EDAM - The ontology of data analysis and management
type: Ontology
next id: 4048
date: 24.09.2024 00:27 UTC
idspace: EDAM http://edamontology.org/ "EDAM relations, concept properties, and subsets"
idspace: EDAM_data http://edamontology.org/data_ "EDAM types of data"
idspace: EDAM_format http://edamontology.org/format_ "EDAM data formats"
idspace: EDAM_operation http://edamontology.org/operation_ "EDAM operations"
idspace: EDAM_topic http://edamontology.org/topic_ "EDAM topics"
remark: EDAM 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.
remark: EDAM is a community project and its development can be followed and contributed to at https://github.com/edamontology/edamontology.
contributor: https://github.com/edamontology/edamontology/graphs/contributors and many more!
creator: Federico Bianchini
creator: Hervé Ménager
creator: Jon Ison
creator: Matúš Kalaš
format: application/rdf+xml
format: rdf+xml
has format: RDF/XML
has format: OWL format
description: 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.
version: unstable(1.26)
license: https://creativecommons.org/licenses/by-sa/4.0
has subset: properties
has subset: data
has subset: bio
has subset: events
has subset: obsolete
has subset: formats
has subset: identifiers
has subset: operations
has subset: topics
prior version: http://edamontology.org/1.25
version IRI: 1.25-20240924T0027Z-unstable(1.26)
version info: 1.25-20240924T0027Z-unstable(1.26)
Repository: edamontology
Citation: f1000research.1118900.1

Citation
type: AnnotationProperty
Created in: 1.13
is metadata tag: true
has broad synonym: Publication reference
has definition: 'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferably including a DOI, pointing to a citeable publication of the given data format.
has related synonym: Publication
in subset: properties

Created in
type: AnnotationProperty
is metadata tag: true
has definition: Version in which a concept was created.
in subset: properties

deprecation_comment
type: AnnotationProperty
is metadata tag: true
has definition: A comment explaining why the comment should be or was deprecated, including name of person commenting (jison, mkalas etc.).
in subset: properties

Documentation
type: AnnotationProperty
is metadata tag: true
has definition: '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.
has related synonym: Specification
in subset: properties

Example
type: AnnotationProperty
is metadata tag: true
has definition: 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.
in subset: properties
comment: Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead.

File extension
type: AnnotationProperty
is metadata tag: true
has definition: 'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats.
in subset: properties
comment: 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.
comment: Separated by bar ('|'), without a dot ('.') prefix, preferably not all capital characters.

Information standard
type: AnnotationProperty
is metadata tag: true
comment: "Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard.
has definition: '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.
has narrow synonym: Minimum information checklist
has narrow synonym: Minimum information standard
in subset: properties

deprecation_candidate
type: AnnotationProperty
is metadata tag: true
has definition: When 'true', the concept has been proposed to be deprecated.
in subset: properties

refactor_candidate
type: AnnotationProperty
is metadata tag: true
has definition: When 'true', the concept has been proposed to be refactored.
in subset: properties

isdebtag
type: AnnotationProperty
is metadata tag: true
has definition: When 'true', the concept has been proposed or is supported within Debian as a tag.
in subset: properties

Media type
type: AnnotationProperty
is metadata tag: true
has definition: '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.
has narrow synonym: MIME type
in subset: properties

notRecommendedForAnnotation
type: AnnotationProperty
is metadata tag: true
has definition: Whether terms associated with this concept are recommended for use in annotation.
in subset: properties

Obsolete since
type: AnnotationProperty
is metadata tag: true
has definition: Version in which a concept was made obsolete.
in subset: properties

Old parent
type: AnnotationProperty
is metadata tag: true
has definition: EDAM concept URI of the erstwhile "parent" of a now deprecated concept.
in subset: properties

Old related
type: AnnotationProperty
is metadata tag: true
has definition: EDAM concept URI of an erstwhile related concept (by has_input, has_output, has_topic, is_format_of, etc.) of a now deprecated concept.
in subset: properties

Ontology used
type: AnnotationProperty
is metadata tag: true
has definition: '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.
in subset: properties

Organisation
type: AnnotationProperty
is metadata tag: true
has definition: '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.
has exact synonym: Organization
in subset: properties

refactor_comment
type: AnnotationProperty
is metadata tag: true
has definition: A comment explaining the proposed refactoring, including name of person commenting (jison, mkalas etc.).
in subset: properties

Regular expression
type: AnnotationProperty
is metadata tag: true
has definition: 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.
in subset: properties

Related term
type: AnnotationProperty
sub property of: hasRelatedSynonym
has definition: '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.
in subset: properties

Repository
type: AnnotationProperty
is metadata tag: true
has definition: '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.
has exact synonym: Public repository
has exact synonym: Source-code repository
in subset: properties

thematic_editor
type: AnnotationProperty
is metadata tag: true
has definition: Name of thematic editor (http://biotools.readthedocs.io/en/latest/governance.html#registry-editors) responsible for this concept and its children.
in subset: properties

has format
type: ObjectProperty
inverse of: is format of
domain: Data
range: Format
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A has_format B' defines for the subject A, that it has the object B as its data format.
in subset: properties
is cyclic: false
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'.
broad match: OBI_0000298
broad match: has-quality

has function
type: ObjectProperty
inverse of: is function of
range: Operation
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A has_function B' defines for the subject A, that it has the object B as its function.
has related synonym: OBO_REL:bearer_of
in subset: properties
is cyclic: true
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts.
broad match: has-quality

Axiom
annotated source: has function
annotated property: hasRelatedSynonym
annotated target: OBO_REL:bearer_of
comment: 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.

Axiom
annotated source: has function
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

has identifier
type: ObjectProperty
inverse of: is identifier of
domain: Data
range: Identifier
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
in subset: properties
is cyclic: false
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'.

has input
type: ObjectProperty
inverse of: is input of
domain: Operation
range: Data
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument.
has related synonym: OBO_REL:has_participant
in subset: properties
is cyclic: true
comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined.

Axiom
annotated source: has input
annotated property: hasRelatedSynonym
annotated target: OBO_REL:has_participant
comment: '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.

Axiom
annotated source: has input
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

has output
type: ObjectProperty
inverse of: is output of
domain: Operation
range: Data
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument.
has related synonym: OBO_REL:has_participant
in subset: properties
is cyclic: true
comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined.

Axiom
annotated source: has output
annotated property: hasRelatedSynonym
annotated target: OBO_REL:has_participant
comment: '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.

Axiom
annotated source: has output
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

has topic
type: ObjectProperty
inverse of: is topic of
domain: Class
  union of: Data
  union of: Operation
range: Topic
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: '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).
in subset: properties
is cyclic: true
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
broad match: IAO_0000136
broad match: OBI_0000298
broad match: has-quality

Axiom
annotated source: has topic
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

is format of
type: ObjectProperty
domain: Format
range: Data
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A is_format_of B' defines for the subject A, that it is a data format of the object B.
has related synonym: OBO_REL:quality_of
in subset: properties
is cyclic: false
comment: Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined.
broad match: inherent-in

Axiom
annotated source: is format of
annotated property: hasRelatedSynonym
annotated target: OBO_REL:quality_of
comment: 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.

is function of
type: ObjectProperty
domain: Operation
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A is_function_of B' defines for the subject A, that it is a function of the object B.
has narrow synonym: OBO_REL:function_of
has related synonym: OBO_REL:inheres_in
in subset: properties
is cyclic: true
comment: Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used.
broad match: inherent-in

Axiom
annotated source: is function of
annotated property: hasNarrowSynonym
annotated target: OBO_REL:function_of
comment: 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.

Axiom
annotated source: is function of
annotated property: hasRelatedSynonym
annotated target: OBO_REL:inheres_in
comment: 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.

Axiom
annotated source: is function of
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

is identifier of
type: ObjectProperty
domain: Identifier
range: Data
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B.
in subset: properties
is cyclic: false
comment: Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined.

is input of
type: ObjectProperty
domain: Data
range: Operation
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: '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.
has related synonym: OBO_REL:participates_in
in subset: properties
is cyclic: true
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'.

Axiom
annotated source: is input of
annotated property: hasRelatedSynonym
annotated target: OBO_REL:participates_in
comment: '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.

Axiom
annotated source: is input of
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

is output of
type: ObjectProperty
domain: Data
range: Operation
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: '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.
has related synonym: OBO_REL:participates_in
in subset: properties
is cyclic: true
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.

Axiom
annotated source: is output of
annotated property: hasRelatedSynonym
annotated target: OBO_REL:participates_in
comment: '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.

Axiom
annotated source: is output of
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

is topic of
type: ObjectProperty
domain: Topic
range: Class
  union of: Data
  union of: Operation
is anti symmetric: false
is reflexive: false
is symmetric: false
transitive over: OBO_REL:is_a
has definition: '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).
has related synonym: OBO_REL:quality_of
in subset: properties
is cyclic: true
comment: Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'.
broad match: inherent-in

Axiom
annotated source: is topic of
annotated property: hasRelatedSynonym
annotated target: OBO_REL:quality_of
comment: 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.

Axiom
annotated source: is topic of
annotated property: isCyclic
annotated target: true
comment: In very unusual cases.

Resource type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: A type of computational resource used in bioinformatics.
in subset: obsolete
deprecated: true

Data
type: Class
disjoint with: Format
disjoint with: Operation
disjoint with: Topic
disjoint with: DeprecatedClass
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: 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.
has exact synonym: Data record
has narrow synonym: Data set
has narrow synonym: Datum
in subset: bio
in subset: data
narrow match: IAO_0000027
broad match: IAO_0000030
related match: SIO_000088
broad match: BFO_0000002
broad match: Perpetuant

Axiom
annotated source: Data
annotated property: hasExactSynonym
annotated target: Data record
comment: 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).

Axiom
annotated source: Data
annotated property: hasNarrowSynonym
annotated target: Data set
comment: EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).

Axiom
annotated source: Data
annotated property: hasNarrowSynonym
annotated target: Datum
comment: EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).

Tool
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A bioinformatics package or tool, e.g. a standalone application or web service.
in subset: obsolete
replaced by: Tool metadata
deprecated: true

Database
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.
in subset: obsolete
replaced by: Database metadata
deprecated: true

Ontology
type: Class
subclass of: Ontology data
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
Created in: beta12orEarlier
has definition: An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.
in subset: bio
in subset: data

Directory metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: A directory on disk from which files are read.
in subset: obsolete
deprecated: true

MeSH vocabulary
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology
has definition: Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.
in subset: obsolete
deprecated: true

HGNC vocabulary
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology
has definition: Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.
in subset: obsolete
deprecated: true

UMLS vocabulary
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology
has definition: Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).
in subset: obsolete
deprecated: true

Identifier
type: Class
subclass of: Data
subclass of: Restriction
  on property: is identifier of
  some values from: Data
disjoint with: Report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: 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).
has exact synonym: ID
in subset: bio
in subset: data
in subset: identifiers
narrow match: identifier

Axiom
annotated source: Identifier
annotated property: narrowMatch
annotated target: identifier
comment: Almost exact but limited to identifying resources, and being unambiguous.

Database entry
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: An entry (retrievable via URL) from a biological database.
in subset: obsolete
deprecated: true

Molecular mass
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
has definition: Mass of a molecule.
in subset: bio
in subset: data

Molecular charge
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
has db xref: PDBML:pdbx_formal_charge
has definition: Net charge of a molecule.
in subset: bio
in subset: data

Chemical formula
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
has definition: A specification of a chemical structure.
has exact synonym: Chemical structure specification
in subset: bio
in subset: data

QSAR descriptor
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
has definition: A QSAR quantitative descriptor (name-value pair) of chemical structure.
in subset: bio
in subset: data
comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.

Raw sequence
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: 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).
Obsolete since: 1.23
Old parent: Sequence
has definition: A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.
in subset: obsolete
replaced by: Sequence
comment: Non-sequence characters may be used for example for gaps and translation stop.
deprecated: true

Sequence record
type: Class
subclass of: Sequence
Created in: beta12orEarlier
has db xref: SO:2000061
has definition: A molecular sequence and associated metadata.
in subset: bio
in subset: data

Sequence set
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: 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.
has narrow synonym: Alignment reference
has related synonym: SO:0001260
in subset: bio
in subset: data
comment: 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.
comment: This concept may be used for arbitrary sequence sets and associated data arising from processing.

Sequence mask character
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence attribute
has definition: A character used to replace (mask) other characters in a molecular sequence.
in subset: obsolete
deprecated: true

Sequence mask type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of sequence masking to perform.
in subset: obsolete
comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
deprecated: true

DNA sense specification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Sequence attribute
consider: Sequence attribute
has definition: The strand of a DNA sequence (forward or reverse).
in subset: obsolete
comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.
deprecated: true

Sequence length specification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence length
has definition: A specification of sequence length(s).
in subset: obsolete
deprecated: true

Sequence metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence report
has definition: Basic or general information concerning molecular sequences.
in subset: obsolete
comment: This is used for such things as a report including the sequence identifier, type and length.
deprecated: true

Sequence feature source
type: Class
subclass of: Sequence features metadata
Created in: beta12orEarlier
has definition: How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.
in subset: bio
in subset: data
comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).

Sequence search results
type: Class
subclass of: Database search results
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Database hits (sequence)
has exact synonym: Sequence database hits
has exact synonym: Sequence database search results
has exact synonym: Sequence search hits
in subset: bio
in subset: data
comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.

Sequence signature matches
type: Class
subclass of: Sequence signature data
subclass of: Alignment
Created in: beta12orEarlier
has definition: Report on the location of matches ("hits") between sequences, sequence profiles, motifs (conserved or functional patterns) and other types of sequence signatures.
has narrow synonym: Profile-profile alignment
has narrow synonym: Protein secondary database search results
has narrow synonym: Search results (protein secondary database)
has narrow synonym: Sequence motif hits
has narrow synonym: Sequence motif matches
has narrow synonym: Sequence profile alignment
has narrow synonym: Sequence profile hits
has narrow synonym: Sequence profile matches
has narrow synonym: Sequence-profile alignment
in subset: bio
in subset: data
comment: A "profile-profile alignment" is an alignment of two sequence profiles, each profile typically representing a sequence alignment.
comment: 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).
comment: 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 model
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Mathematical model
has definition: Data files used by motif or profile methods.
in subset: obsolete
deprecated: true

Sequence signature data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: 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 alignment (words)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence alignment
has definition: Alignment of exact matches between subsequences (words) within two or more molecular sequences.
in subset: obsolete
deprecated: true

Dotplot
type: Class
subclass of: Sequence alignment report
Created in: beta12orEarlier
has definition: A dotplot of sequence similarities identified from word-matching or character comparison.
in subset: bio
in subset: data

Sequence alignment
type: Class
subclass of: Alignment
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
Created in: beta12orEarlier
has definition: Alignment of multiple molecular sequences.
has exact synonym: Multiple sequence alignment
has exact synonym: msa
in subset: bio
in subset: data

Sequence alignment parameter
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence attribute
has definition: Some simple value controlling a sequence alignment (or similar 'match') operation.
in subset: obsolete
deprecated: true

Sequence similarity score
type: Class
subclass of: Score
Created in: beta12orEarlier
has definition: A value representing molecular sequence similarity.
in subset: bio
in subset: data

Sequence alignment metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence alignment report
has definition: Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.
in subset: obsolete
deprecated: true

Sequence alignment report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: An informative report of molecular sequence alignment-derived data or metadata.
has exact synonym: Sequence alignment metadata
in subset: bio
in subset: data
comment: 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.

Profile-profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: "Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data.
Obsolete since: 1.25 or earlier
Old parent: Alignment
has definition: A profile-profile alignment (each profile typically representing a sequence alignment).
in subset: obsolete
replaced by: Sequence signature matches
deprecated: true

Sequence-profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: "Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data.
Obsolete since: 1.24
Old parent: Alignment
has definition: Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).
in subset: obsolete
replaced by: Sequence signature matches
deprecated: true

Sequence distance matrix
type: Class
subclass of: Distance matrix
Created in: beta12orEarlier
has db xref: Moby:phylogenetic_distance_matrix
has definition: A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.
has exact synonym: Phylogenetic distance matrix
in subset: bio
in subset: data
comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.

Phylogenetic character data
type: Class
subclass of: Phylogenetic data
Created in: beta12orEarlier
has definition: Basic character data from which a phylogenetic tree may be generated.
in subset: bio
in subset: data
comment: As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments

Phylogenetic tree
type: Class
subclass of: Phylogenetic data
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has db xref: Moby:Tree
has db xref: Moby:myTree
has db xref: Moby:phylogenetic_tree
has definition: 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.
has exact synonym: Phylogeny
in subset: bio
in subset: data
comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.

Comparison matrix
type: Class
subclass of: Matrix
Created in: beta12orEarlier
has definition: Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.
has exact synonym: Substitution matrix
in subset: bio
in subset: data
comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).

Protein topology
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Predicted or actual protein topology represented as a string of protein secondary structure elements.
in subset: obsolete
replaced by: Protein features
comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated.
deprecated: true

Protein features report (secondary structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Secondary structure (predicted or real) of a protein.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features report (super-secondary)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Super-secondary structure of protein sequence(s).
in subset: obsolete
replaced by: Protein features
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
deprecated: true

Protein secondary structure alignment
type: Class
subclass of: Secondary structure alignment
Created in: beta12orEarlier
deprecation_candidate: true
has definition: Alignment of the (1D representations of) secondary structure of two or more proteins.
has exact synonym: Secondary structure alignment (protein)
in subset: bio
in subset: data

Secondary structure alignment metadata (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment report
has definition: An informative report on protein secondary structure alignment-derived data or metadata.
in subset: obsolete
deprecated: true

RNA secondary structure
type: Class
subclass of: RNA structure
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: beta12orEarlier
has db xref: Moby:RNAStructML
has definition: An informative report of secondary structure (predicted or real) of an RNA molecule.
has exact synonym: Secondary structure (RNA)
in subset: bio
in subset: data
comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.

