topic_3263 1.3 true 1.26 The protection of data, such as patient health data, from damage or unwanted access from unauthorised users. Data privacy Data_security The concept of data security was ambiguous, and therefore replaced by two distinct concepts: data protection (incl. sensitive data etc.), and cybersecurity. Data security true topic_3277 1.3 Biological samples and specimens. Specimen collections Sample_collections biosamples samples Sample collections topic_3292 1.3 true VT 1.5.4 Biochemistry and molecular biology Chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry Biochemistry Glycomics Pathobiochemistry Phytochemistry Biochemistry topic_3293 1.3 true The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). Phylogenetics Phylogenetics http://purl.bioontology.org/ontology/MSH/D010802 topic_3295 1.3 true Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. Epigenetics DNA methylation Histone modification Methylation profiles This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.) Epigenetics http://purl.bioontology.org/ontology/MSH/D019175 topic_3297 1.3 true The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. Biotechnology Applied microbiology Biotechnology topic_3298 1.3 true Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. Phenomics Phenomics topic_3299 1.3 true VT 1.5.16 Evolutionary biology The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. Evolution Evolutionary_biology Evolutionary biology topic_3300 1.3 true VT 3.1.8 Physiology The functions of living organisms and their constituent parts. Physiology Electrophysiology Physiology topic_3301 1.3 true VT 1.5.20 Microbiology The biology of microorganisms. Microbiology Antimicrobial stewardship Medical microbiology Microbial genetics Microbial physiology Microbial surveillance Microbiological surveillance Molecular infection biology Molecular microbiology Microbiology topic_3302 1.3 true The biology of parasites. Parasitology Parasitology topic_3303 1.3 true VT 3.1 Basic medicine VT 3.2 Clinical medicine VT 3.2.9 General and internal medicine Research in support of healing by diagnosis, treatment, and prevention of disease. Biomedical research Clinical medicine Experimental medicine Medicine General medicine Internal medicine Medicine topic_3304 1.3 true Neuroscience VT 3.1.5 Neuroscience The study of the nervous system and brain; its anatomy, physiology and function. Neurobiology Molecular neuroscience Neurophysiology Systemetic neuroscience Neurobiology topic_3305 1.3 true VT 3.3.1 Epidemiology Topic concerning the the patterns, cause, and effect of disease within populations. Public_health_and_epidemiology Epidemiology Public health Public health and epidemiology topic_3306 1.3 true VT 1.5.9 Biophysics The use of physics to study biological system. Biophysics Medical physics Biophysics topic_3307 1.3 true VT 1.5.12 Computational biology VT 1.5.19 Mathematical biology VT 1.5.26 Theoretical biology The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. Computational_biology Biomathematics Mathematical biology Theoretical biology This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). Computational biology topic_3308 1.3 true The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Transcriptomics Comparative transcriptomics Transcriptome Transcriptomics topic_3314 1.3 Chemical science Polymer science VT 1.7.10 Polymer science VT 1.7 Chemical sciences VT 1.7.2 Chemistry VT 1.7.3 Colloid chemistry VT 1.7.5 Electrochemistry VT 1.7.6 Inorganic and nuclear chemistry VT 1.7.7 Mathematical chemistry VT 1.7.8 Organic chemistry VT 1.7.9 Physical chemistry The composition and properties of matter, reactions, and the use of reactions to create new substances. Chemistry Inorganic chemistry Mathematical chemistry Nuclear chemistry Organic chemistry Physical chemistry Chemistry topic_3315 1.3 VT 1.1.99 Other VT:1.1 Mathematics The study of numbers (quantity) and other topics including structure, space, and change. Maths Mathematics Dynamic systems Dynamical systems Dynymical systems theory Graph analytics Monte Carlo methods Multivariate analysis Mathematics topic_3316 1.3 VT 1.2 Computer sciences VT 1.2.99 Other The theory and practical use of computer systems. Computer_science Cloud computing HPC High performance computing High-performance computing Computer science topic_3318 1.3 The study of matter, space and time, and related concepts such as energy and force. Physics Physics topic_3320 1.3 true RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. Alternative splicing RNA_splicing Splice sites This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc.. RNA splicing topic_3321 1.3 true The structure and function of genes at a molecular level. Molecular_genetics Molecular genetics topic_3322 1.3 true VT 3.2.25 Respiratory systems The study of respiratory system. Pulmonary medicine Pulmonology Respiratory_medicine Pulmonary disorders Respiratory disease Respiratory medicine topic_3323 1.3 1.4 The study of metabolic diseases. Metabolic disease true topic_3324 1.3 VT 3.3.4 Infectious diseases The branch of medicine that deals with the prevention, diagnosis and management of transmissible disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). Communicable disease Transmissible disease Infectious_disease Infectious disease topic_3325 1.3 The study of rare diseases. Rare_diseases Rare diseases topic_3332 1.3 true VT 1.7.4 Computational chemistry Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. Computational_chemistry Computational chemistry topic_3334 1.3 true The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. Neurology Neurological disorders Neurology topic_3335 1.3 true VT 3.2.22 Peripheral vascular disease VT 3.2.4 Cardiac and Cardiovascular systems The diseases and abnormalities of the heart and circulatory system. Cardiovascular medicine Cardiology Cardiovascular disease Heart disease Cardiology topic_3336 1.3 true The discovery and design of drugs or potential drug compounds. Drug_discovery This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Drug discovery topic_3337 1.3 true Repositories of biological samples, typically human, for basic biological and clinical research. Tissue collection biobanking Biobank Biobank topic_3338 1.3 Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. Laboratory mouse Mouse_clinic Mouse clinic topic_3339 1.3 Collections of microbial cells including bacteria, yeasts and moulds. Microbial_collection Microbial collection topic_3340 1.3 Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. Cell_culture_collection Cell culture collection topic_3341 1.3 Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. Clone_library Clone library topic_3342 1.3 true 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. Translational_medicine Translational medicine topic_3343 1.3 Collections of chemicals, typically for use in high-throughput screening experiments. Compound_libraries_and_screening Chemical library Chemical screening Compound library Small chemical compounds libraries Small compounds libraries Target identification and validation Compound libraries and screening topic_3344 1.3 true VT 3.3 Health sciences Topic concerning biological science that is (typically) performed in the context of medicine. Biomedical sciences Health science Biomedical_science Biomedical science topic_3345 1.3 Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. Data_identity_and_mapping Data identity and mapping topic_3346 1.3 1.12 The search and retrieval from a database on the basis of molecular sequence similarity. Sequence search true topic_3360 1.4 true Objective indicators of biological state often used to assess health, and determinate treatment. Diagnostic markers Biomarkers Biomarkers topic_3361 1.4 This was merged into Data acquisition. Laboratory_techniques 1.26 The procedures used to conduct an experiment. Experimental techniques Lab method Lab techniques Laboratory method Experiments Laboratory experiments Laboratory techniques true topic_3365 1.4 The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data. Data_architecture_analysis_and_design Data analysis Data architecture Data design Data architecture, analysis and design topic_3366 1.4 The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. Data_integration_and_warehousing Data integration Data warehousing Data integration and warehousing topic_3368 1.4 Any matter, surface or construct that interacts with a biological system. Biomaterials Biomaterials topic_3369 1.4 true The use of synthetic chemistry to study and manipulate biological systems. Chemical_biology Chemical biology topic_3370 1.4 VT 1.7.1 Analytical chemistry The study of the separation, identification, and quantification of the chemical components of natural and artificial materials. Analytical_chemistry Analytical chemistry topic_3371 1.4 The use of chemistry to create new compounds. Synthetic_chemistry Synthetic organic chemistry Synthetic chemistry topic_3372 1.4 1.2.12 Programming languages Software engineering VT 1.2.1 Algorithms VT 1.2.14 Software engineering VT 1.2.7 Data structures The process that leads from an original formulation of a computing problem to executable programs. Computer programming Software development Software_engineering Algorithms Data structures Programming languages Software engineering topic_3373 1.4 true The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Drug development science Medicine development Medicines development Drug_development Drug development topic_3374 1.4 Drug delivery Drug formulation Drug formulation and delivery The process of formulating and administering a pharmaceutical compound to achieve a therapeutic effect. Biotherapeutics Biotherapeutics topic_3375 1.4 true The study of how a drug interacts with the body. Drug_metabolism ADME Drug absorption Drug distribution Drug excretion Pharmacodynamics Pharmacokinetics Pharmacokinetics and pharmacodynamics Drug metabolism topic_3376 1.4 Health care research Health care science The discovery, development and approval of medicines. Drug discovery and development Medicines_research_and_development Medicines research and development topic_3377 1.4 The safety (or lack) of drugs and other medical interventions. Patient safety Safety_sciences Drug safety Safety sciences topic_3378 1.4 The detection, assessment, understanding and prevention of adverse effects of medicines. Pharmacovigilence Pharmacovigilence concerns safety once a drug has gone to market. Pharmacovigilance topic_3379 1.4 The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. Preclinical_and_clinical_studies Clinical studies Clinical study Clinical trial Drug trials Preclinical studies Preclinical study Preclinical and clinical studies topic_3382 1.4 true The visual representation of an object. Imaging Diffraction experiment Microscopy Microscopy imaging Optical super resolution microscopy Photonic force microscopy Photonic microscopy This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. Imaging