RNA secondary structure alignment
type: Class
subclass of: Secondary structure alignment
Created in: beta12orEarlier
deprecation_candidate: true
has db xref: Moby:RNAStructAlignmentML
has definition: Alignment of the (1D representations of) secondary structure of two or more RNA molecules.
has exact synonym: Secondary structure alignment (RNA)
in subset: bio
in subset: data

Secondary structure alignment metadata (RNA)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment report
has definition: An informative report of RNA secondary structure alignment-derived data or metadata.
in subset: obsolete
deprecated: true

Structure
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.
has exact synonym: Coordinate model
has exact synonym: Structure data
in subset: bio
in subset: data
comment: The coordinate data may be predicted or real.

Tertiary structure record
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure
has definition: An entry from a molecular tertiary (3D) structure database.
in subset: obsolete
deprecated: true

Structure database search results
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Database search results
has definition: Results (hits) from searching a database of tertiary structure.
in subset: obsolete
deprecated: true

Structure alignment
type: Class
subclass of: Alignment
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Alignment (superimposition) of molecular tertiary (3D) structures.
in subset: bio
in subset: data
comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.

Structure alignment report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: An informative report of molecular tertiary structure alignment-derived data.
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Structure similarity score
type: Class
subclass of: Score
Created in: beta12orEarlier
has definition: A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.
in subset: bio
in subset: data

Structural profile
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Some type of structural (3D) profile or template (representing a structure or structure alignment).
has exact synonym: 3D profile
has exact synonym: Structural (3D) profile
in subset: bio
in subset: data

Structural (3D) profile alignment
type: Class
subclass of: Alignment
Created in: beta12orEarlier
has definition: A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).
has exact synonym: Structural profile alignment
in subset: bio
in subset: data

Sequence-3D profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence-structure alignment
has definition: An alignment of a sequence to a 3D profile (representing structures or a structure alignment).
in subset: obsolete
deprecated: true

Protein sequence-structure scoring matrix
type: Class
subclass of: Matrix
Created in: beta12orEarlier
has definition: Matrix of values used for scoring sequence-structure compatibility.
in subset: bio
in subset: data

Sequence-structure alignment
type: Class
subclass of: Alignment
Created in: beta12orEarlier
has definition: An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).
in subset: bio
in subset: data

Amino acid annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report about a specific amino acid.
in subset: obsolete
deprecated: true

Peptide annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report about a specific peptide.
in subset: obsolete
deprecated: true

Protein report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Gene product annotation
in subset: bio
in subset: data

Protein property
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
has definition: A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.
has exact synonym: Protein physicochemical property
has exact synonym: Protein properties
has narrow synonym: Protein sequence statistics
in subset: bio
in subset: data
comment: 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 structural motifs and surfaces
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: 3D structural motifs in a protein.
replaced by: Protein features
deprecated: true

Protein domain classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Data concerning the classification of the sequences and/or structures of protein structural domain(s).
in subset: obsolete
deprecated: true

Protein features report (domains)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: structural domains or 3D folds in a protein or polypeptide chain.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein architecture report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Protein structure report
has definition: An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.
in subset: obsolete
deprecated: true

Protein folding report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Protein structure report
deprecated: true

Protein features (mutation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein report
has definition: Data on the effect of (typically point) mutation on protein folding, stability, structure and function.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

Protein interaction raw data
type: Class
subclass of: Experimental measurement
Created in: beta12orEarlier
has definition: Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.

Protein interaction data
type: Class
subclass of: Protein property
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Protein interaction record
has exact synonym: Protein interaction report
has exact synonym: Protein report (interaction)
has exact synonym: Protein-protein interaction data
has narrow synonym: Atom interaction data
has narrow synonym: Protein non-covalent interactions report
has narrow synonym: Residue interaction data
in subset: bio
in subset: data

Protein family report
type: Class
subclass of: Protein report
subclass of: Restriction
  on property: has topic
  some values from: Gene and protein families
Created in: beta12orEarlier
has broad synonym: Protein classification data
has definition: An informative report on a specific protein family or other classification or group of protein sequences or structures.
has exact synonym: Protein family annotation
in subset: bio
in subset: data

Vmax
type: Class
subclass of: Enzyme kinetics data
Created in: beta12orEarlier
has definition: The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.
in subset: bio
in subset: data

Km
type: Class
subclass of: Enzyme kinetics data
Created in: beta12orEarlier
has definition: Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.
in subset: bio
in subset: data

Nucleotide base annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report about a specific nucleotide base.
in subset: obsolete
deprecated: true

Nucleic acid property
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
comment: Nucleic acid structural properties stiffness, curvature, twist/roll data or other conformational parameters or properties.
has definition: A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.
has exact synonym: Nucleic acid physicochemical property
has narrow synonym: GC-content
has narrow synonym: Nucleic acid property (structural)
has narrow synonym: Nucleic acid structural property
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Codon usage data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.
has exact synonym: Codon usage report
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Gene report
type: Class
subclass of: Nucleic acid report
Created in: beta12orEarlier
has db xref: Moby:GeneInfo
has db xref: Moby:gene
has db xref: Moby_namespace:Human_Readable_Description
has definition: A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
has exact synonym: Gene and transcript structure (report)
has exact synonym: Gene annotation
has exact synonym: Gene features report
has exact synonym: Gene function (report)
has exact synonym: Gene structure (repot)
has exact synonym: Nucleic acid features (gene and transcript structure)
in subset: bio
in subset: data
comment: 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 classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene report
has definition: A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.
in subset: obsolete
deprecated: true

DNA variation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Chromosome report
type: Class
subclass of: Nucleic acid report
Created in: beta12orEarlier
has definition: A human-readable collection of information about a specific chromosome.
in subset: bio
in subset: data
comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.

Genotype/phenotype report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Genotype/phenotype annotation
in subset: bio
in subset: data

PCR experiment report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: PCR experiments, e.g. quantitative real-time PCR.
in subset: obsolete
replaced by: Protocol
deprecated: true

Sequence trace
type: Class
subclass of: Sequence set (nucleic acid)
subclass of: Experimental measurement
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: This is the raw data produced by a DNA sequencing machine.

Sequence assembly
type: Class
subclass of: Sequence set (nucleic acid)
Created in: beta12orEarlier
has definition: An assembly of fragments of a (typically genomic) DNA sequence.
has exact synonym: Contigs
has exact synonym: SO:0000353
has narrow synonym: SO:0001248
in subset: bio
in subset: data
comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.

Axiom
annotated source: Sequence assembly
annotated property: hasNarrowSynonym
annotated target: SO:0001248
comment: Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'.

RH scores
type: Class
subclass of: Experimental measurement
Created in: beta12orEarlier
has definition: Radiation hybrid scores (RH) scores for one or more markers.
has exact synonym: Radiation Hybrid (RH) scores
in subset: bio
in subset: data
comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.

Genetic linkage report
type: Class
subclass of: Nucleic acid report
Created in: beta12orEarlier
has definition: A human-readable collection of information about the linkage of alleles.
has exact synonym: Gene annotation (linkage)
has narrow synonym: Linkage disequilibrium (report)
in subset: bio
in subset: data
comment: This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).

Gene expression profile
type: Class
subclass of: Expression data
Created in: beta12orEarlier
has definition: Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.
has related synonym: Gene expression pattern
in subset: bio
in subset: data

Microarray experiment report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: microarray experiments including conditions, protocol, sample:data relationships etc.
in subset: obsolete
replaced by: Protocol
deprecated: true

Oligonucleotide probe data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Oligonucleotide probe annotation
has definition: Data on oligonucleotide probes (typically for use with DNA microarrays).
in subset: obsolete
deprecated: true

SAGE experimental data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence tag profile
has definition: Output from a serial analysis of gene expression (SAGE) experiment.
in subset: obsolete
deprecated: true

MPSS experimental data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence tag profile
has definition: Massively parallel signature sequencing (MPSS) data.
in subset: obsolete
deprecated: true

SBS experimental data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence tag profile
has definition: Sequencing by synthesis (SBS) data.
in subset: obsolete
deprecated: true

Sequence tag profile (with gene assignment)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.14
Old parent: Thing
has definition: Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.
in subset: obsolete
replaced by: Sequence tag profile
deprecated: true

Electron density map
type: Class
subclass of: Protein structure raw data
Created in: beta12orEarlier
has broad synonym: Protein X-ray crystallographic data
has definition: X-ray crystallography data.
in subset: bio
in subset: data

Raw NMR data
type: Class
subclass of: Protein structure raw data
Created in: beta12orEarlier
has definition: Nuclear magnetic resonance (NMR) raw data, typically for a protein.
has narrow synonym: Protein NMR data
in subset: bio
in subset: data

CD spectra
type: Class
subclass of: Protein structure raw data
Created in: beta12orEarlier
has definition: Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.
has exact synonym: CD spectrum
has exact synonym: Protein circular dichroism (CD) spectroscopic data
in subset: bio
in subset: data

Volume map
type: Class
subclass of: Experimental measurement
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: beta12orEarlier
has definition: Volume map data from electron microscopy.
has exact synonym: 3D volume map
has exact synonym: EM volume map
has exact synonym: Electron microscopy volume map
in subset: bio
in subset: data

Electron microscopy model
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Structure
has definition: Annotation on a structural 3D model (volume map) from electron microscopy.
in subset: obsolete
replaced by: 3D EM Mask
deprecated: true

2D PAGE image
type: Class
subclass of: Raw image
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: Two-dimensional gel electrophoresis image.
in subset: bio
in subset: data

Mass spectrum
type: Class
subclass of: Mass spectrometry data
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: Spectra from mass spectrometry.
has exact synonym: Mass spectrometry spectra
in subset: bio
in subset: data

Peptide mass fingerprint
type: Class
subclass of: Mass spectrometry data
subclass of: Peptide property
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: A set of peptide masses (peptide mass fingerprint) from mass spectrometry.
has exact synonym: Peak list
has exact synonym: Protein fingerprint
has narrow synonym: Molecular weights standard fingerprint
in subset: bio
in subset: data
comment: A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides.

Peptide identification
type: Class
subclass of: Protein property
subclass of: Peptide property
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: 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.
has exact synonym: 'Protein identification'
has exact synonym: Peptide spectrum match
in subset: bio
in subset: data

Pathway or network annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Pathway or network report
has definition: An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.
in subset: obsolete
deprecated: true

Biological pathway map
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Pathway or network
has definition: A map (typically a diagram) of a biological pathway.
in subset: obsolete
deprecated: true

Data resource definition
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Annotated URI
has definition: A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.
in subset: obsolete
deprecated: true

Workflow metadata
type: Class
subclass of: Resource metadata
Created in: beta12orEarlier
has definition: Basic information, annotation or documentation concerning a workflow (but not the workflow itself).
in subset: bio
in subset: data

Mathematical model
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Computational biology
Created in: beta12orEarlier
has definition: A biological model represented in mathematical terms.
has exact synonym: Biological model
in subset: bio
in subset: data

Statistical estimate score
type: Class
subclass of: Score
Created in: beta12orEarlier
has definition: A value representing estimated statistical significance of some observed data; typically sequence database hits.
in subset: bio
in subset: data

EMBOSS database resource definition
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Database metadata
has definition: Resource definition for an EMBOSS database.
in subset: obsolete
deprecated: true

Version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Resource metadata
has definition: Information on a version of software or data, for example name, version number and release date.
in subset: obsolete
comment: Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
deprecated: true

Database cross-mapping
type: Class
subclass of: Data reference
Created in: beta12orEarlier
has definition: A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.
in subset: bio
in subset: data
comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.

Data index
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Database management
Created in: beta12orEarlier
has definition: An index of data of biological relevance.
in subset: bio
in subset: data

Data index report
type: Class
subclass of: Report
subclass of: Restriction
  on property: has topic
  some values from: Database management
Created in: beta12orEarlier
has definition: A human-readable collection of information concerning an analysis of an index of biological data.
has exact synonym: Database index annotation
in subset: bio
in subset: data

Database metadata
type: Class
subclass of: Resource metadata
Created in: beta12orEarlier
has definition: Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.
in subset: bio
in subset: data

Tool metadata
type: Class
subclass of: Resource metadata
Created in: beta12orEarlier
has definition: Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.
in subset: bio
in subset: data

Job metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: Textual metadata on a submitted or completed job.
in subset: obsolete
deprecated: true

User metadata
type: Class
subclass of: Resource metadata
Created in: beta12orEarlier
has definition: Textual metadata on a software author or end-user, for example a person or other software.
in subset: bio
in subset: data

Small molecule report
type: Class
subclass of: Structure report
subclass of: Restriction
  on property: has topic
  some values from: Small molecules
Created in: beta12orEarlier
has definition: A human-readable collection of information about a specific chemical compound.
has exact synonym: Chemical compound annotation
has exact synonym: Chemical structure report
has exact synonym: Small molecule annotation
in subset: bio
in subset: data

Cell line report
type: Class
subclass of: Organism report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Cell line annotation
has exact synonym: Organism strain data
in subset: bio
in subset: data

Scent annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report about a specific scent.
in subset: obsolete
deprecated: true

Ontology term
type: Class
subclass of: Ontology concept data
Created in: beta12orEarlier
has definition: A term (name) from an ontology.
has exact synonym: Ontology class name
has exact synonym: Ontology terms
in subset: bio
in subset: data

Ontology concept data
type: Class
subclass of: Ontology data
Created in: beta12orEarlier
has definition: Data concerning or derived from a concept from a biological ontology.
has exact synonym: Ontology class metadata
has exact synonym: Ontology term metadata
in subset: bio
in subset: data

Keyword
type: Class
subclass of: Data
Created in: beta12orEarlier
has db xref: Moby:BooleanQueryString
has db xref: Moby:Global_Keyword
has db xref: Moby:QueryString
has db xref: Moby:Wildcard_Query
has definition: Keyword(s) or phrase(s) used (typically) for text-searching purposes.
has exact synonym: Phrases
has exact synonym: Term
in subset: bio
in subset: data
comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.

Citation
type: Class
subclass of: Text data
Created in: beta12orEarlier
has db xref: Moby:GCP_SimpleCitation
has db xref: Moby:Publication
has definition: Bibliographic data that uniquely identifies a scientific article, book or other published material.
has exact synonym: Bibliographic reference
has exact synonym: Reference
in subset: bio
in subset: data
comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.

Article
type: Class
subclass of: Text data
subclass of: Text
Created in: beta12orEarlier
has definition: A scientific text, typically a full text article from a scientific journal.
has narrow synonym: Article text
has narrow synonym: Scientific article
in subset: bio
in subset: data

Text mining report
type: Class
subclass of: Report
subclass of: Text data
Created in: beta12orEarlier
has definition: A human-readable collection of information resulting from text mining.
has exact synonym: Text mining output
in subset: bio
in subset: data
comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.

Entity identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: An identifier of a biological entity or phenomenon.
in subset: obsolete
deprecated: true

Data resource identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: An identifier of a data resource.
in subset: obsolete
deprecated: true

Identifier (by type of entity)
type: Class
subclass of: Identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier that identifies a particular type of data.
has exact synonym: Identifier (typed)
in subset: bio
in subset: data
in subset: identifiers
comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.

Tool identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a bioinformatics tool, e.g. an application or web service.
in subset: bio
in subset: data
in subset: identifiers

Discrete entity identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).
in subset: obsolete
deprecated: true

Entity feature identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: 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).
in subset: obsolete
deprecated: true

Entity collection identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: Name or other identifier of a collection of discrete biological entities.
in subset: obsolete
deprecated: true

Phenomenon identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: Name or other identifier of a physical, observable biological occurrence or event.
in subset: obsolete
deprecated: true

Molecule identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Name or other identifier of a molecule.
in subset: bio
in subset: data
in subset: identifiers

Atom ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier (e.g. character symbol) of a specific atom.
has exact synonym: Atom identifier
in subset: bio
in subset: data
in subset: identifiers

Molecule name
type: Class
subclass of: Molecule identifier
subclass of: Name
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Name of a specific molecule.
in subset: bio
in subset: data
in subset: identifiers

Molecule type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type a molecule.
in subset: obsolete
comment: For example, 'Protein', 'DNA', 'RNA' etc.
deprecated: true

Chemical identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Compound identifier
has definition: Unique identifier of a chemical compound.
in subset: obsolete
deprecated: true

Chromosome name
type: Class
subclass of: Molecule name
subclass of: Nucleic acid identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Chromosome report
Created in: beta12orEarlier
has definition: Name of a chromosome.
in subset: bio
in subset: data
in subset: identifiers

Peptide identifier
type: Class
subclass of: Molecule identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a peptide chain.
in subset: bio
in subset: data
in subset: identifiers

Protein identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Protein report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a protein.
in subset: bio
in subset: data
in subset: identifiers

Compound name
type: Class
subclass of: Molecule name
subclass of: Compound identifier
Created in: beta12orEarlier
has definition: Unique name of a chemical compound.
has exact synonym: Chemical name
in subset: bio
in subset: data
in subset: identifiers

Chemical registry number
type: Class
subclass of: Compound accession
Created in: beta12orEarlier
has definition: Unique registry number of a chemical compound.
in subset: bio
in subset: data
in subset: identifiers

Ligand identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Compound identifier
has definition: Code word for a ligand, for example from a PDB file.
in subset: obsolete
deprecated: true

Drug identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Drug structure
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a drug.
in subset: bio
in subset: data
in subset: identifiers

Amino acid identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Amino acid property
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an amino acid.
has exact synonym: Residue identifier
in subset: bio
in subset: data
in subset: identifiers

Nucleotide identifier
type: Class
subclass of: Compound identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Name or other identifier of a nucleotide.
in subset: bio
in subset: data
in subset: identifiers

Monosaccharide identifier
type: Class
subclass of: Compound identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a monosaccharide.
in subset: bio
in subset: data
in subset: identifiers

Chemical name (ChEBI)
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.
has exact synonym: ChEBI chemical name
in subset: bio
in subset: data
in subset: identifiers
comment: This is the recommended chemical name for use for example in database annotation.