topic_3383 1.4 The use of imaging techniques to understand biology. Biological imaging Biological_imaging Bioimaging topic_3384 1.4 VT 3.2.13 Medical imaging VT 3.2.14 Nuclear medicine VT 3.2.24 Radiology The use of imaging techniques for clinical purposes for medical research. Medical_imaging Neuroimaging Nuclear medicine Radiology Medical imaging topic_3385 1.4 The use of optical instruments to magnify the image of an object. Light_microscopy Light microscopy topic_3386 1.4 The use of animals and alternatives in experimental research. Animal experimentation Animal research Animal testing In vivo testing Laboratory_animal_science Laboratory animal science topic_3387 1.4 true VT 1.5.18 Marine and Freshwater biology The study of organisms in the ocean or brackish waters. Marine_biology Marine biology topic_3388 1.4 true The identification of molecular and genetic causes of disease and the development of interventions to correct them. Molecular_medicine Molecular medicine topic_3390 1.4 VT 3.3.7 Nutrition and Dietetics The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. Nutrition Nutrition science Nutritional_science Dietetics Nutritional science topic_3391 1.4 true The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. Omics Omics topic_3393 1.4 The processes that need to be in place to ensure the quality of products for human or animal use. Quality assurance Quality_affairs Good clinical practice Good laboratory practice Good manufacturing practice Quality affairs topic_3394 1.4 The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. Healthcare RA Regulatory_affairs Regulatory affairs topic_3395 1.4 true Biomedical approaches to clinical interventions that involve the use of stem cells. Stem cell research Regenerative_medicine Regenerative medicine topic_3396 1.4 true An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incorporating biochemical, physiological, and environmental interactions that sustain life. Systems_medicine Systems medicine topic_3397 1.4 Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. Veterinary_medicine Clinical veterinary medicine Veterinary medicine topic_3398 1.4 The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. Biological engineering Bioengineering Bioengineering topic_3399 1.4 true Ageing Aging Gerontology VT 3.2.10 Geriatrics and gerontology The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. Geriatrics Geriatric_medicine Geriatric medicine topic_3400 1.4 true VT 3.2.1 Allergy Health issues related to the immune system and their prevention, diagnosis and management. Allergy_clinical_immunology_and_immunotherapeutics Allergy Clinical immunology Immune disorders Immunomodulators Immunotherapeutics Allergy, clinical immunology and immunotherapeutics topic_3401 1.4 true The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. Algiatry Pain management Pain_medicine Pain medicine topic_3402 1.4 VT 3.2.2 Anaesthesiology Anaesthesia and anaesthetics. Anaesthetics Anaesthesiology Anaesthesiology topic_3403 1.4 VT 3.2.5 Critical care/Emergency medicine The multidisciplinary that cares for patients with acute, life-threatening illness or injury. Acute medicine Emergency medicine Intensive care medicine Critical_care_medicine Critical care medicine topic_3404 1.4 VT 3.2.7 Dermatology and venereal diseases The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. Dermatology Dermatological disorders Dermatology topic_3405 1.4 The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. Dentistry Dentistry topic_3406 1.4 VT 3.2.20 Otorhinolaryngology The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. Audiovestibular medicine Otolaryngology Otorhinolaryngology Ear_nose_and_throat_medicine Head and neck disorders Ear, nose and throat medicine topic_3407 1.4 true The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Endocrinology_and_metabolism Endocrine disorders Endocrinology Metabolic disorders Metabolism Endocrinology and metabolism topic_3408 1.4 true VT 3.2.11 Hematology The branch of medicine that deals with the blood, blood-forming organs and blood diseases. Haematology Blood disorders Haematological disorders Haematology topic_3409 1.4 true VT 3.2.8 Gastroenterology and hepatology The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. Gastroenterology Gastrointestinal disorders Gastroenterology topic_3410 1.4 The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. Gender_medicine Gender medicine topic_3411 1.4 true VT 3.2.15 Obstetrics and gynaecology The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. Gynaecology_and_obstetrics Gynaecological disorders Gynaecology Obstetrics Gynaecology and obstetrics topic_3412 1.4 true The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. Hepatology Hepatic_and_biliary_medicine Liver disorders Hepatic and biliary medicine Hepatobiliary medicine topic_3413 1.4 1.13 The branch of medicine that deals with the infectious diseases of the tropics. Infectious tropical disease true topic_3414 1.4 The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. Traumatology Trauma_medicine Trauma medicine topic_3415 1.4 true The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. Medical_toxicology Medical toxicology topic_3416 1.4 VT 3.2.19 Orthopaedics VT 3.2.26 Rheumatology The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. Musculoskeletal_medicine Musculoskeletal disorders Orthopaedics Rheumatology Musculoskeletal medicine topic_3417 1.4 Optometry VT 3.2.17 Ophthalmology VT 3.2.18 Optometry