Chemical name (IUPAC)
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: IUPAC recommended name of a chemical compound.
has exact synonym: IUPAC chemical name
in subset: bio
in subset: data
in subset: identifiers

Chemical name (INN)
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO).
has exact synonym: INN chemical name
in subset: bio
in subset: data
in subset: identifiers

Chemical name (brand)
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: Brand name of a chemical compound.
has exact synonym: Brand chemical name
in subset: bio
in subset: data
in subset: identifiers

Chemical name (synonymous)
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: Synonymous name of a chemical compound.
has exact synonym: Synonymous chemical name
in subset: bio
in subset: data
in subset: identifiers

CAS number
type: Class
subclass of: Chemical registry number
subclass of: Accession
subclass of: Drug accession
Created in: beta12orEarlier
has definition: CAS registry number of a chemical compound; a unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
has exact synonym: CAS chemical registry number
has exact synonym: Chemical registry number (CAS)
in subset: bio
in subset: data
in subset: identifiers

Chemical registry number (Beilstein)
type: Class
subclass of: Chemical registry number
subclass of: Accession
Created in: beta12orEarlier
has definition: Beilstein registry number of a chemical compound.
has exact synonym: Beilstein chemical registry number
in subset: bio
in subset: data
in subset: identifiers

Chemical registry number (Gmelin)
type: Class
subclass of: Chemical registry number
subclass of: Accession
Created in: beta12orEarlier
has definition: Gmelin registry number of a chemical compound.
has exact synonym: Gmelin chemical registry number
in subset: bio
in subset: data
in subset: identifiers

HET group name
type: Class
subclass of: Compound name
Created in: beta12orEarlier
has definition: 3-letter code word for a ligand (HET group) from a PDB file, for example ATP.
has exact synonym: Component identifier code
has exact synonym: Short ligand name
in subset: bio
in subset: data
in subset: identifiers

Amino acid name
type: Class
subclass of: Amino acid identifier
Created in: beta12orEarlier
has definition: String of one or more ASCII characters representing an amino acid.
in subset: bio
in subset: data
in subset: identifiers

Nucleotide code
type: Class
subclass of: Compound name
subclass of: Nucleotide identifier
Created in: beta12orEarlier
has definition: String of one or more ASCII characters representing a nucleotide.
in subset: bio
in subset: data
in subset: identifiers

Polypeptide chain ID
type: Class
subclass of: Peptide identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Protein chain
Created in: beta12orEarlier
has db xref: PDBML:pdbx_PDB_strand_id
has db xref: WHATIF: chain
has definition: Identifier of a polypeptide chain from a protein.
has exact synonym: Chain identifier
has exact synonym: PDB chain identifier
has exact synonym: PDB strand id
has exact synonym: Polypeptide chain identifier
has exact synonym: Protein chain identifier
in subset: bio
in subset: data
in subset: identifiers
comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA

Protein name
type: Class
subclass of: Molecule name
subclass of: Protein identifier
Created in: beta12orEarlier
has definition: Name of a protein.
in subset: bio
in subset: data
in subset: identifiers

Enzyme identifier
type: Class
subclass of: Protein identifier
Created in: beta12orEarlier
has definition: Name or other identifier of an enzyme or record from a database of enzymes.
in subset: bio
in subset: data
in subset: identifiers

EC number
type: Class
subclass of: Accession
subclass of: Enzyme ID
Created in: beta12orEarlier
Regular expression: [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+
has db xref: Moby:Annotated_EC_Number
has db xref: Moby:EC_Number
has definition: An Enzyme Commission (EC) number of an enzyme.
has exact synonym: EC
has exact synonym: EC code
has exact synonym: Enzyme Commission number
in subset: bio
in subset: data
in subset: identifiers

Enzyme name
type: Class
subclass of: Protein name
subclass of: Enzyme identifier
Created in: beta12orEarlier
has definition: Name of an enzyme.
in subset: bio
in subset: data
in subset: identifiers

Restriction enzyme name
type: Class
subclass of: Enzyme name
Created in: beta12orEarlier
has definition: Name of a restriction enzyme.
in subset: bio
in subset: data
in subset: identifiers

Sequence position specification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence position
has definition: A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.
in subset: obsolete
deprecated: true

Sequence feature ID
type: Class
subclass of: Sequence feature identifier
Created in: beta12orEarlier
has definition: A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.
in subset: bio
in subset: data
in subset: identifiers

Sequence position
type: Class
subclass of: Sequence attribute
Created in: beta12orEarlier
has db xref: PDBML:_atom_site.id
has db xref: WHATIF: PDBx_atom_site
has db xref: WHATIF: number
has definition: A position of one or more points (base or residue) in a sequence, or part of such a specification.
has related synonym: SO:0000735
in subset: bio
in subset: data

Sequence range
type: Class
subclass of: Sequence attribute
Created in: beta12orEarlier
has definition: Specification of range(s) of sequence positions.
in subset: bio
in subset: data

Nucleic acid feature identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence feature ID
has definition: Name or other identifier of an nucleic acid feature.
in subset: obsolete
deprecated: true

Protein feature identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence feature ID
has definition: Name or other identifier of a protein feature.
in subset: obsolete
deprecated: true

Sequence feature key
type: Class
subclass of: Sequence features metadata
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Sequence feature method
has exact synonym: Sequence feature type
in subset: bio
in subset: data
comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.

Sequence feature qualifier
type: Class
subclass of: Sequence features metadata
Created in: beta12orEarlier
has definition: Typically one of the EMBL or Swiss-Prot feature qualifiers.
in subset: bio
in subset: data
comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location.

Sequence feature label
type: Class
subclass of: Name
subclass of: Sequence features metadata
subclass of: Sequence feature identifier
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Sequence feature name
in subset: bio
in subset: data
comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.

EMBOSS Uniform Feature Object
type: Class
subclass of: Name
subclass of: Sequence feature identifier
Created in: beta12orEarlier
has definition: The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.
has exact synonym: UFO
in subset: bio
in subset: data

Codon name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: String of one or more ASCII characters representing a codon.
in subset: obsolete
deprecated: true

Gene identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Gene report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has db xref: Moby:GeneAccessionList
has definition: An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.
in subset: bio
in subset: data
in subset: identifiers

Gene symbol
type: Class
subclass of: Gene name
Created in: beta12orEarlier
has db xref: Moby_namespace:Global_GeneCommonName
has db xref: Moby_namespace:Global_GeneSymbol
has definition: The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (NCBI)
type: Class
subclass of: RefSeq accession
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene
has definition: An NCBI unique identifier of a gene.
has exact synonym: Entrez gene ID
has exact synonym: Gene identifier (Entrez)
has exact synonym: Gene identifier (NCBI)
has exact synonym: NCBI gene ID
has exact synonym: NCBI geneid
in subset: bio
in subset: data
in subset: identifiers

Gene identifier (NCBI RefSeq)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene ID (NCBI)
has definition: An NCBI RefSeq unique identifier of a gene.
in subset: obsolete
deprecated: true

Gene identifier (NCBI UniGene)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence cluster ID (UniGene)
has definition: An NCBI UniGene unique identifier of a gene.
in subset: obsolete
deprecated: true

Gene identifier (Entrez)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene ID (NCBI)
has definition: An Entrez unique identifier of a gene.
in subset: obsolete
deprecated: true

Gene ID (CGD)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of a gene or feature from the CGD database.
has exact synonym: CGD ID
in subset: bio
in subset: data
in subset: identifiers

Gene ID (DictyBase)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of a gene from DictyBase.
in subset: bio
in subset: data
in subset: identifiers

Ensembl gene ID
type: Class
subclass of: Accession
subclass of: Gene ID
subclass of: Ensembl ID
Created in: beta12orEarlier
has definition: Unique identifier for a gene (or other feature) from the Ensembl database.
has exact synonym: Gene ID (Ensembl)
in subset: bio
in subset: data
in subset: identifiers

Gene ID (SGD)
type: Class
subclass of: Accession
subclass of: Gene ID
subclass of: SGD ID
Created in: beta12orEarlier
Regular expression: S[0-9]+
has definition: Identifier of an entry from the SGD database.
has exact synonym: SGD identifier
in subset: bio
in subset: data
in subset: identifiers

Gene ID (GeneDB)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9\.-]*
has db xref: Moby_namespace:GeneDB
has definition: Identifier of a gene from the GeneDB database.
has exact synonym: GeneDB identifier
in subset: bio
in subset: data
in subset: identifiers

TIGR identifier
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of an entry from the TIGR database.
in subset: bio
in subset: data
in subset: identifiers

TAIR accession (gene)
type: Class
subclass of: Gene ID
subclass of: TAIR accession
Created in: beta12orEarlier
Regular expression: Gene:[0-9]{7}
has definition: Identifier of an gene from the TAIR database.
in subset: bio
in subset: data
in subset: identifiers

Protein domain ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Protein domain
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a protein structural domain.
in subset: bio
in subset: data
in subset: identifiers
comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier.

SCOP domain identifier
type: Class
subclass of: Protein domain ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a protein domain (or other node) from the SCOP database.
in subset: bio
in subset: data
in subset: identifiers

CATH domain ID
type: Class
subclass of: CATH identifier
Created in: beta12orEarlier
Example: 1nr3A00
has definition: Identifier of a protein domain from CATH.
has exact synonym: CATH domain identifier
in subset: bio
in subset: data
in subset: identifiers

SCOP concise classification string (sccs)
type: Class
subclass of: SCOP domain identifier
Created in: beta12orEarlier
has definition: A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.
in subset: bio
in subset: data
in subset: identifiers
comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.

SCOP sunid
type: Class
subclass of: SCOP domain identifier
Created in: beta12orEarlier
Example: 33229
has definition: Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.
has exact synonym: SCOP unique identifier
has exact synonym: sunid
in subset: bio
in subset: data
in subset: identifiers
comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.

CATH node ID
type: Class
subclass of: CATH identifier
Created in: beta12orEarlier
Example: 3.30.1190.10.1.1.1.1.1
has definition: A code number identifying a node from the CATH database.
has exact synonym: CATH code
has exact synonym: CATH node identifier
in subset: bio
in subset: data
in subset: identifiers

Kingdom name
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).
in subset: bio
in subset: data
in subset: identifiers

Species name
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a species (typically a taxonomic group) of organism.
has exact synonym: Organism species
in subset: bio
in subset: data
in subset: identifiers

Strain name
type: Class
subclass of: Strain identifier
subclass of: Organism name
Created in: beta12orEarlier
has definition: The name of a strain of an organism variant, typically a plant, virus or bacterium.
in subset: bio
in subset: data
in subset: identifiers

URI
type: Class
subclass of: Identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A string of characters that name or otherwise identify a resource on the Internet.
has exact synonym: URIs
in subset: bio
in subset: data

Database ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Database metadata
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a biological or bioinformatics database.
has exact synonym: Database identifier
in subset: bio
in subset: data
in subset: identifiers

Directory name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a directory.
in subset: bio
in subset: data
in subset: identifiers

File name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name (or part of a name) of a file (of any type).
in subset: bio
in subset: data
in subset: identifiers

Ontology name
type: Class
subclass of: Name
subclass of: Ontology identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Ontology
Created in: beta12orEarlier
has definition: Name of an ontology of biological or bioinformatics concepts and relations.
in subset: bio
in subset: data
in subset: identifiers

URL
type: Class
subclass of: URI
Created in: beta12orEarlier
has db xref: Moby:Link
has db xref: Moby:URL
has definition: A Uniform Resource Locator (URL).
in subset: bio
in subset: data

URN
type: Class
subclass of: URI
Created in: beta12orEarlier
has definition: A Uniform Resource Name (URN).
in subset: bio
in subset: data

LSID
type: Class
subclass of: URN
Created in: beta12orEarlier
has definition: A Life Science Identifier (LSID) - a unique identifier of some data.
has exact synonym: Life Science Identifier
in subset: bio
in subset: data
comment: 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>]

Database name
type: Class
subclass of: Database ID
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a biological or bioinformatics database.
in subset: bio
in subset: data
in subset: identifiers

Sequence database name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Database name
has definition: The name of a molecular sequence database.
in subset: obsolete
deprecated: true

Enumerated file name
type: Class
subclass of: File name
Created in: beta12orEarlier
has definition: The name of a file (of any type) with restricted possible values.
in subset: bio
in subset: data
in subset: identifiers

File name extension
type: Class
subclass of: File name
Created in: beta12orEarlier
has definition: The extension of a file name.
in subset: bio
in subset: data
in subset: identifiers
comment: A file extension is the characters appearing after the final '.' in the file name.

File base name
type: Class
subclass of: File name
Created in: beta12orEarlier
has definition: The base name of a file.
in subset: bio
in subset: data
in subset: identifiers
comment: A file base name is the file name stripped of its directory specification and extension.

QSAR descriptor name
type: Class
subclass of: Name
subclass of: Molecular property identifier
subclass of: Restriction
  on property: is identifier of
  some values from: QSAR descriptor
Created in: beta12orEarlier
has definition: Name of a QSAR descriptor.
in subset: bio
in subset: data
in subset: identifiers

Database entry identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.
in subset: obsolete
comment: This concept is required for completeness. It should never have child concepts.
deprecated: true

Sequence identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of molecular sequence(s) or entries from a molecular sequence database.
in subset: bio
in subset: data
in subset: identifiers

Sequence set ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence set
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a set of molecular sequence(s).
in subset: bio
in subset: data
in subset: identifiers

Sequence signature identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence motif identifier
consider: Sequence profile ID
has definition: Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.
in subset: obsolete
deprecated: true

Sequence alignment ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence alignment
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a molecular sequence alignment, for example a record from an alignment database.
in subset: bio
in subset: data
in subset: identifiers

Phylogenetic distance matrix identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier (by type of entity)
has definition: Identifier of a phylogenetic distance matrix.
in subset: obsolete
deprecated: true

Phylogenetic tree ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Phylogenetic tree
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a phylogenetic tree for example from a phylogenetic tree database.
in subset: bio
in subset: data
in subset: identifiers

Comparison matrix identifier
type: Class
subclass of: Matrix identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Comparison matrix
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a comparison matrix.
has exact synonym: Substitution matrix identifier
in subset: bio
in subset: data
in subset: identifiers

Structure ID
type: Class
subclass of: Structure identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.
in subset: bio
in subset: data
in subset: identifiers

Structural (3D) profile ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Structural profile
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).
has exact synonym: Structural profile identifier
in subset: bio
in subset: data
in subset: identifiers

Structure alignment ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Structure alignment
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of tertiary structure alignments.
in subset: bio
in subset: data
in subset: identifiers

Amino acid index ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Matrix identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Amino acid index
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an index of amino acid physicochemical and biochemical property data.
in subset: bio
in subset: data
in subset: identifiers

Protein interaction ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Protein interaction data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has broad synonym: Molecular interaction ID
has definition: Identifier of a report of protein interactions from a protein interaction database (typically).
in subset: bio
in subset: data
in subset: identifiers

Protein family identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Protein family report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a protein family.
has exact synonym: Protein secondary database record identifier
in subset: bio
in subset: data
in subset: identifiers

Codon usage table name
type: Class
subclass of: Name
subclass of: Codon usage table ID
subclass of: Restriction
  on property: is identifier of
  some values from: Codon usage table
subclass of: Restriction
  on property: is identifier of
  some values from: Genetic code
Created in: beta12orEarlier
has definition: Unique name of a codon usage table.
in subset: bio
in subset: data
in subset: identifiers

Transcription factor identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Protein identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a transcription factor (or a TF binding site).
in subset: bio
in subset: data
in subset: identifiers

Experiment annotation ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Protocol
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of microarray data.
in subset: bio
in subset: data
in subset: identifiers

Electron microscopy model ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: 3D EM Map
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of electron microscopy data.
in subset: bio
in subset: data
in subset: identifiers

Gene expression report ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Processed microarray data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a report of gene expression (e.g. a gene expression profile) from a database.
has exact synonym: Gene expression profile identifier
in subset: bio
in subset: data
in subset: identifiers

Genotype and phenotype annotation ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Genotype/phenotype report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of genotypes and phenotypes.
in subset: bio
in subset: data
in subset: identifiers

Pathway or network identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Pathway or network
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of biological pathways or networks.
in subset: bio
in subset: data
in subset: identifiers

Workflow ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a biological or biomedical workflow, typically from a database of workflows.
in subset: bio
in subset: data
in subset: identifiers

Data resource definition ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a data type definition from some provider.
has exact synonym: Data resource definition identifier
in subset: bio
in subset: data
in subset: identifiers

Biological model ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Mathematical model
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a mathematical model, typically an entry from a database.
has exact synonym: Biological model identifier
in subset: bio
in subset: data
in subset: identifiers

Compound identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Small molecule report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of chemicals.
has exact synonym: Chemical compound identifier
has exact synonym: Compound ID
has exact synonym: Small molecule identifier
in subset: bio
in subset: data
in subset: identifiers

Ontology concept ID
type: Class
subclass of: Ontology concept identifier
Created in: beta12orEarlier
has definition: A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
in subset: bio
in subset: data
in subset: identifiers

Article ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Article
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Unique identifier of a scientific article.
has exact synonym: Article identifier
in subset: bio
in subset: data
in subset: identifiers

FlyBase ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
Regular expression: FB[a-zA-Z_0-9]{2}[0-9]{7}
has definition: Identifier of an object from the FlyBase database.
in subset: bio
in subset: data
in subset: identifiers

WormBase name
type: Class
subclass of: Name
subclass of: WormBase identifier
Created in: beta12orEarlier
has definition: Name of an object from the WormBase database, usually a human-readable name.
in subset: bio
in subset: data
in subset: identifiers

WormBase class
type: Class
subclass of: WormBase identifier
Created in: beta12orEarlier
has definition: Class of an object from the WormBase database.
in subset: bio
in subset: data
in subset: identifiers
comment: A WormBase class describes the type of object such as 'sequence' or 'protein'.