The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. Ophthalmology Eye disoders Ophthalmology topic_3418 1.4 VT 3.2.21 Paediatrics The branch of medicine that deals with the medical care of infants, children and adolescents. Child health Paediatrics Paediatrics topic_3419 1.4 Mental health VT 3.2.23 Psychiatry The branch of medicine that deals with the management of mental illness, emotional disturbance and abnormal behaviour. Psychiatry Psychiatric disorders Psychiatry topic_3420 1.4 VT 3.2.3 Andrology The health of the reproductive processes, functions and systems at all stages of life. Reproductive_health Andrology Family planning Fertility medicine Reproductive disorders Reproductive health topic_3421 1.4 VT 3.2.28 Transplantation The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. Surgery Transplantation Surgery topic_3422 1.4 VT 3.2.29 Urology and nephrology The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. Urology_and_nephrology Kidney disease Nephrology Urological disorders Urology Urology and nephrology topic_3423 1.4 Alternative medicine Holistic medicine Integrative medicine VT 3.2.12 Integrative and Complementary medicine Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. Complementary_medicine Complementary medicine topic_3444 1.7 Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. MRT Magnetic resonance imaging Magnetic resonance tomography NMRI Nuclear magnetic resonance imaging MRI MRI topic_3448 1.7 The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. Neutron diffraction experiment Neutron_diffraction Elastic neutron scattering Neutron microscopy Neutron diffraction topic_3452 1.7 Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). CT Computed tomography TDM Tomography Electron tomography PET Positron emission tomography X-ray tomography Tomography topic_3473 1.7 true KDD Knowledge discovery in databases VT 1.3.2 Data mining The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. Data_mining Pattern recognition Data mining topic_3474 1.7 Artificial Intelligence VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics) A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an output, rather than relying on explicitly encoded information only. Machine_learning Active learning Ensembl learning Kernel methods Knowledge representation Neural networks Recommender system Reinforcement learning Supervised learning Unsupervised learning Machine learning topic_3489 1.8 Database administration Information systems Databases The general handling of data stored in digital archives such as databases, databanks, web portals, and other data resources. Database_management Content management Document management File management Record management This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files, and reports. Database management topic_3500 1.8 VT 1.5.29 Zoology Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. Animal Animal biology Animals Metazoa Zoology Animal genetics Animal physiology Entomology The study of the animal kingdom. Zoology topic_3510 1.8 The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Protein_sites_features_and_motifs Protein sequence features Signal peptide cleavage sites A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. Protein sites, features and motifs topic_3511 1.8 The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Nucleic_acid_sites_features_and_motifs Nucleic acid functional sites Nucleic acid sequence features Primer binding sites Sequence tagged sites Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. Nucleic acid sites, features and motifs topic_3512 1.8 Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. Gene_transcripts Coding RNA EST Exons Fusion transcripts Gene transcript features Introns PolyA signal PolyA site Signal peptide coding sequence Transit peptide coding sequence cDNA mRNA mRNA features This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences. This includes coding sequences for a signal or transit peptide. A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. This includes regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. Gene transcripts topic_3514 1.8 1.13 Protein-ligand (small molecule) interaction(s). Protein-ligand interactions true topic_3515 1.8 1.13 Protein-drug interaction(s). Protein-drug interactions true topic_3516 1.8 Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. Genotyping_experiment Genotyping experiment topic_3517 1.8 Genome-wide association study experiments. GWAS GWAS analysis Genome-wide association study GWAS_study GWAS study topic_3518 1.8 Microarray experiments including conditions, protocol, sample:data relationships etc. Microarrays Microarray_experiment Gene expression microarray Genotyping array Methylation array MicroRNA array Multichannel microarray One channel microarray Proprietary platform micoarray RNA chips RNA microarrays Reverse phase protein array SNP array Tiling arrays Tissue microarray Two channel microarray aCGH microarray mRNA microarray miRNA array This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. Microarray experiment topic_3519 1.8 PCR experiments, e.g. quantitative real-time PCR. Polymerase chain reaction PCR_experiment Quantitative PCR RT-qPCR Real Time Quantitative PCR PCR experiment topic_3520 1.8 Proteomics experiments. Proteomics_experiment 2D PAGE experiment DIA Data-independent acquisition MS MS experiments Mass spectrometry Mass spectrometry experiments Northern blot experiment Spectrum demultiplexing