Sequence accession
type: Class
subclass of: Sequence identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A persistent, unique identifier of a molecular sequence database entry.
has exact synonym: Sequence accession number
in subset: bio
in subset: data
in subset: identifiers

Sequence type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing a type of molecular sequence.
in subset: obsolete
comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
deprecated: true

EMBOSS Uniform Sequence Address
type: Class
subclass of: Sequence identifier
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.
has exact synonym: EMBOSS USA
in subset: bio
in subset: data
in subset: identifiers

Sequence accession (protein)
type: Class
subclass of: Sequence accession
subclass of: Restriction
  on property: is identifier of
  some values from: Protein sequence
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession number of a protein sequence database entry.
has exact synonym: Protein sequence accession number
in subset: bio
in subset: data
in subset: identifiers

Sequence accession (nucleic acid)
type: Class
subclass of: Sequence accession
subclass of: Restriction
  on property: is identifier of
  some values from: Nucleic acid sequence
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession number of a nucleotide sequence database entry.
has exact synonym: Nucleotide sequence accession number
in subset: bio
in subset: data
in subset: identifiers

RefSeq accession
type: Class
subclass of: Accession
subclass of: Sequence accession (hybrid)
Created in: beta12orEarlier
Regular expression: (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+
has definition: Accession number of a RefSeq database entry.
has exact synonym: RefSeq ID
in subset: bio
in subset: data
in subset: identifiers

UniProt accession (extended)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: UniProt accession
has definition: Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.
in subset: obsolete
deprecated: true

PIR identifier
type: Class
subclass of: Sequence accession (protein)
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of PIR sequence database entry.
has exact synonym: PIR ID
has exact synonym: PIR accession number
in subset: bio
in subset: data
in subset: identifiers

TREMBL accession
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.2
Old parent: Thing
has definition: Identifier of a TREMBL sequence database entry.
in subset: obsolete
replaced by: UniProt accession
deprecated: true

Gramene primary identifier
type: Class
subclass of: Gramene identifier
Created in: beta12orEarlier
has definition: Primary identifier of a Gramene database entry.
has exact synonym: Gramene primary ID
in subset: bio
in subset: data
in subset: identifiers

EMBL/GenBank/DDBJ ID
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (UniGene)
type: Class
subclass of: Sequence cluster ID
subclass of: Accession
Created in: beta12orEarlier
has definition: A unique identifier of an entry (gene cluster) from the NCBI UniGene database.
has exact synonym: UniGene ID
has exact synonym: UniGene cluster ID
has exact synonym: UniGene identifier
in subset: bio
in subset: data
in subset: identifiers

dbEST accession
type: Class
subclass of: Accession
subclass of: GenBank accession
subclass of: EST accession
Created in: beta12orEarlier
has definition: Identifier of a dbEST database entry.
has exact synonym: dbEST ID
in subset: bio
in subset: data
in subset: identifiers

dbSNP ID
type: Class
subclass of: Accession
subclass of: Sequence variation ID
Created in: beta12orEarlier
has definition: Identifier of a dbSNP database entry.
has exact synonym: dbSNP identifier
in subset: bio
in subset: data
in subset: identifiers

EMBOSS sequence type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence attribute
has definition: The EMBOSS type of a molecular sequence.
in subset: obsolete
comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.
deprecated: true

EMBOSS listfile
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: ID list
has definition: List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).
in subset: obsolete
deprecated: true

Sequence cluster ID
type: Class
subclass of: Sequence set ID
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence cluster
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a cluster of molecular sequence(s).
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (COG)
type: Class
subclass of: Sequence cluster ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the COG database.
has exact synonym: COG ID
in subset: bio
in subset: data
in subset: identifiers

Sequence motif identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence motif
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a sequence motif, for example an entry from a motif database.
in subset: bio
in subset: data
in subset: identifiers

Sequence profile ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence profile
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a sequence profile.
in subset: bio
in subset: data
in subset: identifiers
comment: A sequence profile typically represents a sequence alignment.

ELM ID
type: Class
subclass of: Sequence motif identifier
Created in: beta12orEarlier
has definition: Identifier of an entry from the ELMdb database of protein functional sites.
in subset: bio
in subset: data
in subset: identifiers

Prosite accession number
type: Class
subclass of: Sequence motif identifier
Created in: beta12orEarlier
Regular expression: PS[0-9]{5}
has definition: Accession number of an entry from the Prosite database.
has exact synonym: Prosite ID
in subset: bio
in subset: data
in subset: identifiers

HMMER hidden Markov model ID
type: Class
subclass of: Sequence profile ID
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Hidden Markov model
Created in: beta12orEarlier
has definition: Unique identifier or name of a HMMER hidden Markov model.
in subset: bio
in subset: data
in subset: identifiers

JASPAR profile ID
type: Class
subclass of: Sequence profile ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier or name of a profile from the JASPAR database.
in subset: bio
in subset: data
in subset: identifiers

Sequence alignment type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of a sequence alignment.
in subset: obsolete
comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
deprecated: true

BLAST sequence alignment type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence attribute
has definition: The type of a BLAST sequence alignment.
in subset: obsolete
deprecated: true

Phylogenetic tree type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of a phylogenetic tree.
in subset: obsolete
comment: For example 'nj', 'upgmp' etc.
deprecated: true

TreeBASE study accession number
type: Class
subclass of: Phylogenetic tree ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession number of an entry from the TreeBASE database.
in subset: bio
in subset: data
in subset: identifiers

TreeFam accession number
type: Class
subclass of: Phylogenetic tree ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession number of an entry from the TreeFam database.
in subset: bio
in subset: data
in subset: identifiers

Comparison matrix type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of a comparison matrix.
in subset: obsolete
comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.
deprecated: true

Comparison matrix name
type: Class
subclass of: Comparison matrix identifier
subclass of: Name
subclass of: Restriction
  on property: is identifier of
  some values from: Comparison matrix
Created in: beta12orEarlier
has definition: Unique name or identifier of a comparison matrix.
has exact synonym: Substitution matrix name
in subset: bio
in subset: data
in subset: identifiers
comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.

PDB ID
type: Class
subclass of: Structure ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9][a-zA-Z_0-9]{3}
has definition: An identifier of an entry from the PDB database.
has exact synonym: PDB identifier
has exact synonym: PDBID
in subset: bio
in subset: data
in subset: identifiers
comment: 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)

AAindex ID
type: Class
subclass of: Amino acid index ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the AAindex database.
in subset: bio
in subset: data
in subset: identifiers

BIND accession number
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession number of an entry from the BIND database.
in subset: bio
in subset: data
in subset: identifiers

IntAct accession number
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: EBI\-[0-9]+
has definition: Accession number of an entry from the IntAct database.
in subset: bio
in subset: data
in subset: identifiers

Protein family name
type: Class
subclass of: Protein family identifier
subclass of: Name
Created in: beta12orEarlier
has definition: Name of a protein family.
in subset: bio
in subset: data
in subset: identifiers

InterPro entry name
type: Class
subclass of: Protein family name
subclass of: Restriction
  on property: is identifier of
  some values from: Protein signature
Created in: beta12orEarlier
has definition: Name of an InterPro entry, usually indicating the type of protein matches for that entry.
in subset: bio
in subset: data
in subset: identifiers

InterPro accession
type: Class
subclass of: Accession
subclass of: Protein family accession
subclass of: Restriction
  on property: is identifier of
  some values from: Protein signature
Created in: beta12orEarlier
Example: IPR015590
Regular expression: IPR[0-9]{6}
has definition: Primary accession number of an InterPro entry.
has exact synonym: InterPro primary accession
has exact synonym: InterPro primary accession number
in subset: bio
in subset: data
in subset: identifiers
comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records.

InterPro secondary accession
type: Class
subclass of: InterPro accession
subclass of: Restriction
  on property: is identifier of
  some values from: Protein signature
Created in: beta12orEarlier
has definition: Secondary accession number of an InterPro entry.
has exact synonym: InterPro secondary accession number
in subset: bio
in subset: data
in subset: identifiers

Gene3D ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the Gene3D database.
in subset: bio
in subset: data
in subset: identifiers

PIRSF ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: PIRSF[0-9]{6}
has definition: Unique identifier of an entry from the PIRSF database.
in subset: bio
in subset: data
in subset: identifiers

PRINTS code
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: PR[0-9]{5}
has definition: The unique identifier of an entry in the PRINTS database.
in subset: bio
in subset: data
in subset: identifiers

Pfam accession number
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: PF[0-9]{5}
has definition: Accession number of a Pfam entry.
in subset: bio
in subset: data
in subset: identifiers

SMART accession number
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: SM[0-9]{5}
has definition: Accession number of an entry from the SMART database.
in subset: bio
in subset: data
in subset: identifiers

Superfamily hidden Markov model number
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Unique identifier (number) of a hidden Markov model from the Superfamily database.
in subset: bio
in subset: data
in subset: identifiers

TIGRFam ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Accession number of an entry (family) from the TIGRFam database.
has exact synonym: TIGRFam accession number
in subset: bio
in subset: data
in subset: identifiers

ProDom accession number
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: PD[0-9]+
has definition: A ProDom domain family accession number.
in subset: bio
in subset: data
in subset: identifiers
comment: ProDom is a protein domain family database.

TRANSFAC accession number
type: Class
subclass of: Accession
subclass of: Transcription factor accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the TRANSFAC database.
in subset: bio
in subset: data
in subset: identifiers

ArrayExpress accession number
type: Class
subclass of: Experiment annotation ID
Created in: beta12orEarlier
Regular expression: [AEP]-[a-zA-Z_0-9]{4}-[0-9]+
has definition: Accession number of an entry from the ArrayExpress database.
has exact synonym: ArrayExpress experiment ID
in subset: bio
in subset: data
in subset: identifiers

PRIDE experiment accession number
type: Class
subclass of: Experiment annotation ID
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: PRIDE experiment accession number.
in subset: bio
in subset: data
in subset: identifiers

EMDB ID
type: Class
subclass of: Electron microscopy model ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the EMDB electron microscopy database.
in subset: bio
in subset: data
in subset: identifiers

GEO accession number
type: Class
subclass of: Gene expression report ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [GDS|GPL|GSE|GSM][0-9]+
has definition: Accession number of an entry from the GEO database.
in subset: bio
in subset: data
in subset: identifiers

GermOnline ID
type: Class
subclass of: Gene expression report ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the GermOnline database.
in subset: bio
in subset: data
in subset: identifiers

EMAGE ID
type: Class
subclass of: Gene expression report ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the EMAGE database.
in subset: bio
in subset: data
in subset: identifiers

Disease ID
type: Class
subclass of: Disease identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession number of an entry from a database of disease.
in subset: bio
in subset: data
in subset: identifiers

HGVbase ID
type: Class
subclass of: Genotype and phenotype annotation ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the HGVbase database.
in subset: bio
in subset: data
in subset: identifiers

HIVDB identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Identifier
has definition: Identifier of an entry from the HIVDB database.
in subset: obsolete
deprecated: true

OMIM ID
type: Class
subclass of: Genotype and phenotype annotation ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [*#+%^]?[0-9]{6}
has definition: Identifier of an entry from the OMIM database.
in subset: bio
in subset: data
in subset: identifiers

KEGG object identifier
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Unique identifier of an object from one of the KEGG databases (excluding the GENES division).
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (reactome)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: REACT_[0-9]+(\.[0-9]+)?
has definition: Identifier of an entry from the Reactome database.
has exact synonym: Reactome ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (aMAZE)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Pathway or network identifier
has definition: Identifier of an entry from the aMAZE database.
in subset: obsolete
deprecated: true

Pathway ID (BioCyc)
type: Class
subclass of: Accession
subclass of: BioCyc ID
subclass of: Pathway or network accession
Created in: beta12orEarlier
has definition: Identifier of an pathway from the BioCyc biological pathways database.
has exact synonym: BioCyc pathway ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (INOH)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the INOH database.
has exact synonym: INOH identifier
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (PATIKA)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the PATIKA database.
has exact synonym: PATIKA ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (CPDB)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.
has exact synonym: CPDB ID
in subset: bio
in subset: data
in subset: identifiers
comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.

Pathway ID (Panther)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: PTHR[0-9]{5}
has definition: Identifier of a biological pathway from the Panther Pathways database.
has exact synonym: Panther Pathways ID
in subset: bio
in subset: data
in subset: identifiers

MIRIAM identifier
type: Class
subclass of: Accession
subclass of: Data resource definition accession
subclass of: Restriction
  on property: is identifier of
  some values from: Database metadata
Created in: beta12orEarlier
Example: MIR:00100005
Regular expression: MIR:[0-9]{8}
has definition: Unique identifier of a MIRIAM data resource.
in subset: bio
in subset: data
in subset: identifiers
comment: This is the identifier used internally by MIRIAM for a data type.

MIRIAM data type name
type: Class
subclass of: Data resource definition name
subclass of: Restriction
  on property: is identifier of
  some values from: Database metadata
Created in: beta12orEarlier
has definition: The name of a data type from the MIRIAM database.
in subset: bio
in subset: data
in subset: identifiers

MIRIAM URI
type: Class
subclass of: URI
subclass of: Accession
subclass of: Data resource definition accession
subclass of: Restriction
  on property: is identifier of
  some values from: Database metadata
Created in: beta12orEarlier
Example: urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202
has definition: The URI (URL or URN) of a data entity from the MIRIAM database.
has exact synonym: identifiers.org synonym
in subset: bio
in subset: data
in subset: identifiers
comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.

MIRIAM data type primary name
type: Class
subclass of: MIRIAM data type name
Created in: beta12orEarlier
Example: UniProt|Enzyme Nomenclature
has definition: The primary name of a data type from the MIRIAM database.
in subset: bio
in subset: data
in subset: identifiers
comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary.

Axiom
annotated source: MIRIAM data type primary name
annotated property: Example
annotated target: UniProt|Enzyme Nomenclature
comment: A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'.

MIRIAM data type synonymous name
type: Class
subclass of: MIRIAM data type name
Created in: beta12orEarlier
has definition: A synonymous name of a data type from the MIRIAM database.
in subset: bio
in subset: data
in subset: identifiers
comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary.

Taverna workflow ID
type: Class
subclass of: Workflow ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of a Taverna workflow.
in subset: bio
in subset: data
in subset: identifiers

Biological model name
type: Class
subclass of: Biological model ID
subclass of: Name
Created in: beta12orEarlier
has definition: Name of a biological (mathematical) model.
in subset: bio
in subset: data
in subset: identifiers

BioModel ID
type: Class
subclass of: Accession
subclass of: Biological model accession
Created in: beta12orEarlier
Regular expression: (BIOMD|MODEL)[0-9]{10}
has definition: Unique identifier of an entry from the BioModel database.
in subset: bio
in subset: data
in subset: identifiers

PubChem CID
type: Class
subclass of: PubChem ID
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.
has exact synonym: PubChem compound accession identifier
in subset: bio
in subset: data
in subset: identifiers

ChemSpider ID
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of an entry from the ChemSpider database.
in subset: bio
in subset: data
in subset: identifiers

ChEBI ID
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: CHEBI:[0-9]+
has definition: Identifier of an entry from the ChEBI database.
has exact synonym: ChEBI IDs
has exact synonym: ChEBI identifier
in subset: bio
in subset: data
in subset: identifiers

BioPax concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the BioPax ontology.
in subset: bio
in subset: data
in subset: identifiers

GO concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
has definition: An identifier of a concept from The Gene Ontology.
has exact synonym: GO concept identifier
in subset: bio
in subset: data
in subset: identifiers

MeSH concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the MeSH vocabulary.
in subset: bio
in subset: data
in subset: identifiers

HGNC concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the HGNC controlled vocabulary.
in subset: bio
in subset: data
in subset: identifiers

NCBI taxonomy ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
subclass of: Organism accession
Created in: beta12orEarlier
Example: 9662|3483|182682
Regular expression: [1-9][0-9]{0,8}
has definition: A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.
has exact synonym: NCBI tax ID
has exact synonym: NCBI taxonomy identifier
in subset: bio
in subset: data
in subset: identifiers

Plant Ontology concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the Plant Ontology (PO).
in subset: bio
in subset: data
in subset: identifiers

UMLS concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the UMLS vocabulary.
in subset: bio
in subset: data
in subset: identifiers

FMA concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: FMA:[0-9]+
has definition: An identifier of a concept from Foundational Model of Anatomy.
in subset: bio
in subset: data
in subset: identifiers
comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.

EMAP concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the EMAP mouse ontology.
in subset: bio
in subset: data
in subset: identifiers

ChEBI concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the ChEBI ontology.
in subset: bio
in subset: data
in subset: identifiers

MGED concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the MGED ontology.
in subset: bio
in subset: data
in subset: identifiers

myGrid concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a concept from the myGrid ontology.
in subset: bio
in subset: data
in subset: identifiers
comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.