This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. Also Northern blot experiments. Proteomics experiment topic_3521 1.8 1.13 Two-dimensional gel electrophoresis experiments, gels or spots in a gel. 2D PAGE experiment true topic_3522 1.8 1.13 Northern Blot experiments. Northern blot experiment true topic_3523 1.8 RNAi experiments. RNAi_experiment RNAi experiment topic_3524 1.8 Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. Simulation_experiment Simulation experiment topic_3525 1.8 1.13 Protein-DNA/RNA interaction(s). Protein-nucleic acid interactions true topic_3526 1.8 1.13 Protein-protein interaction(s), including interactions between protein domains. Protein-protein interactions true topic_3527 1.8 1.13 Cellular process pathways. Cellular process pathways true topic_3528 1.8 1.13 Disease pathways, typically of human disease. Disease pathways true topic_3529 1.8 1.13 Environmental information processing pathways. Environmental information processing pathways true topic_3530 1.8 1.13 Genetic information processing pathways. Genetic information processing pathways true topic_3531 1.8 1.13 Super-secondary structure of protein sequence(s). Protein super-secondary structure true topic_3533 1.8 1.13 Catalytic residues (active site) of an enzyme. Protein active sites true topic_3534 1.8 Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc. Protein_binding_sites Enzyme active site Protein cleavage sites Protein functional sites Protein key folding sites Protein-nucleic acid binding sites Protein binding sites topic_3535 1.8 1.13 RNA and DNA-binding proteins and binding sites in protein sequences. Protein-nucleic acid binding sites true topic_3536 1.8 1.13 Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. Protein cleavage sites true topic_3537 1.8 1.13 Chemical modification of a protein. Protein chemical modifications true topic_3538 1.8 Disordered structure in a protein. Protein features (disordered structure) Protein_disordered_structure Protein disordered structure topic_3539 1.8 1.13 Structural domains or 3D folds in a protein or polypeptide chain. Protein domains true topic_3540 1.8 1.13 Key residues involved in protein folding. Protein key folding sites true topic_3541 1.8 1.13 Post-translation modifications in a protein sequence, typically describing the specific sites involved. Protein post-translational modifications true topic_3542 1.8 Secondary structure (predicted or real) of a protein, including super-secondary structure. Protein features (secondary structure) Protein_secondary_structure Protein super-secondary structure Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). Protein secondary structure topic_3543 1.8 1.13 Short repetitive subsequences (repeat sequences) in a protein sequence. Protein sequence repeats true topic_3544 1.8 1.13 Signal peptides or signal peptide cleavage sites in protein sequences. Protein signal peptides true topic_3569 1.10 VT 1.1.1 Applied mathematics The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models. Applied_mathematics Applied mathematics topic_3570 1.10 VT 1.1.1 Pure mathematics The study of abstract mathematical concepts. Pure_mathematics Linear algebra Pure mathematics topic_3571 1.10 Data governance is the control of data entry and maintenance to ensure the data meets defined standards, qualities, or constraints. Data_governance Data stewardship Data governance topic_3572 1.10 The quality, integrity, and cleaning up of data. Data_quality_management Data clean-up Data cleaning Data integrity Data quality Data quality management topic_3573 1.10 Freshwater science VT 1.5.18 Marine and Freshwater biology The study of organisms in freshwater ecosystems. Freshwater_biology Freshwater biology topic_3574 1.10 true VT 3.1.2 Human genetics The study of inheritance in human beings. Human_genetics Human genetics topic_3575 1.10 VT 3.3.14 Tropical medicine Health problems that are prevalent in tropical and subtropical regions. Tropical_medicine Tropical medicine topic_3576 1.10 true VT 3.3.14 Tropical medicine VT 3.4 Medical biotechnology VT 3.4.1 Biomedical devices VT 3.4.2 Health-related biotechnology Biotechnology applied to the medical sciences and the development of medicines. Medical_biotechnology Pharmaceutical biotechnology Medical biotechnology topic_3577 1.10 true VT 3.4.5 Molecular diagnostics An approach to medicine whereby decisions, practices and are tailored to the individual patient based on their predicted response or risk of disease. Precision medicine Personalised_medicine Molecular diagnostics Personalised medicine topic_3656 1.12 Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq. Chromatin immunoprecipitation Immunoprecipitation_experiment Immunoprecipitation experiment topic_3673 1.12 Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. Genome sequencing WGS Whole_genome_sequencing De novo genome sequencing Whole genome resequencing Whole genome sequencing topic_3674 1.12 Laboratory technique to sequence the methylated regions in DNA. MeDIP-chip MeDIP-seq mDIP Methylated_DNA_immunoprecipitation BS-Seq Bisulfite sequencing MeDIP Methylated DNA immunoprecipitation (MeDIP) Methylation sequencing WGBS Whole-genome bisulfite sequencing methy-seq methyl-seq Methylated DNA immunoprecipitation topic_3676 1.12 Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome. Exome Exome analysis Exome capture Targeted exome capture WES Whole exome sequencing Exome_sequencing Exome sequencing is considered a cheap alternative to whole