PubMed ID
type: Class
subclass of: Article ID
subclass of: Accession
Created in: beta12orEarlier
Example: 4963447
Regular expression: [1-9][0-9]{0,8}
has definition: PubMed unique identifier of an article.
has exact synonym: PMID
in subset: bio
in subset: data
in subset: identifiers

DOI
type: Class
subclass of: Article ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: (doi\:)?[0-9]{2}\.[0-9]{4}/.*
has definition: Digital Object Identifier (DOI) of a published article.
has exact synonym: Digital Object Identifier
in subset: bio
in subset: data
in subset: identifiers

Medline UI
type: Class
subclass of: Article ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Medline UI (unique identifier) of an article.
has exact synonym: Medline unique identifier
in subset: bio
in subset: data
in subset: identifiers
comment: The use of Medline UI has been replaced by the PubMed unique identifier.

Tool name
type: Class
subclass of: Tool identifier
Created in: beta12orEarlier
has definition: The name of a computer package, application, method or function.
in subset: bio
in subset: data
in subset: identifiers

Tool name (signature)
type: Class
subclass of: Tool name
Created in: beta12orEarlier
has definition: The unique name of a signature (sequence classifier) method.
in subset: bio
in subset: data
in subset: identifiers
comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.

Tool name (BLAST)
type: Class
subclass of: Tool name
Created in: beta12orEarlier
has definition: The name of a BLAST tool.
has exact synonym: BLAST name
in subset: bio
in subset: data
in subset: identifiers
comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.

Tool name (FASTA)
type: Class
subclass of: Tool name
Created in: beta12orEarlier
has definition: The name of a FASTA tool.
in subset: bio
in subset: data
in subset: identifiers
comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.

Tool name (EMBOSS)
type: Class
subclass of: Tool name
Created in: beta12orEarlier
has definition: The name of an EMBOSS application.
in subset: bio
in subset: data
in subset: identifiers

Tool name (EMBASSY package)
type: Class
subclass of: Tool name
Created in: beta12orEarlier
has definition: The name of an EMBASSY package.
in subset: bio
in subset: data
in subset: identifiers

QSAR descriptor (constitutional)
type: Class
subclass of: QSAR descriptor
Created in: beta12orEarlier
has definition: A QSAR constitutional descriptor.
has exact synonym: QSAR constitutional descriptor
in subset: bio
in subset: data

QSAR descriptor (electronic)
type: Class
subclass of: QSAR descriptor
Created in: beta12orEarlier
has definition: A QSAR electronic descriptor.
has exact synonym: QSAR electronic descriptor
in subset: bio
in subset: data

QSAR descriptor (geometrical)
type: Class
subclass of: QSAR descriptor
Created in: beta12orEarlier
has definition: A QSAR geometrical descriptor.
has exact synonym: QSAR geometrical descriptor
in subset: bio
in subset: data

QSAR descriptor (topological)
type: Class
subclass of: QSAR descriptor
Created in: beta12orEarlier
has definition: A QSAR topological descriptor.
has exact synonym: QSAR topological descriptor
in subset: bio
in subset: data

QSAR descriptor (molecular)
type: Class
subclass of: QSAR descriptor
Created in: beta12orEarlier
has definition: A QSAR molecular descriptor.
has exact synonym: QSAR molecular descriptor
in subset: bio
in subset: data

Sequence set (protein)
type: Class
subclass of: Sequence set
Created in: beta12orEarlier
has definition: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
in subset: bio
in subset: data

Sequence set (nucleic acid)
type: Class
subclass of: Sequence set
Created in: beta12orEarlier
has definition: Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
in subset: bio
in subset: data

Sequence cluster
type: Class
subclass of: Sequence set
subclass of: Restriction
  on property: has topic
  some values from: Gene and protein families
Created in: beta12orEarlier
has definition: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
in subset: bio
in subset: data
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.

Psiblast checkpoint file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.
in subset: obsolete
comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.
deprecated: true

HMMER synthetic sequences set
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: Sequences generated by HMMER package in FASTA-style format.
in subset: obsolete
deprecated: true

Proteolytic digest
type: Class
subclass of: Sequence set (protein)
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.
in subset: bio
in subset: data

Restriction digest
type: Class
subclass of: Sequence set (nucleic acid)
Created in: beta12orEarlier
has db xref: SO:0000412
has definition: Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.
in subset: bio
in subset: data

PCR primers
type: Class
subclass of: Sequence set (nucleic acid)
Created in: beta12orEarlier
has definition: Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.
in subset: bio
in subset: data

vectorstrip cloning vector definition file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.
in subset: obsolete
deprecated: true

Primer3 internal oligo mishybridizing library
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: 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.
in subset: obsolete
deprecated: true

Primer3 mispriming library file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: 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.
in subset: obsolete
deprecated: true

primersearch primer pairs sequence record
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.
in subset: obsolete
deprecated: true

Sequence cluster (protein)
type: Class
subclass of: Sequence set (protein)
subclass of: Sequence cluster
Created in: beta12orEarlier
has definition: A cluster of protein sequences.
has exact synonym: Protein sequence cluster
in subset: bio
in subset: data
comment: The sequences are typically related, for example a family of sequences.

Sequence cluster (nucleic acid)
type: Class
subclass of: Sequence set (nucleic acid)
subclass of: Sequence cluster
Created in: beta12orEarlier
has definition: A cluster of nucleotide sequences.
has exact synonym: Nucleotide sequence cluster
in subset: bio
in subset: data
comment: The sequences are typically related, for example a family of sequences.

Sequence length
type: Class
subclass of: Sequence attribute
Created in: beta12orEarlier
has definition: The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
in subset: bio
in subset: data

Word size
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence length
has definition: Size of a sequence word.
in subset: obsolete
comment: Word size is used for example in word-based sequence database search methods.
deprecated: true

Window size
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence length
has definition: Size of a sequence window.
in subset: obsolete
comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.
deprecated: true

Sequence length range
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence length
has definition: Specification of range(s) of length of sequences.
in subset: obsolete
deprecated: true

Sequence information report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.
in subset: obsolete
replaced by: Sequence report
deprecated: true

Sequence property
type: Class
subclass of: Sequence report
Created in: beta12orEarlier
has definition: An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.
has exact synonym: Sequence properties report
in subset: bio
in subset: data

Sequence features
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.
has exact synonym: Feature record
has exact synonym: Features
has exact synonym: General sequence features
has exact synonym: Sequence features report
has related synonym: SO:0000110
in subset: bio
in subset: data
comment: 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 (comparative)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence features
has definition: Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

Sequence property (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein property
has definition: A report of general sequence properties derived from protein sequence data.
in subset: obsolete
deprecated: true

Sequence property (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid property
has definition: A report of general sequence properties derived from nucleotide sequence data.
in subset: obsolete
deprecated: true

Sequence complexity report
type: Class
subclass of: Sequence property
Created in: beta12orEarlier
has definition: A report on sequence complexity, for example low-complexity or repeat regions in sequences.
has exact synonym: Sequence property (complexity)
in subset: bio
in subset: data

Sequence ambiguity report
type: Class
subclass of: Sequence property
Created in: beta12orEarlier
has definition: A report on ambiguity in molecular sequence(s).
has exact synonym: Sequence property (ambiguity)
in subset: bio
in subset: data

Sequence composition report
type: Class
subclass of: Sequence property
Created in: beta12orEarlier
has definition: A report (typically a table) on character or word composition / frequency of a molecular sequence(s).
has exact synonym: Sequence composition
has exact synonym: Sequence property (composition)
in subset: bio
in subset: data

Peptide molecular weight hits
type: Class
subclass of: Sequence set (protein)
Created in: beta12orEarlier
has definition: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.
in subset: bio
in subset: data

Base position variability plot
type: Class
subclass of: Sequence composition report
Created in: beta12orEarlier
has definition: A plot of third base position variability in a nucleotide sequence.
in subset: bio
in subset: data

Sequence composition table
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence composition report
has definition: A table of character or word composition / frequency of a molecular sequence.
in subset: obsolete
deprecated: true

Base frequencies table
type: Class
subclass of: Sequence composition report
subclass of: Matrix
Created in: beta12orEarlier
has definition: A table of base frequencies of a nucleotide sequence.
in subset: bio
in subset: data

Base word frequencies table
type: Class
subclass of: Sequence composition report
subclass of: Matrix
Created in: beta12orEarlier
has definition: A table of word composition of a nucleotide sequence.
in subset: bio
in subset: data

Amino acid frequencies table
type: Class
subclass of: Sequence composition report
subclass of: Matrix
Created in: beta12orEarlier
has definition: A table of amino acid frequencies of a protein sequence.
has exact synonym: Sequence composition (amino acid frequencies)
in subset: bio
in subset: data

Amino acid word frequencies table
type: Class
subclass of: Sequence composition report
subclass of: Matrix
Created in: beta12orEarlier
has definition: A table of amino acid word composition of a protein sequence.
has exact synonym: Sequence composition (amino acid words)
in subset: bio
in subset: data

DAS sequence feature annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: DASGFF
has definition: Annotation of a molecular sequence in DAS format.
in subset: obsolete
deprecated: true

Feature table
type: Class
subclass of: Sequence features
Created in: beta12orEarlier
has definition: Annotation of positional sequence features, organised into a standard feature table.
has exact synonym: Sequence feature table
in subset: bio
in subset: data

Map
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: A map of (typically one) DNA sequence annotated with positional or non-positional features.
has exact synonym: DNA map
in subset: bio
in subset: data

Nucleic acid features
type: Class
subclass of: Sequence features
Created in: beta12orEarlier
has definition: An informative report on intrinsic positional features of a nucleotide sequence, formatted to be machine-readable.
has exact synonym: Feature table (nucleic acid)
has exact synonym: Nucleic acid feature table
has narrow synonym: Genome features
has narrow synonym: Genomic features
in subset: bio
in subset: data
comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.

Protein features
type: Class
subclass of: Protein report
subclass of: Sequence features
Created in: beta12orEarlier
has definition: An informative report on intrinsic positional features of a protein sequence.
has exact synonym: Feature table (protein)
has exact synonym: Protein feature table
in subset: bio
in subset: data
comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.

Genetic map
type: Class
subclass of: Map
Created in: beta12orEarlier
has db xref: Moby:GeneticMap
has definition: 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.
has exact synonym: Linkage map
in subset: bio
in subset: data
comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.

Sequence map
type: Class
subclass of: Physical map
Created in: beta12orEarlier
has definition: A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.
in subset: bio
in subset: data
comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.

Physical map
type: Class
subclass of: Map
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.

Sequence signature map
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Image of a sequence with matches to signatures, motifs or profiles.
in subset: obsolete
replaced by: Sequence image
deprecated: true

Cytogenetic map
type: Class
subclass of: Physical map
Created in: beta12orEarlier
has definition: A map showing banding patterns derived from direct observation of a stained chromosome.
has exact synonym: Chromosome map
has exact synonym: Cytogenic map
has exact synonym: Cytologic map
in subset: bio
in subset: data
comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.

DNA transduction map
type: Class
subclass of: Genetic map
Created in: beta12orEarlier
has definition: A gene map showing distances between loci based on relative cotransduction frequencies.
in subset: bio
in subset: data

Gene map
type: Class
subclass of: Sequence map
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Plasmid map
type: Class
subclass of: Sequence map
Created in: beta12orEarlier
has definition: Sequence map of a plasmid (circular DNA).
in subset: bio
in subset: data

Genome map
type: Class
subclass of: Sequence map
Created in: beta12orEarlier
has definition: Sequence map of a whole genome.
in subset: bio
in subset: data

Restriction map
type: Class
subclass of: Sequence map
subclass of: Sequence image
Created in: beta12orEarlier
has definition: Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.
in subset: bio
in subset: data

InterPro compact match image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Image showing matches between protein sequence(s) and InterPro Entries.
in subset: obsolete
replaced by: Sequence image
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
deprecated: true

InterPro detailed match image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Image showing detailed information on matches between protein sequence(s) and InterPro Entries.
in subset: obsolete
replaced by: Sequence image
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.
deprecated: true

InterPro architecture image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Image showing the architecture of InterPro domains in a protein sequence.
in subset: obsolete
replaced by: Sequence image
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.
deprecated: true

SMART protein schematic
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence image
has definition: SMART protein schematic in PNG format.
in subset: obsolete
deprecated: true

GlobPlot domain image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.
in subset: obsolete
replaced by: Sequence image
deprecated: true

Sequence motif matches
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.
in subset: obsolete
replaced by: Sequence signature matches
deprecated: true

Sequence features (repeats)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence features
has definition: Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
in subset: obsolete
comment: The report might include derived data map such as classification, annotation, organisation, periodicity etc.
deprecated: true

Gene and transcript structure (report)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Gene report
has definition: A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
in subset: obsolete
deprecated: true

Mobile genetic elements
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: regions of a nucleic acid sequence containing mobile genetic elements.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Nucleic acid features (quadruplexes)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Nucleic acid structure report
has definition: A report on quadruplex-forming motifs in a nucleotide sequence.
in subset: obsolete
deprecated: true

Nucleosome exclusion sequences
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Report on nucleosome formation potential or exclusion sequence(s).
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Gene features (exonic splicing enhancer)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: A report on exonic splicing enhancers (ESE) in an exon.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Nucleic acid features (microRNA)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Nucleic acid features
has definition: A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.
in subset: obsolete
deprecated: true

Coding region
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Gene features (SECIS element)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene report
has definition: A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.
in subset: obsolete
deprecated: true

Transcription factor binding sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: transcription factor binding sites (TFBS) in a DNA sequence.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Protein features (sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein features
has definition: A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.
in subset: obsolete
comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.
deprecated: true

Protein features report (signal peptides)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: signal peptides or signal peptide cleavage sites in protein sequences.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features report (cleavage sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features (post-translation modifications)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: post-translation modifications in a protein sequence, typically describing the specific sites involved.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features report (active sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: catalytic residues (active site) of an enzyme.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features report (binding sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein features (epitopes)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.
in subset: obsolete
replaced by: Protein features
comment: Epitope mapping is commonly done during vaccine design.
deprecated: true

Protein features report (nucleic acid binding sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: RNA and DNA-binding proteins and binding sites in protein sequences.
in subset: obsolete
replaced by: Protein features
deprecated: true

MHC Class I epitopes report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein features
has definition: A report on epitopes that bind to MHC class I molecules.
in subset: obsolete
deprecated: true

MHC Class II epitopes report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein features
has definition: A report on predicted epitopes that bind to MHC class II molecules.
in subset: obsolete
deprecated: true

Protein features (PEST sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: A report or plot of PEST sites in a protein sequence.
in subset: obsolete
replaced by: Protein features
comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.
deprecated: true

Sequence database hits scores list
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence search results
has definition: Scores from a sequence database search (for example a BLAST search).
in subset: obsolete
deprecated: true

Sequence database hits alignments list
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence search results
has definition: Alignments from a sequence database search (for example a BLAST search).
in subset: obsolete
deprecated: true

Sequence database hits evaluation data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence search results
has definition: A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).
in subset: obsolete
deprecated: true

MEME motif alphabet
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Mathematical model
has definition: Alphabet for the motifs (patterns) that MEME will search for.
in subset: obsolete
deprecated: true

MEME background frequencies file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Mathematical model
has definition: MEME background frequencies file.
in subset: obsolete
deprecated: true

MEME motifs directive file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Mathematical model
has definition: File of directives for ordering and spacing of MEME motifs.
in subset: obsolete
deprecated: true

Dirichlet distribution
type: Class
subclass of: Mathematical model
Created in: beta12orEarlier
has definition: Dirichlet distribution used by hidden Markov model analysis programs.
in subset: bio
in subset: data

HMM emission and transition counts
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Transition matrix
consider: Emission matrix
has definition: 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.
in subset: obsolete
deprecated: true

Regular expression
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Regular expression pattern.
in subset: bio
in subset: data

Sequence motif
type: Class
subclass of: Sequence signature data
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.
in subset: bio
in subset: data

Sequence profile
type: Class
subclass of: Sequence signature data
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Some type of statistical model representing a (typically multiple) sequence alignment.
in subset: bio
in subset: data

Protein signature
type: Class
subclass of: Sequence signature report
Created in: beta12orEarlier
has definition: An informative report about a specific or conserved protein sequence pattern.
has narrow synonym: InterPro entry
has narrow synonym: Protein domain signature
has narrow synonym: Protein family signature
has narrow synonym: Protein region signature
has narrow synonym: Protein repeat signature
has narrow synonym: Protein site signature
in subset: bio
in subset: data

Prosite nucleotide pattern
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence motif
has definition: A nucleotide regular expression pattern from the Prosite database.
in subset: obsolete
deprecated: true

Prosite protein pattern
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence motif
has definition: A protein regular expression pattern from the Prosite database.
in subset: obsolete
deprecated: true

Position frequency matrix
type: Class
subclass of: Position-specific scoring matrix
Created in: beta12orEarlier
has definition: A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.
has exact synonym: PFM
in subset: bio
in subset: data

Position weight matrix
type: Class
subclass of: Position-specific scoring matrix
Created in: beta12orEarlier
has definition: A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.
has exact synonym: PWM
in subset: bio
in subset: data
comment: Contributions of individual sequences to the matrix might be uneven (weighted).

Information content matrix
type: Class
subclass of: Position-specific scoring matrix
Created in: beta12orEarlier
has definition: 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.
has exact synonym: ICM
in subset: bio
in subset: data

Hidden Markov model
type: Class
subclass of: Mathematical model
Created in: beta12orEarlier
has definition: 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.
has exact synonym: HMM
in subset: bio
in subset: data

Fingerprint
type: Class
subclass of: Position-specific scoring matrix
Created in: beta12orEarlier
has definition: One or more fingerprints (sequence classifiers) as used in the PRINTS database.
in subset: bio
in subset: data

Domainatrix signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence profile
has definition: A protein signature of the type used in the EMBASSY Signature package.
in subset: obsolete
deprecated: true

HMMER NULL hidden Markov model
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Hidden Markov model
has definition: NULL hidden Markov model representation used by the HMMER package.
in subset: obsolete
deprecated: true

Protein family signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein signature
has definition: A protein family signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.
deprecated: true

Protein domain signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein signature
has definition: A protein domain signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries.
deprecated: true

Protein region signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein signature
has definition: A protein region signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein region signature defines a region which cannot be described as a protein family or domain signature.
deprecated: true

Protein repeat signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein signature
has definition: A protein repeat signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
deprecated: true

Protein site signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein signature
has definition: A protein site signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein site signature is a classifier for a specific site in a protein.
deprecated: true

Protein conserved site signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence motif (protein)
has definition: A protein conserved site signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.
deprecated: true

Protein active site signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence motif (protein)
has definition: A protein active site signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
deprecated: true

Protein binding site signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence motif (protein)
has definition: A protein binding site signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
deprecated: true

Protein post-translational modification signature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence motif (protein)
has definition: A protein post-translational modification signature (sequence classifier) from the InterPro database.
in subset: obsolete
comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
deprecated: true

Pair sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
deprecation_candidate: true
has definition: Alignment of exactly two molecular sequences.
has exact synonym: Sequence alignment (pair)
in subset: bio
in subset: data

Sequence alignment (multiple)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment
has definition: Alignment of more than two molecular sequences.
in subset: obsolete
deprecated: true

Nucleic acid sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Alignment of multiple nucleotide sequences.
has exact synonym: Sequence alignment (nucleic acid)
has narrow synonym: DNA sequence alignment
has narrow synonym: RNA sequence alignment
in subset: bio
in subset: data

Protein sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Alignment of multiple protein sequences.
has exact synonym: Sequence alignment (protein)
in subset: bio
in subset: data

Hybrid sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Alignment of multiple molecular sequences of different types.
has exact synonym: Sequence alignment (hybrid)
in subset: bio
in subset: data
comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.

Sequence alignment (nucleic acid pair)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Pair sequence alignment
consider: Nucleic acid sequence alignment
has definition: Alignment of exactly two nucleotide sequences.
in subset: obsolete
deprecated: true

Sequence alignment (protein pair)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Pair sequence alignment
consider: Protein sequence alignment
has definition: Alignment of exactly two protein sequences.
in subset: obsolete
deprecated: true

Hybrid sequence alignment (pair)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Hybrid sequence alignment
has definition: Alignment of exactly two molecular sequences of different types.
in subset: obsolete
deprecated: true

Multiple nucleotide sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment
has definition: Alignment of more than two nucleotide sequences.
in subset: obsolete
deprecated: true

Multiple protein sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment
has definition: Alignment of more than two protein sequences.
in subset: obsolete
deprecated: true

Alignment score or penalty
type: Class
subclass of: Score
Created in: beta12orEarlier
has definition: A simple floating point number defining the penalty for opening or extending a gap in an alignment.
in subset: bio
in subset: data

Score end gaps control
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence attribute
has definition: Whether end gaps are scored or not.
in subset: obsolete
deprecated: true

Aligned sequence order
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence attribute
has definition: Controls the order of sequences in an output sequence alignment.
in subset: obsolete
deprecated: true

Gap opening penalty
type: Class
subclass of: Gap penalty
Created in: beta12orEarlier
has definition: A penalty for opening a gap in an alignment.
in subset: bio
in subset: data

Gap extension penalty
type: Class
subclass of: Gap penalty
Created in: beta12orEarlier
has definition: A penalty for extending a gap in an alignment.
in subset: bio
in subset: data

Gap separation penalty
type: Class
subclass of: Gap penalty
Created in: beta12orEarlier
has definition: A penalty for gaps that are close together in an alignment.
in subset: bio
in subset: data

Terminal gap penalty
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Terminal gap opening penalty
consider: Terminal gap extension penalty
has definition: 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.
in subset: obsolete
deprecated: true

Match reward score
type: Class
subclass of: Alignment score or penalty
Created in: beta12orEarlier
has definition: The score for a 'match' used in various sequence database search applications with simple scoring schemes.
in subset: bio
in subset: data

Mismatch penalty score
type: Class
subclass of: Alignment score or penalty
Created in: beta12orEarlier
has definition: The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes.
in subset: bio
in subset: data

Drop off score
type: Class
subclass of: Alignment score or penalty
Created in: beta12orEarlier
has definition: This is the threshold drop in score at which extension of word alignment is halted.
in subset: bio
in subset: data

Gap opening penalty (integer)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap opening penalty
has definition: A simple floating point number defining the penalty for opening a gap in an alignment.
in subset: obsolete
deprecated: true

Gap opening penalty (float)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap opening penalty
has definition: A simple floating point number defining the penalty for opening a gap in an alignment.
in subset: obsolete
deprecated: true

Gap extension penalty (integer)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap extension penalty
has definition: A simple floating point number defining the penalty for extending a gap in an alignment.
in subset: obsolete
deprecated: true

Gap extension penalty (float)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap extension penalty
has definition: A simple floating point number defining the penalty for extending a gap in an alignment.
in subset: obsolete
deprecated: true

Gap separation penalty (integer)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap separation penalty
has definition: A simple floating point number defining the penalty for gaps that are close together in an alignment.
in subset: obsolete
deprecated: true

Gap separation penalty (float)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gap separation penalty
has definition: A simple floating point number defining the penalty for gaps that are close together in an alignment.
in subset: obsolete
deprecated: true

Terminal gap opening penalty
type: Class
subclass of: Gap opening penalty
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Terminal gap extension penalty
type: Class
subclass of: Gap extension penalty
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Sequence identity
type: Class
subclass of: Sequence similarity score
Created in: beta12orEarlier
has definition: Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.
in subset: bio
in subset: data

Sequence similarity
type: Class
subclass of: Sequence similarity score
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: Data Type is float probably.

Sequence alignment metadata (quality report)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment report
has definition: Data on molecular sequence alignment quality (estimated accuracy).
in subset: obsolete
deprecated: true

Sequence alignment report (site conservation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence similarity plot
has definition: Data on character conservation in a molecular sequence alignment.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
deprecated: true

Sequence alignment report (site correlation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence alignment report
has definition: 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.
in subset: obsolete
deprecated: true

Sequence-profile alignment (Domainatrix signature)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence signature matches
has definition: Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).
in subset: obsolete
deprecated: true

Sequence-profile alignment (HMM)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence signature matches
has definition: Alignment of molecular sequence(s) to a hidden Markov model(s).
in subset: obsolete
deprecated: true

Sequence-profile alignment (fingerprint)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence signature matches
has definition: Alignment of molecular sequences to a protein fingerprint from the PRINTS database.
in subset: obsolete
deprecated: true

Phylogenetic continuous quantitative data
type: Class
subclass of: Phylogenetic character data
Created in: beta12orEarlier
has definition: Continuous quantitative data that may be read during phylogenetic tree calculation.
has exact synonym: Phylogenetic continuous quantitative characters
has exact synonym: Quantitative traits
in subset: bio
in subset: data

Phylogenetic discrete data
type: Class
subclass of: Phylogenetic character data
Created in: beta12orEarlier
has definition: Character data with discrete states that may be read during phylogenetic tree calculation.
has exact synonym: Discrete characters
has exact synonym: Discretely coded characters
has exact synonym: Phylogenetic discrete states
in subset: bio
in subset: data

Phylogenetic character cliques
type: Class
subclass of: Phylogenetic data
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Phylogenetic report (cliques)
in subset: bio
in subset: data

Phylogenetic invariants
type: Class
subclass of: Phylogenetic data
subclass of: Restriction
  on property: has topic
  some values from: Genetic variation
Created in: beta12orEarlier
has definition: Phylogenetic invariants data for testing alternative tree topologies.
has exact synonym: Phylogenetic report (invariants)
in subset: bio
in subset: data

Phylogenetic report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Phylogenetic data
has definition: A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.
in subset: obsolete
comment: 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.
deprecated: true

DNA substitution model
type: Class
subclass of: Mathematical model
Created in: beta12orEarlier
has definition: A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.
has exact synonym: Phylogenetic tree report (DNA substitution model)
has exact synonym: Sequence alignment report (DNA substitution model)
has exact synonym: Substitution model
in subset: bio
in subset: data

Phylogenetic tree report (tree shape)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Phylogenetic data
has definition: Data about the shape of a phylogenetic tree.
in subset: obsolete
deprecated: true

Phylogenetic tree report (tree evaluation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Phylogenetic data
has definition: Data on the confidence of a phylogenetic tree.
in subset: obsolete
deprecated: true

Phylogenetic tree distances
type: Class
subclass of: Phylogenetic data
Created in: beta12orEarlier
has definition: Distances, such as Branch Score distance, between two or more phylogenetic trees.
has exact synonym: Phylogenetic tree report (tree distances)
in subset: bio
in subset: data

Phylogenetic tree report (tree stratigraphic)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Phylogenetic data
has definition: Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.
in subset: obsolete
deprecated: true

Phylogenetic character contrasts
type: Class
subclass of: Phylogenetic data
Created in: beta12orEarlier
has definition: Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.
has exact synonym: Phylogenetic report (character contrasts)
in subset: bio
in subset: data

Comparison matrix (integers)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix
has definition: Matrix of integer numbers for sequence comparison.
in subset: obsolete
deprecated: true

Comparison matrix (floats)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix
has definition: Matrix of floating point numbers for sequence comparison.
in subset: obsolete
deprecated: true

Comparison matrix (nucleotide)
type: Class
subclass of: Comparison matrix
Created in: beta12orEarlier
has definition: Matrix of integer or floating point numbers for nucleotide comparison.
has exact synonym: Nucleotide comparison matrix
has exact synonym: Nucleotide substitution matrix
in subset: bio
in subset: data

Comparison matrix (amino acid)
type: Class
subclass of: Comparison matrix
subclass of: Amino acid property
Created in: beta12orEarlier
has definition: Matrix of integer or floating point numbers for amino acid comparison.
has exact synonym: Amino acid comparison matrix
has exact synonym: Amino acid substitution matrix
in subset: bio
in subset: data

Nucleotide comparison matrix (integers)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix (nucleotide)
has definition: Matrix of integer numbers for nucleotide comparison.
in subset: obsolete
deprecated: true

Nucleotide comparison matrix (floats)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix (nucleotide)
has definition: Matrix of floating point numbers for nucleotide comparison.
in subset: obsolete
deprecated: true

Amino acid comparison matrix (integers)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix (amino acid)
has definition: Matrix of integer numbers for amino acid comparison.
in subset: obsolete
deprecated: true

Amino acid comparison matrix (floats)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Comparison matrix (amino acid)
has definition: Matrix of floating point numbers for amino acid comparison.
in subset: obsolete
deprecated: true

Nucleic acid structure
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a nucleic acid tertiary (3D) structure.
in subset: bio
in subset: data

Protein structure
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Protein structure analysis
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules.
has exact synonym: Protein structures
in subset: bio
in subset: data

Protein-ligand complex
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.

Carbohydrate structure
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Carbohydrates
subclass of: Restriction
  on property: has topic
  some values from: Lipidomics
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a carbohydrate (3D) structure.
in subset: bio
in subset: data

Small molecule structure
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Small molecules
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.
has related synonym: CHEBI:23367
in subset: bio
in subset: data

DNA structure
type: Class
subclass of: Nucleic acid structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a DNA tertiary (3D) structure.
in subset: bio
in subset: data

RNA structure
type: Class
subclass of: Nucleic acid structure
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for an RNA tertiary (3D) structure.
in subset: bio
in subset: data

tRNA structure
type: Class
subclass of: RNA structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.
in subset: bio
in subset: data

Protein chain
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.
in subset: bio
in subset: data

Protein domain
type: Class
subclass of: Protein structure
subclass of: Restriction
  on property: has topic
  some values from: Protein folds and structural domains
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for the tertiary (3D) structure of a protein domain.
in subset: bio
in subset: data

Protein structure (all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein structure
has definition: 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).
in subset: obsolete
deprecated: true

C-alpha trace
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).
has exact synonym: Protein structure (C-alpha atoms)
in subset: bio
in subset: data
comment: C-beta atoms from amino acid side-chains may be included.

Protein chain (all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein chain
has definition: 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).
in subset: obsolete
deprecated: true

Protein chain (C-alpha atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein chain
has definition: 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).
in subset: obsolete
comment: C-beta atoms from amino acid side-chains may be included.
deprecated: true

Protein domain (all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein domain
has definition: 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).
in subset: obsolete
deprecated: true

Protein domain (C-alpha atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein domain
has definition: 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).
in subset: obsolete
comment: C-beta atoms from amino acid side-chains may be included.
deprecated: true

Structure alignment (pair)
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Alignment (superimposition) of exactly two molecular tertiary (3D) structures.
has exact synonym: Pair structure alignment
in subset: bio
in subset: data

Structure alignment (multiple)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure alignment
has definition: Alignment (superimposition) of more than two molecular tertiary (3D) structures.
in subset: obsolete
deprecated: true

Protein structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Alignment (superimposition) of protein tertiary (3D) structures.
has exact synonym: Structure alignment (protein)
in subset: bio
in subset: data

Nucleic acid structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Alignment (superimposition) of nucleic acid tertiary (3D) structures.
has exact synonym: Structure alignment (nucleic acid)
in subset: bio
in subset: data

Structure alignment (protein pair)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Structure alignment (pair)
consider: Protein structure alignment
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures.
in subset: obsolete
deprecated: true

Multiple protein tertiary structure alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of more than two protein tertiary (3D) structures.
in subset: obsolete
deprecated: true

Structure alignment (protein all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).
in subset: obsolete
deprecated: true

Structure alignment (protein C-alpha atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).
in subset: obsolete
comment: C-beta atoms from amino acid side-chains may be considered.
deprecated: true

Pairwise protein tertiary structure alignment (all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).
in subset: obsolete
deprecated: true

Pairwise protein tertiary structure alignment (C-alpha atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).
in subset: obsolete
comment: C-beta atoms from amino acid side-chains may be included.
deprecated: true

Multiple protein tertiary structure alignment (all atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).
in subset: obsolete
deprecated: true

Multiple protein tertiary structure alignment (C-alpha atoms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure alignment
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).
in subset: obsolete
comment: C-beta atoms from amino acid side-chains may be included.
deprecated: true

Structure alignment (nucleic acid pair)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Structure alignment (pair)
consider: Nucleic acid structure alignment
has definition: Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.
in subset: obsolete
deprecated: true

Multiple nucleic acid tertiary structure alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid structure alignment
has definition: Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.
in subset: obsolete
deprecated: true

RNA structure alignment
type: Class
subclass of: Nucleic acid structure alignment
Created in: beta12orEarlier
has definition: Alignment (superimposition) of RNA tertiary (3D) structures.
has exact synonym: Structure alignment (RNA)
in subset: bio
in subset: data

Structural transformation matrix
type: Class
subclass of: Matrix
Created in: beta12orEarlier
has definition: Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.
in subset: bio
in subset: data

DaliLite hit table
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure alignment report
has definition: DaliLite hit table of protein chain tertiary structure alignment data.
in subset: obsolete
comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.
deprecated: true

Molecular similarity score
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure similarity score
has definition: A score reflecting structural similarities of two molecules.
in subset: obsolete
deprecated: true

Root-mean-square deviation
type: Class
subclass of: Structure similarity score
Created in: beta12orEarlier
has definition: Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.
has exact synonym: RMSD
in subset: bio
in subset: data

Tanimoto similarity score
type: Class
subclass of: Structure similarity score
Created in: beta12orEarlier
has definition: A measure of the similarity between two ligand fingerprints.
in subset: bio
in subset: data
comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.

3D-1D scoring matrix
type: Class
subclass of: Protein sequence-structure scoring matrix
Created in: beta12orEarlier
has definition: A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.
in subset: bio
in subset: data

Amino acid index
type: Class
subclass of: Amino acid property
subclass of: Matrix
Created in: beta12orEarlier
has definition: A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.
in subset: bio
in subset: data

Amino acid index (chemical classes)
type: Class
subclass of: Amino acid index
Created in: beta12orEarlier
has definition: Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.
has exact synonym: Chemical classes (amino acids)
in subset: bio
in subset: data

Amino acid pair-wise contact potentials
type: Class
subclass of: Amino acid property
Created in: beta12orEarlier
has definition: Statistical protein contact potentials.
has exact synonym: Contact potentials (amino acid pair-wise)
in subset: bio
in subset: data

Amino acid index (molecular weight)
type: Class
subclass of: Amino acid index
Created in: beta12orEarlier
has definition: Molecular weights of amino acids.
has exact synonym: Molecular weight (amino acids)
in subset: bio
in subset: data

Amino acid index (hydropathy)
type: Class
subclass of: Amino acid index
Created in: beta12orEarlier
has definition: Hydrophobic, hydrophilic or charge properties of amino acids.
has exact synonym: Hydropathy (amino acids)
in subset: bio
in subset: data

Amino acid index (White-Wimley data)
type: Class
subclass of: Amino acid index
Created in: beta12orEarlier
has definition: Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.
has exact synonym: White-Wimley data (amino acids)
in subset: bio
in subset: data

Amino acid index (van der Waals radii)
type: Class
subclass of: Amino acid index
Created in: beta12orEarlier
has definition: Van der Waals radii of atoms for different amino acid residues.
has exact synonym: van der Waals radii (amino acids)
in subset: bio
in subset: data

Enzyme report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein report
has definition: An informative report on a specific enzyme.
in subset: obsolete
deprecated: true

Restriction enzyme report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein report
has definition: An informative report on a specific restriction enzyme such as enzyme reference data.
in subset: obsolete
comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
deprecated: true

Peptide molecular weights
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.
in subset: bio
in subset: data
comment: The report might include associated data such as frequency of peptide fragment molecular weights.