genome sequencing. Exome sequencing topic_3678 1.12 true The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. Design of experiments Experimental design Studies Experimental_design_and_studies Experimental design and studies topic_3679 1.12 The design of an experiment involving non-human animals. Animal_study Challenge study Animal study topic_3697 1.13 true The ecology of microorganisms including their relationship with one another and their environment. Environmental microbiology Microbial_ecology Community analysis Microbiome Molecular community analysis Microbial ecology topic_3794 1.17 An antibody-based technique used to map in vivo RNA-protein interactions. RIP RNA_immunoprecipitation CLIP CLIP-seq HITS-CLIP PAR-CLIP iCLIP RNA immunoprecipitation topic_3796 1.17 Large-scale study (typically comparison) of DNA sequences of populations. Population_genomics Population genomics topic_3810 1.20 Agriculture Agroecology Agronomy Multidisciplinary study, research and development within the field of agriculture. Agricultural_science Agricultural biotechnology Agricultural economics Animal breeding Animal husbandry Animal nutrition Farming systems research Food process engineering Food security Horticulture Phytomedicine Plant breeding Plant cultivation Plant nutrition Plant pathology Soil science Agricultural science topic_3837 1.20 Approach which samples, in parallel, all genes in all organisms present in a given sample, e.g. to provide insight into biodiversity and function. Shotgun metagenomic sequencing Metagenomic_sequencing Metagenomic sequencing topic_3855 1.21 Environment Study of the environment, the interactions between its physical, chemical, and biological components and it's effect on life. Also how humans impact upon the environment, and how we can manage and utilise natural resources. Environmental_science Environmental sciences topic_3892 1.22 The study and simulation of molecular conformations using a computational model and computer simulations. This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc. Biomolecular simulation topic_3895 1.22 The application of multi-disciplinary science and technology for the construction of artificial biological systems for diverse applications. Biomimeic chemistry Synthetic biology topic_3912 1.22 The application of biotechnology to directly manipulate an organism's genes. Genetic manipulation Genetic modification Genetic_engineering Genome editing Genome engineering Genetic engineering topic_3922 1.24 A field of biological research focused on the discovery and identification of peptides, typically by comparing mass spectra against a protein database. Proteogenomics Proteogenomics topic_3923 1.24 Amplicon panels Resequencing Laboratory experiment to identify the differences between a specific genome (of an individual) and a reference genome (developed typically from many thousands of individuals). WGS re-sequencing is used as golden standard to detect variations compared to a given reference genome, including small variants (SNP and InDels) as well as larger genome re-organisations (CNVs, translocations, etc.). Highly targeted resequencing Whole genome resequencing (WGR) Whole-genome re-sequencing (WGSR) Amplicon sequencing Amplicon-based sequencing Ultra-deep sequencing Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions. Genome resequencing topic_3930 1.24 A biomedical field that bridges immunology and genetics, to study the genetic basis of the immune system. Immune system genetics Immungenetics Immunology and genetics Immunogenetics Immunogenes This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology. Immunogenetics topic_3931 1.24 Interdisciplinary science focused on extracting information from chemical systems by data analytical approaches, for example multivariate statistics, applied mathematics, and computer science. Chemometrics Chemometrics topic_3934 1.24 Cytometry is the measurement of the characteristics of cells. Cytometry Flow cytometry Image cytometry Mass cytometry Cytometry topic_3939 1.24 Biotechnology approach that seeks to optimize cellular genetic and regulatory processes in order to increase the cells' production of a certain substance. Metabolic engineering topic_3940 1.24 Molecular biology methods used to analyze the spatial organization of chromatin in a cell. 3C technologies 3C-based methods Chromosome conformation analysis Chromosome_conformation_capture Chromatin accessibility Chromatin accessibility assay Chromosome conformation capture topic_3941 1.24 The study of microbe gene expression within natural environments (i.e. the metatranscriptome). Metatranscriptomics Metatranscriptomics methods can be used for whole gene expression profiling of complex microbial communities. Metatranscriptomics topic_3943 1.24 The reconstruction and analysis of genomic information in extinct species. Paleogenomics Ancestral genomes Paleogenetics Paleogenomics topic_3944 1.24 The biological classification of organisms by categorizing them in groups ("clades") based on their most recent common ancestor. Cladistics Tree of life Cladistics topic_3945 1.24 The study of the process and mechanism of change of biomolecules such as DNA, RNA, and proteins across generations. Molecular_evolution Molecular evolution topic_3948 1.24 Immunoinformatics is the field of computational biology that deals with the study of immunoloogical questions. Immunoinformatics is at the interface between immunology and computer science. It takes advantage of