Peptide hydrophobic moment
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: Report on the hydrophobic moment of a polypeptide sequence.
in subset: bio
in subset: data
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.

Protein aliphatic index
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: The aliphatic index of a protein.
in subset: bio
in subset: data
comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains.

Protein sequence hydropathy plot
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.
in subset: bio
in subset: data
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.

Protein charge plot
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Protein solubility
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: The solubility or atomic solvation energy of a protein sequence or structure.
has exact synonym: Protein solubility data
in subset: bio
in subset: data

Protein crystallizability
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: Data on the crystallizability of a protein sequence.
has exact synonym: Protein crystallizability data
in subset: bio
in subset: data

Protein globularity
type: Class
subclass of: Protein hydropathy data
Created in: beta12orEarlier
has definition: Data on the stability, intrinsic disorder or globularity of a protein sequence.
has exact synonym: Protein globularity data
in subset: bio
in subset: data

Protein titration curve
type: Class
subclass of: Protein property
subclass of: Plot
Created in: beta12orEarlier
has definition: The titration curve of a protein.
in subset: bio
in subset: data

Protein isoelectric point
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: The isoelectric point of one proteins.
in subset: bio
in subset: data

Protein pKa value
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: The pKa value of a protein.
in subset: bio
in subset: data

Protein hydrogen exchange rate
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: The hydrogen exchange rate of a protein.
in subset: bio
in subset: data

Protein extinction coefficient
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: The extinction coefficient of a protein.
in subset: bio
in subset: data

Protein optical density
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: The optical density of a protein.
in subset: bio
in subset: data

Protein subcellular localisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein report
has definition: An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).
in subset: obsolete
deprecated: true

Peptide immunogenicity data
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: An report on allergenicity / immunogenicity of peptides and proteins.
has exact synonym: Peptide immunogenicity
has exact synonym: Peptide immunogenicity report
in subset: bio
in subset: data
comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.

MHC peptide immunogenicity report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Peptide immunogenicity data
has definition: A report on the immunogenicity of MHC class I or class II binding peptides.
in subset: obsolete
deprecated: true

Protein structure report
type: Class
subclass of: Protein report
subclass of: Structure report
Created in: beta12orEarlier
has definition: A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains.
has exact synonym: Protein property (structural)
has exact synonym: Protein report (structure)
has exact synonym: Protein structural property
has exact synonym: Protein structure report (domain)
has exact synonym: Protein structure-derived report
in subset: bio
in subset: data

Protein structural quality report
type: Class
subclass of: Protein structure report
Created in: beta12orEarlier
has definition: Report on the quality of a protein three-dimensional model.
has exact synonym: Protein property (structural quality)
has exact synonym: Protein report (structural quality)
has exact synonym: Protein structure report (quality evaluation)
has exact synonym: Protein structure validation report
in subset: bio
in subset: data
comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.

Protein non-covalent interactions report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Protein interaction data
deprecated: true

Protein flexibility or motion report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Protein structure report
has definition: Informative report on flexibility or motion of a protein structure.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

Protein solvent accessibility
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: Data on the solvent accessible or buried surface area of a protein structure.
in subset: bio
in subset: data
comment: This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.

Protein surface report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Protein structure report
has definition: Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

Ramachandran plot
type: Class
subclass of: Protein geometry data
Created in: beta12orEarlier
has definition: Phi/psi angle data or a Ramachandran plot of a protein structure.
in subset: bio
in subset: data

Protein dipole moment
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: Data on the net charge distribution (dipole moment) of a protein structure.
in subset: bio
in subset: data

Protein distance matrix
type: Class
subclass of: Protein interaction data
subclass of: Distance matrix
Created in: beta12orEarlier
has definition: A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.
in subset: bio
in subset: data

Protein contact map
type: Class
subclass of: Protein interaction data
Created in: beta12orEarlier
has definition: An amino acid residue contact map for a protein structure.
in subset: bio
in subset: data

Protein residue 3D cluster
type: Class
subclass of: Protein interaction data
Created in: beta12orEarlier
has definition: Report on clusters of contacting residues in protein structures such as a key structural residue network.
in subset: bio
in subset: data

Protein hydrogen bonds
type: Class
subclass of: Protein interaction data
Created in: beta12orEarlier
has definition: Patterns of hydrogen bonding in protein structures.
in subset: bio
in subset: data

Protein non-canonical interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Protein structure report
has definition: Non-canonical atomic interactions in protein structures.
in subset: obsolete
deprecated: true

CATH node
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a node from the CATH database.
in subset: obsolete
comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.
deprecated: true

SCOP node
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a node from the SCOP database.
in subset: obsolete
deprecated: true

EMBASSY domain classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.
in subset: obsolete
replaced by: Protein family report
deprecated: true

CATH class
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'class' node from the CATH database.
in subset: obsolete
deprecated: true

CATH architecture
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'architecture' node from the CATH database.
in subset: obsolete
deprecated: true

CATH topology
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'topology' node from the CATH database.
in subset: obsolete
deprecated: true

CATH homologous superfamily
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'homologous superfamily' node from the CATH database.
in subset: obsolete
deprecated: true

CATH structurally similar group
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'structurally similar group' node from the CATH database.
in subset: obsolete
deprecated: true

CATH functional category
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a protein 'functional category' node from the CATH database.
in subset: obsolete
deprecated: true

Protein fold recognition report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein features
has definition: A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s).
in subset: obsolete
comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
deprecated: true

Protein-protein interaction report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: protein-protein interaction(s), including interactions between protein domains.
in subset: obsolete
replaced by: Protein interaction data
deprecated: true

Protein-ligand interaction report
type: Class
subclass of: Protein interaction data
Created in: beta12orEarlier
has definition: An informative report on protein-ligand (small molecule) interaction(s).
has narrow synonym: Protein-drug interaction report
in subset: bio
in subset: data

Protein-nucleic acid interactions report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: protein-DNA/RNA interaction(s).
in subset: obsolete
replaced by: Protein interaction data
deprecated: true

Nucleic acid melting profile
type: Class
subclass of: Nucleic acid thermodynamic data
Created in: beta12orEarlier
comment: 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.
comment: 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
comment: 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.
comment: Nucleic acid temperature profile: a temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Plots melting temperature versus base position.
has definition: Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.
has exact synonym: Nucleic acid stability profile
has narrow synonym: Melting map
has narrow synonym: Nucleic acid melting curve
in subset: bio
in subset: data
comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.

Nucleic acid enthalpy
type: Class
subclass of: Nucleic acid thermodynamic data
Created in: beta12orEarlier
has definition: Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
in subset: bio
in subset: data

Nucleic acid entropy
type: Class
subclass of: Nucleic acid thermodynamic data
Created in: beta12orEarlier
has definition: Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
in subset: bio
in subset: data

Nucleic acid melting temperature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid melting temperature
has definition: Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
in subset: obsolete
deprecated: true

Nucleic acid stitch profile
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Nucleic acid melting profile
has definition: Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
in subset: obsolete
replaced by: Nucleic acid melting profile
deprecated: true

DNA base pair stacking energies data
type: Class
subclass of: DNA base structural data
Created in: beta12orEarlier
has definition: DNA base pair stacking energies data.
in subset: bio
in subset: data

DNA base pair twist angle data
type: Class
subclass of: DNA base structural data
Created in: beta12orEarlier
has definition: DNA base pair twist angle data.
in subset: bio
in subset: data

DNA base trimer roll angles data
type: Class
subclass of: DNA base structural data
Created in: beta12orEarlier
has definition: DNA base trimer roll angles data.
in subset: bio
in subset: data

Vienna RNA parameters
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: RNA parameters used by the Vienna package.
in subset: obsolete
deprecated: true

Vienna RNA structure constraints
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: Structure constraints used by the Vienna package.
in subset: obsolete
deprecated: true

Vienna RNA concentration data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: RNA concentration data used by the Vienna package.
in subset: obsolete
deprecated: true

Vienna RNA calculated energy
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid enthalpy
has definition: RNA calculated energy data generated by the Vienna package.
in subset: obsolete
deprecated: true

Base pairing probability matrix dotplot
type: Class
subclass of: DNA base structural data
subclass of: Plot
Created in: beta12orEarlier
has definition: Dotplot of RNA base pairing probability matrix.
in subset: bio
in subset: data
comment: Such as generated by the Vienna package.

Nucleic acid folding report
type: Class
subclass of: Nucleic acid report
Created in: beta12orEarlier
has definition: A human-readable collection of information about RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.
has exact synonym: Nucleic acid report (folding model)
has exact synonym: Nucleic acid report (folding)
has narrow synonym: RNA secondary structure folding classification
has narrow synonym: RNA secondary structure folding probabilities
in subset: bio
in subset: data

Codon usage table
type: Class
subclass of: Codon usage data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Table of codon usage data calculated from one or more nucleic acid sequences.
in subset: bio
in subset: data
comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.

Genetic code
type: Class
subclass of: Codon usage data
Created in: beta12orEarlier
has definition: A genetic code for an organism.
in subset: bio
in subset: data
comment: A genetic code need not include detailed codon usage information.

Codon adaptation index
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Codon usage bias
has definition: A simple measure of synonymous codon usage bias often used to predict gene expression levels.
in subset: obsolete
deprecated: true

Codon usage bias plot
type: Class
subclass of: Codon usage data
Created in: beta12orEarlier
has definition: A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.
has exact synonym: Synonymous codon usage statistic plot
in subset: bio
in subset: data

Nc statistic
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Codon usage bias
has definition: 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.
in subset: obsolete
deprecated: true

Codon usage fraction difference
type: Class
subclass of: Codon usage data
Created in: beta12orEarlier
has definition: The differences in codon usage fractions between two codon usage tables.
in subset: bio
in subset: data

Pharmacogenomic test report
type: Class
subclass of: Genotype/phenotype report
Created in: beta12orEarlier
has definition: A human-readable collection of information about the influence of genotype on drug response.
in subset: bio
in subset: data
comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.

Disease report
type: Class
subclass of: Genotype/phenotype report
subclass of: Restriction
  on property: has topic
  some values from: Pathology
Created in: beta12orEarlier
has definition: A human-readable collection of information about a specific disease.
in subset: bio
in subset: data
comment: 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.

Linkage disequilibrium (report)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
in subset: obsolete
replaced by: Genetic linkage report
deprecated: true

Heat map
type: Class
subclass of: Image
subclass of: Clustered expression profiles
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Affymetrix probe sets library file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Oligonucleotide probe annotation
has definition: Affymetrix library file of information about which probes belong to which probe set.
in subset: obsolete
deprecated: true

Affymetrix probe sets information library file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Oligonucleotide probe annotation
has definition: Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.
has related synonym: GIN file
in subset: obsolete
deprecated: true

Molecular weights standard fingerprint
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.
in subset: obsolete
replaced by: Peptide mass fingerprint
deprecated: true

Metabolic pathway report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A report typically including a map (diagram) of a metabolic pathway.
in subset: obsolete
replaced by: Pathway or network report
comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
deprecated: true

Genetic information processing pathway report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: genetic information processing pathways.
in subset: obsolete
replaced by: Pathway or network report
deprecated: true

Environmental information processing pathway report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: environmental information processing pathways.
in subset: obsolete
replaced by: Pathway or network report
deprecated: true

Signal transduction pathway report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A report typically including a map (diagram) of a signal transduction pathway.
in subset: obsolete
replaced by: Pathway or network report
deprecated: true

Cellular process pathways report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Topic concernning cellular process pathways.
in subset: obsolete
replaced by: Pathway or network report
deprecated: true

Disease pathway or network report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: disease pathways, typically of human disease.
in subset: obsolete
replaced by: Protein interaction data
deprecated: true

Drug structure relationship map
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Drug report
has definition: A report typically including a map (diagram) of drug structure relationships.
in subset: obsolete
replaced by: Drug report
deprecated: true

Protein interaction networks
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Pathway or network
has definition: networks of protein interactions.
in subset: obsolete
deprecated: true

MIRIAM datatype
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Annotated URI
has definition: An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.
in subset: obsolete
comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
deprecated: true

E-value
type: Class
subclass of: Statistical estimate score
Created in: beta12orEarlier
has definition: A simple floating point number defining the lower or upper limit of an expectation value (E-value).
has exact synonym: Expectation value
in subset: bio
in subset: data
comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.

Z-value
type: Class
subclass of: Statistical estimate score
Created in: beta12orEarlier
has definition: The z-value is the number of standard deviations a data value is above or below a mean value.
in subset: bio
in subset: data
comment: A z-value might be specified as a threshold for reporting hits from database searches.

P-value
type: Class
subclass of: Statistical estimate score
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: A z-value might be specified as a threshold for reporting hits from database searches.

Database version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Database metadata
has definition: Information on a database (or ontology) version, for example name, version number and release date.
in subset: obsolete
deprecated: true

Tool version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Tool metadata
has definition: Information on an application version, for example name, version number and release date.
in subset: obsolete
deprecated: true

CATH version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: Information on a version of the CATH database.
in subset: obsolete
deprecated: true

Swiss-Prot to PDB mapping
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Database cross-mapping
has definition: Cross-mapping of Swiss-Prot codes to PDB identifiers.
in subset: obsolete
deprecated: true

Sequence database cross-references
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data reference
has definition: Cross-references from a sequence record to other databases.
in subset: obsolete
deprecated: true

Job status
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: Metadata on the status of a submitted job.
in subset: obsolete
comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
deprecated: true

Job ID
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: System metadata
has definition: The (typically numeric) unique identifier of a submitted job.
in subset: obsolete
deprecated: true

Job type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of job, for example interactive or non-interactive.
in subset: obsolete
deprecated: true

Tool log
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.
in subset: obsolete
deprecated: true

DaliLite log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.
in subset: obsolete
deprecated: true

STRIDE log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: STRIDE log file.
in subset: obsolete
deprecated: true

NACCESS log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: NACCESS log file.
in subset: obsolete
deprecated: true

EMBOSS wordfinder log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS wordfinder log file.
in subset: obsolete
deprecated: true

EMBOSS domainatrix log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS (EMBASSY) domainatrix application log file.
in subset: obsolete
deprecated: true

EMBOSS sites log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS (EMBASSY) sites application log file.
in subset: obsolete
deprecated: true

EMBOSS supermatcher error file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS (EMBASSY) supermatcher error file.
in subset: obsolete
deprecated: true

EMBOSS megamerger log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS megamerger log file.
in subset: obsolete
deprecated: true

EMBOSS whichdb log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS megamerger log file.
in subset: obsolete
deprecated: true

EMBOSS vectorstrip log file
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: EMBOSS vectorstrip log file.
in subset: obsolete
deprecated: true

Username
type: Class
subclass of: Account authentication
Created in: beta12orEarlier
has definition: A username on a computer system or a website.
in subset: bio
in subset: data
in subset: identifiers

Password
type: Class
subclass of: Account authentication
Created in: beta12orEarlier
has definition: A password on a computer system, or a website.
in subset: bio
in subset: data
in subset: identifiers

Email address
type: Class
subclass of: Account authentication
Created in: beta12orEarlier
has db xref: Moby:Email
has db xref: Moby:EmailAddress
has definition: A valid email address of an end-user.
in subset: bio
in subset: data
in subset: identifiers

Person name
type: Class
subclass of: Person identifier
Created in: beta12orEarlier
has definition: The name of a person.
in subset: bio
in subset: data
in subset: identifiers

Number of iterations
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: Number of iterations of an algorithm.
in subset: obsolete
deprecated: true

Number of output entities
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: Number of entities (for example database hits, sequences, alignments etc) to write to an output file.
in subset: obsolete
deprecated: true

Hit sort order
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: Controls the order of hits (reported matches) in an output file from a database search.
in subset: obsolete
deprecated: true

Drug report
type: Class
subclass of: Small molecule report
subclass of: Restriction
  on property: has topic
  some values from: Small molecules
Created in: beta12orEarlier
comment: A drug structure relationship map is report (typically a map diagram) of drug structure relationships.
has definition: A human-readable collection of information about a specific drug.
has exact synonym: Drug annotation
has narrow synonym: Drug structure relationship map
in subset: bio
in subset: data

Phylogenetic tree image
type: Class
subclass of: Image
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: See also 'Phylogenetic tree'

RNA secondary structure image
type: Class
subclass of: Image
Created in: beta12orEarlier
has definition: Image of RNA secondary structure, knots, pseudoknots etc.
in subset: bio
in subset: data

Protein secondary structure image
type: Class
subclass of: Protein image
Created in: beta12orEarlier
has definition: Image of protein secondary structure.
in subset: bio
in subset: data

Structure image
type: Class
subclass of: Image
Created in: beta12orEarlier
has definition: Image of one or more molecular tertiary (3D) structures.
in subset: bio
in subset: data

Sequence alignment image
type: Class
subclass of: Image
Created in: beta12orEarlier
has definition: Image of two or more aligned molecular sequences possibly annotated with alignment features.
in subset: bio
in subset: data

Chemical structure image
type: Class
subclass of: Structure image
Created in: beta12orEarlier
has definition: An image of the structure of a small chemical compound.
has exact synonym: Small molecule structure image
has narrow synonym: Chemical structure sketch
has narrow synonym: Small molecule sketch
in subset: bio
in subset: data
comment: The molecular identifier and formula are typically included.