computational, statistical, mathematical approaches and enhances the understanding of immunological knowledge. Computational immunology Immunoinformatics This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology. Immunoinformatics topic_3954 1.24 A diagnostic imaging technique based on the application of ultrasound. Standardized echography Ultrasound imaging Echography Diagnostic sonography Medical ultrasound Standard echography Ultrasonography Echography topic_3955 1.24 Experimental approaches to determine the rates of metabolic reactions - the metabolic fluxes - within a biological entity. Fluxomics The "fluxome" is the complete set of metabolic fluxes in a cell, and is a dynamic aspect of phenotype. Fluxomics topic_3957 1.12 An experiment for studying protein-protein interactions. Protein_interaction_experiment Co-immunoprecipitation Phage display Yeast one-hybrid Yeast two-hybrid This used to have the ID http://edamontology.org/topic_3557 but the numerical part (owing to an error) duplicated http://edamontology.org/operation_3557 ('Imputation'). ID of this concept set to http://edamontology.org/topic_3957 in EDAM 1.24. Protein interaction experiment topic_3958 1.25 A DNA structural variation, specifically a duplication or deletion event, resulting in sections of the genome to be repeated, or the number of repeats in the genome to vary between individuals. Copy_number_variation CNV deletion CNV duplication CNV insertion / amplification Complex CNV Copy number variant Copy number variation topic_3959 1.25 The branch of genetics concerned with the relationships between chromosomes and cellular behaviour, especially during mitosis and meiosis. Cytogenetics topic_3966 1.25 The design of vaccines to protect against a particular pathogen, including antigens, delivery systems, and adjuvants to elicit a predictable immune response against specific epitopes. Vaccinology Rational vaccine design Reverse vaccinology Structural vaccinology Structure-based immunogen design Vaccine design Vaccinology topic_3967 1.25 The study of immune system as a whole, its regulation and response to pathogens using genome-wide approaches. Immunomics topic_3974 1.25 Epistasis can be defined as the ability of the genotype at one locus to supersede the phenotypic effect of a mutation at another locus. This interaction between genes can occur at different level: gene expression, protein levels, etc... Epistatic genetic interaction Epistatic interactions Epistasis http://purl.bioontology.org/ontology/MSH/D004843 topic_4010 1.26 Open and reliable science Open research Open, reliable, transparent, and trustable science Open science encompasses the practices of making scientific research transparent and participatory, and its outputs publicly accessible. Open science topic_4011 1.26 Data rescue denotes digitalisation, formatting, archival, and publication of data that were not available in accessible or usable form. Examples are data from private archives, data inside publications, or in paper records stored privately or publicly. Data rescue topic_4012 1.26 FAIR data principles FAIR principles FAIRification FAIR data is scientific data that meets the principles of being findable, accessible, interoperable, and reusable. Findable, accessible, interoperable, reusable data Open data A substantially overlapping term is 'open data', i.e. publicly available data that is free to use, distribute, and create derivative work from, without restrictions. Open data does not automatically have to be FAIR (e.g. findable or interoperable), while FAIR data does in some cases not have to be publicly available without restrictions (especially sensitive, protected data, topic_4044). FAIR data topic_4013 1.26 Microbial mechanisms for protecting microorganisms against antimicrobial agents. AMR Antibiotic resistance (ABR) Antifungal resistance Antiprotozoal resistance Antiviral resistance Extensive drug resistance (XDR) Multidrug resistance Multiple drug resistance (MDR) Multiresistance Pandrug resistance (PDR) Total drug resistance (TDR) Antimicrobial resistance topic_4014 1.26 The monitoring method for measuring electrical activity in the brain. EEG Electroencephalography topic_4016 1.26 The monitoring method for measuring electrical activity in the heart. ECG EKG Electrocardiography topic_4017 1.26 A method for studying biomolecules and other structures at very low (cryogenic) temperature using electron microscopy. cryo-EM Cryogenic electron microscopy topic_4019 1.26 Life Biosciences, or life sciences, include fields of study related to life, living beings, and biomolecules. Life sciences Biosciences topic_4020 1.26 Biogeochemical cycle The carbon cycle is the biogeochemical pathway of carbon moving through the different parts of the Earth (such as ocean, atmosphere, soil), or eventually another planet. Note that the carbon-nitrogen-oxygen (CNO) cycle (https://en.wikipedia.org/wiki/CNO_cycle) is a completely different, thermonuclear reaction in stars. Carbon cycle topic_4021 1.26 Multiomics concerns integration of data from multiple omics (e.g. transcriptomics, proteomics, epigenomics). Integrative omics Multi-omics Pan-omics Panomics Multiomics topic_4027 1.26 With ribosome profiling, ribosome-protected mRNA fragments are analyzed with RNA-seq techniques leading to a genome-wide measurement of the translation landscape. RIBO-seq Ribo-Seq RiboSeq ribo-seq ribosomal footprinting translation footprinting Ribosome Profiling topic_4028 1.26 Combined with NGS (Next Generation Sequencing) technologies, single-cell sequencing allows the study of genetic information (DNA, RNA, epigenome...) at a single cell level. It is often used for differential analysis and gene expression profiling. Single-cell genomics Single-cell sequencing topic_4029 1.26 The study of mechanical waves in liquids, solids, and gases. Acoustics topic_4030 1.26 Interdisplinary study of behavior, precise control, and manipulation of low (microlitre) volume fluids in constrained space. Fluidics Microfluidics topic_4037 1.26 Genomic imprinting is a gene regulation mechanism by which a subset of genes are expressed from one of the two parental chromosomes only. Imprinted genes are organized in clusters, their silencing/activation of the imprinted loci involves epigenetic marks (DNA methylation, etc) and so-called imprinting control regions (ICR). It has been described in mammals, but also plants and insects. Gene imprinting Genomic imprinting topic_4038 1.26 Environmental DNA (eDNA) Environmental RNA (eRNA) Environmental sequencing Taxonomic profiling Metabarcoding is the barcoding of (environmental) DNA or RNA to identify multiple taxa from the same sample. DNA metabarcoding Environmental metabarcoding RNA metabarcoding eDNA metabarcoding eRNA metabarcoding Typically, high-throughput sequencing is performed and the resulting sequence reads are matched to DNA barcodes in a reference database. Metabarcoding topic_4044 1.26 Classified information Confidential information Data privacy Information privacy Information sensitivity Personal data Private data Sensitive data Sensitive human data Sensitive information Special category data Data protection is a topic concerning data that should be protected from disclosure, damage, or unauthorised access, due to its sensitive nature. Management of sensitive data Note that the term information security (https://en.wikipedia.org/wiki/Information_security) covers both the data management aspect for protected data (this topic_4044), and the technical aspect of cybersecurity (topic_4045). Sensitive data includes not only personal and commercial data, but also information about e.g. localisation of endangered biological species that could be exploited. Data protection topic_4045 1.26 Cryptography Cryptology IT security System security Cybersecurity is a topic comprising the approaches and technologies that enable the protection of computer systems, networks and programs from digital attacks. It ensures the availability, integrity, and confidentiality of processed and stored information. Computer security Data security Note that the term information security (https://en.wikipedia.org/wiki/Information_security) covers both the technical aspect of security (this topic_4045), and the data management aspect for protected data (topic_4044). Cybersecurity topic_4046 1.26 Version tracking Version control is a technology for consistent management, storing, and sharing of evolving versions of digital artefacts, such as computer programs, scripts, documents, data, or media files. Source control Source control system Version control system Versioning system Distributed version control is particularly useful for open, collaborative development of software and other creative work, enabling global communities to work cohesively. Version control originates from software engineering, with the purpose of managing source code. However, version control is applicable to other digital artefacts, especially any kind of text-based files. With certain limitations, version control can also be applied to binary files. Version control topic_4047 1.26 Code stewardship Service curation Service registry Software archive Software curation Software registry Software stewardship Tool curation Tool registry Workflow curation Workflow registry Software management comprises the practices and principles of taking care of software and software-based or software-like services, other than programming and maintenance. This includes for example taking care of the associated information and documentation, and the processes of contribution, validation, release/publication, or deployment. Service management The purpose of software management is keeping software or service consistent, easy to use, to update, and to expand. Good software management improves the visibility, impact, and lifetime of software and software-based or software-like services. Software management oboInOwl:ObsoleteClass 1.2 An obsolete concept (redefined in EDAM). Needed for conversion to the OBO format. Obsolete concept (EDAM) true owl:DeprecatedClass 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 a community project and its development can be followed and contributed to at https://github.com/edamontology/edamontology. 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. https://github.com/edamontology/edamontology/graphs/contributors and many more! Federico Bianchini Hervé Ménager Jon Ison Matúš Kalaš 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. application/rdf+xml EDAM - The ontology of data analysis and management unstable(1.26) 1.25-20240924T0027Z-unstable(1.26) 1.25-20240924T0027Z-unstable(1.26) format_2197 beta12orEarlier A serialisation format conforming to the Web Ontology Language (OWL) model. OWL format format_3261 1.2 rdf Resource Description Framework (RDF) XML format. RDF/XML can be used as a standard serialisation syntax for OWL DL, but not for OWL Full. RDF/XML http://www.ebi.ac.uk/SWO/data/SWO_3000006