Fate map
type: Class
subclass of: Image
subclass of: Restriction
  on property: has topic
  some values from: Embryology
Created in: beta12orEarlier
has definition: A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.
in subset: bio
in subset: data

Microarray spots image
type: Class
subclass of: Expression data
subclass of: Raw image
Created in: beta12orEarlier
has definition: An image of spots from a microarray experiment.
in subset: bio
in subset: data

BioPax term
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the BioPax ontology.
in subset: obsolete
deprecated: true

GO
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term definition from The Gene Ontology (GO).
in subset: obsolete
deprecated: true

MeSH
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the MeSH vocabulary.
in subset: obsolete
deprecated: true

HGNC
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the HGNC controlled vocabulary.
in subset: obsolete
deprecated: true

NCBI taxonomy vocabulary
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the NCBI taxonomy vocabulary.
in subset: obsolete
deprecated: true

Plant ontology term
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the Plant Ontology (PO).
in subset: obsolete
deprecated: true

UMLS
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the UMLS vocabulary.
in subset: obsolete
deprecated: true

FMA
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from Foundational Model of Anatomy.
in subset: obsolete
comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
deprecated: true

EMAP
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the EMAP mouse ontology.
in subset: obsolete
deprecated: true

ChEBI
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the ChEBI ontology.
in subset: obsolete
deprecated: true

MGED
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the MGED ontology.
in subset: obsolete
deprecated: true

myGrid
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology term
has definition: A term from the myGrid ontology.
in subset: obsolete
comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
deprecated: true

GO (biological process)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept
has definition: A term definition for a biological process from the Gene Ontology (GO).
in subset: obsolete
comment: Data Type is an enumerated string.
deprecated: true

GO (molecular function)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept
has definition: A term definition for a molecular function from the Gene Ontology (GO).
in subset: obsolete
comment: Data Type is an enumerated string.
deprecated: true

GO (cellular component)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept
has definition: A term definition for a cellular component from the Gene Ontology (GO).
in subset: obsolete
comment: Data Type is an enumerated string.
deprecated: true

Ontology relation type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Ontology concept data
has definition: A relation type defined in an ontology.
in subset: obsolete
deprecated: true

Ontology concept definition
type: Class
subclass of: Ontology concept data
Created in: beta12orEarlier
has definition: The definition of a concept from an ontology.
has exact synonym: Ontology class definition
in subset: bio
in subset: data

Ontology concept comment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Ontology concept data
has definition: A comment on a concept from an ontology.
in subset: obsolete
deprecated: true

Ontology concept reference
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data reference
has definition: Reference for a concept from an ontology.
in subset: obsolete
deprecated: true

doc2loc document information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Citation
has definition: Information on a published article provided by the doc2loc program.
in subset: obsolete
comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider.
deprecated: true

PDB residue number
type: Class
subclass of: Sequence position
Created in: beta12orEarlier
has db xref: PDBML:PDB_residue_no
has db xref: WHATIF: pdb_number
has definition: A residue identifier (a string) from a PDB file.
in subset: bio
in subset: data

Atomic coordinate
type: Class
subclass of: Atomic property
Created in: beta12orEarlier
has definition: Cartesian coordinate of an atom (in a molecular structure).
has exact synonym: Cartesian coordinate
in subset: bio
in subset: data

Atomic x coordinate
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Atomic coordinate
has definition: Cartesian x coordinate of an atom (in a molecular structure).
in subset: obsolete
replaced by: Atomic coordinate
deprecated: true

Atomic y coordinate
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Atomic coordinate
has definition: Cartesian y coordinate of an atom (in a molecular structure).
in subset: obsolete
replaced by: Atomic coordinate
deprecated: true

Atomic z coordinate
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Atomic coordinate
has definition: Cartesian z coordinate of an atom (in a molecular structure).
in subset: obsolete
replaced by: Atomic coordinate
deprecated: true

PDB atom name
type: Class
subclass of: Atom name
Created in: beta12orEarlier
has db xref: PDBML:pdbx_PDB_atom_name
has db xref: WHATIF: PDBx_auth_atom_id
has db xref: WHATIF: PDBx_type_symbol
has db xref: WHATIF: alternate_atom
has db xref: WHATIF: atom_type
has definition: Identifier (a string) of a specific atom from a PDB file for a molecular structure.
in subset: bio
in subset: data
in subset: identifiers

Protein atom
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: Data on a single atom from a protein structure.
has exact synonym: Atom data
has related synonym: CHEBI:33250
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.

Protein residue
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: Data on a single amino acid residue position in a protein structure.
has exact synonym: Residue
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.

Atom name
type: Class
subclass of: Atom ID
subclass of: Name
Created in: beta12orEarlier
has definition: Name of an atom.
in subset: bio
in subset: data
in subset: identifiers

PDB residue name
type: Class
subclass of: Amino acid name (three letter)
Created in: beta12orEarlier
has db xref: WHATIF: type
has definition: Three-letter amino acid residue names as used in PDB files.
in subset: bio
in subset: data
in subset: identifiers

PDB model number
type: Class
subclass of: Structure identifier
Created in: beta12orEarlier
has db xref: PDBML:pdbx_PDB_model_num
has db xref: WHATIF: model_number
has definition: Identifier of a model structure from a PDB file.
has exact synonym: Model number
in subset: bio
in subset: data
in subset: identifiers

CATH domain report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein family report
has definition: Summary of domain classification information for a CATH domain.
in subset: obsolete
comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
deprecated: true

CATH representative domain sequences (ATOM)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence cluster
has definition: FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).
in subset: obsolete
deprecated: true

CATH representative domain sequences (COMBS)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence cluster
has definition: FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).
in subset: obsolete
deprecated: true

CATH domain sequences (ATOM)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: FASTA sequence database for all CATH domains (based on PDB ATOM records).
in subset: obsolete
deprecated: true

CATH domain sequences (COMBS)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: FASTA sequence database for all CATH domains (based on COMBS sequence data).
in subset: obsolete
deprecated: true

Sequence version
type: Class
subclass of: Sequence attribute
Created in: beta12orEarlier
has definition: Information on an molecular sequence version.
has exact synonym: Sequence version information
in subset: bio
in subset: data

Score
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: A numerical value, that is some type of scored value arising for example from a prediction method.
in subset: bio
in subset: data

Protein report (function)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein report
has definition: Report on general functional properties of specific protein(s).
in subset: obsolete
comment: For properties that can be mapped to a sequence, use 'Sequence report' instead.
deprecated: true

Gene name (ASPGD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from Aspergillus Genome Database.
in subset: obsolete
deprecated: true

Gene name (CGD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from Candida Genome Database.
in subset: obsolete
deprecated: true

Gene name (dictyBase)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from dictyBase database.
in subset: obsolete
deprecated: true

Gene name (EcoGene primary)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Primary name of a gene from EcoGene Database.
in subset: obsolete
deprecated: true

Gene name (MaizeGDB)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from MaizeGDB (maize genes) database.
in subset: obsolete
deprecated: true

Gene name (SGD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from Saccharomyces Genome Database.
in subset: obsolete
deprecated: true

Gene name (TGD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from Tetrahymena Genome Database.
in subset: obsolete
deprecated: true

Gene name (CGSC)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Symbol of a gene from E.coli Genetic Stock Center.
in subset: obsolete
deprecated: true

Gene name (HGNC)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Symbol of a gene approved by the HUGO Gene Nomenclature Committee.
in subset: obsolete
deprecated: true

Gene name (MGD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Symbol of a gene from the Mouse Genome Database.
in subset: obsolete
deprecated: true

Gene name (Bacillus subtilis)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Symbol of a gene from Bacillus subtilis Genome Sequence Project.
in subset: obsolete
deprecated: true

Gene ID (PlasmoDB)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
has definition: Identifier of a gene from PlasmoDB Plasmodium Genome Resource.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (EcoGene)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of a gene from EcoGene Database.
has exact synonym: EcoGene Accession
has exact synonym: EcoGene ID
in subset: bio
in subset: data
in subset: identifiers

Gene ID (FlyBase)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
has definition: Gene identifier from FlyBase database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (GeneDB Glossina morsitans)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (GeneDB)
has definition: Gene identifier from Glossina morsitans GeneDB database.
in subset: obsolete
deprecated: true

Gene ID (GeneDB Leishmania major)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (GeneDB)
has definition: Gene identifier from Leishmania major GeneDB database.
in subset: obsolete
deprecated: true

Gene ID (GeneDB Plasmodium falciparum)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (GeneDB)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
has definition: Gene identifier from Plasmodium falciparum GeneDB database.
in subset: obsolete
deprecated: true

Gene ID (GeneDB Schizosaccharomyces pombe)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (GeneDB)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
has definition: Gene identifier from Schizosaccharomyces pombe GeneDB database.
in subset: obsolete
deprecated: true

Gene ID (GeneDB Trypanosoma brucei)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (GeneDB)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
has definition: Gene identifier from Trypanosoma brucei GeneDB database.
in subset: obsolete
deprecated: true

Gene ID (Gramene)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene
has definition: Gene identifier from Gramene database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (Virginia microbial)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD
has definition: Gene identifier from Virginia Bioinformatics Institute microbial database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (SGN)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN
has definition: Gene identifier from Sol Genomics Network.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (WormBase)
type: Class
subclass of: Accession
subclass of: WormBase identifier
subclass of: Gene ID
Created in: beta12orEarlier
Regular expression: WBGene[0-9]{8}
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
has definition: Gene identifier used by WormBase database.
in subset: bio
in subset: data
in subset: identifiers

Gene synonym
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene symbol
has definition: Any name (other than the recommended one) for a gene.
in subset: obsolete
deprecated: true

ORF name
type: Class
subclass of: Name
subclass of: ORF identifier
Created in: beta12orEarlier
has definition: The name of an open reading frame attributed by a sequencing project.
in subset: bio
in subset: data
in subset: identifiers

Sequence assembly component
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence assembly
has definition: A component of a larger sequence assembly.
in subset: obsolete
deprecated: true

Chromosome annotation (aberration)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Chromosome report
has definition: A report on a chromosome aberration such as abnormalities in chromosome structure.
in subset: obsolete
deprecated: true

Clone ID
type: Class
subclass of: Transcript ID
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a clone (cloned molecular sequence) from a database.
in subset: bio
in subset: data
in subset: identifiers

PDB insertion code
type: Class
subclass of: Sequence position
Created in: beta12orEarlier
has db xref: PDBML:pdbx_PDB_ins_code
has db xref: WHATIF: insertion_code
has definition: An insertion code (part of the residue number) for an amino acid residue from a PDB file.
in subset: bio
in subset: data

Atomic occupancy
type: Class
subclass of: Atomic property
Created in: beta12orEarlier
has db xref: WHATIF: PDBx_occupancy
has definition: The fraction of an atom type present at a site in a molecular structure.
in subset: bio
in subset: data
comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.

Isotropic B factor
type: Class
subclass of: Atomic property
Created in: beta12orEarlier
has db xref: WHATIF: PDBx_B_iso_or_equiv
has definition: Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.
in subset: bio
in subset: data

Deletion map
type: Class
subclass of: Cytogenetic map
Created in: beta12orEarlier
has definition: A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.
has exact synonym: Deletion-based cytogenetic map
in subset: bio
in subset: data
comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.

QTL map
type: Class
subclass of: Genetic map
Created in: beta12orEarlier
has definition: A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.
has exact synonym: Quantitative trait locus map
in subset: bio
in subset: data

Haplotype map
type: Class
subclass of: Genetic map
Created in: beta12orEarlier
has db xref: Moby:Haplotyping_Study_obj
has definition: A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.
in subset: bio
in subset: data

Map set data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Map data
has definition: Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.
in subset: obsolete
replaced by: Map data
deprecated: true

Map feature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence features
consider: Nucleic acid features
consider: Map data
has definition: A feature which may mapped (positioned) on a genetic or other type of map.
in subset: obsolete
comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
deprecated: true

Map type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A designation of the type of map (genetic map, physical map, sequence map etc) or map set.
in subset: obsolete
comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
deprecated: true

Protein fold name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a protein fold.
in subset: bio
in subset: data
in subset: identifiers

Taxon
type: Class
subclass of: Organism name
Created in: beta12orEarlier
has db xref: Moby:BriefTaxonConcept
has db xref: Moby:PotentialTaxon
has definition: The name of a group of organisms belonging to the same taxonomic rank.
has exact synonym: Taxonomic rank
has exact synonym: Taxonomy rank
in subset: bio
in subset: data
in subset: identifiers
comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.

Organism identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Organism report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique identifier of a (group of) organisms.
in subset: bio
in subset: data
in subset: identifiers

Genus name
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a genus of organism.
in subset: bio
in subset: data
in subset: identifiers

Taxonomic classification
type: Class
subclass of: Organism name
Created in: beta12orEarlier
has db xref: Moby:GCP_Taxon
has db xref: Moby:TaxonName
has db xref: Moby:TaxonScientificName
has db xref: Moby:TaxonTCS
has db xref: Moby:iANT_organism-xml
has definition: The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.
has exact synonym: Taxonomic information
has exact synonym: Taxonomic name
in subset: bio
in subset: data
in subset: identifiers
comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.

iHOP organism ID
type: Class
subclass of: Accession
subclass of: Organism accession
Created in: beta12orEarlier
has db xref: Moby_namespace:iHOPorganism
has definition: A unique identifier for an organism used in the iHOP database.
in subset: bio
in subset: data
in subset: identifiers

Genbank common name
type: Class
subclass of: Organism name
Created in: beta12orEarlier
has definition: Common name for an organism as used in the GenBank database.
in subset: bio
in subset: data
in subset: identifiers

NCBI taxon
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a taxon from the NCBI taxonomy database.
in subset: bio
in subset: data
in subset: identifiers

Synonym
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Keyword
has definition: An alternative for a word.
in subset: obsolete
deprecated: true

Misspelling
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Keyword
has definition: A common misspelling of a word.
in subset: obsolete
deprecated: true

Acronym
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Keyword
has definition: An abbreviation of a phrase or word.
in subset: obsolete
deprecated: true

Misnomer
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Keyword
has definition: A term which is likely to be misleading of its meaning.
in subset: obsolete
deprecated: true

Author ID
type: Class
subclass of: Person identifier
Created in: beta12orEarlier
has db xref: Moby:Author
has definition: Information on the authors of a published work.
in subset: bio
in subset: data
in subset: identifiers

DragonDB author identifier
type: Class
subclass of: Author ID
Created in: beta12orEarlier
has definition: An identifier representing an author in the DragonDB database.
in subset: bio
in subset: data
in subset: identifiers

Annotated URI
type: Class
subclass of: Data reference
Created in: beta12orEarlier
has db xref: Moby:DescribedLink
has definition: A URI along with annotation describing the data found at the address.
in subset: bio
in subset: data

UniProt keywords
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology
has definition: A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.
in subset: obsolete
deprecated: true

Gene ID (GeneFarm)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: Moby_namespace:GENEFARM_GeneID
has definition: Identifier of a gene from the GeneFarm database.
in subset: bio
in subset: data
in subset: identifiers

Blattner number
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: Moby_namespace:Blattner_number
has definition: The blattner identifier for a gene.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (MIPS Maize)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (MIPS)
has db xref: Moby_namespace:MIPS_GE_Maize
has definition: Identifier for genetic elements in MIPS Maize database.
in subset: obsolete
deprecated: true

Gene ID (MIPS Medicago)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Gene ID (MIPS)
has db xref: Moby_namespace:MIPS_GE_Medicago
has definition: Identifier for genetic elements in MIPS Medicago database.
in subset: obsolete
deprecated: true

Gene name (DragonDB)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: The name of an Antirrhinum Gene from the DragonDB database.
in subset: obsolete
deprecated: true

Gene name (Arabidopsis)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.
in subset: obsolete
deprecated: true

iHOP symbol
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
subclass of: Gene ID
subclass of: Protein accession
Created in: beta12orEarlier
has db xref: Moby_namespace:iHOPsymbol
has definition: A unique identifier of a protein or gene used in the iHOP database.
in subset: bio
in subset: data
in subset: identifiers

Gene name (GeneFarm)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of a gene from the GeneFarm database.
in subset: obsolete
deprecated: true

Locus ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence coordinates
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: 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.
has exact synonym: Locus identifier
has exact synonym: Locus name
in subset: bio
in subset: data
in subset: identifiers

Locus ID (AGI)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: AT[1-5]G[0-9]{5}
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode
has definition: Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases).
has exact synonym: AGI ID
has exact synonym: AGI identifier
has exact synonym: AGI locus code
has exact synonym: Arabidopsis gene loci number
in subset: bio
in subset: data
in subset: identifiers

Locus ID (ASPGD)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
has definition: Identifier for loci from ASPGD (Aspergillus Genome Database).
in subset: bio
in subset: data
in subset: identifiers

Locus ID (MGG)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
has definition: Identifier for loci from Magnaporthe grisea Database at the Broad Institute.
in subset: bio
in subset: data
in subset: identifiers

Locus ID (CGD)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
has definition: Identifier for loci from CGD (Candida Genome Database).
has exact synonym: CGD locus identifier
has exact synonym: CGDID
in subset: bio
in subset: data
in subset: identifiers

Locus ID (CMR)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
has definition: Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.
in subset: bio
in subset: data
in subset: identifiers

NCBI locus tag
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby_namespace:LocusID
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
has definition: Identifier for loci from NCBI database.
has exact synonym: Locus ID (NCBI)
in subset: bio
in subset: data
in subset: identifiers

Locus ID (SGD)
type: Class
subclass of: Locus ID
subclass of: Accession
subclass of: SGD ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
has definition: Identifier for loci from SGD (Saccharomyces Genome Database).
has exact synonym: SGDID
in subset: bio
in subset: data
in subset: identifiers

Locus ID (MMP)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby_namespace:MMP_Locus
has definition: Identifier of loci from Maize Mapping Project.
in subset: bio
in subset: data
in subset: identifiers

Locus ID (DictyBase)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby_namespace:DDB_gene
has definition: Identifier of locus from DictyBase (Dictyostelium discoideum).
in subset: bio
in subset: data
in subset: identifiers

Locus ID (EntrezGene)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby_namespace:EntrezGene_EntrezGeneID
has db xref: Moby_namespace:EntrezGene_ID
has definition: Identifier of a locus from EntrezGene database.
in subset: bio
in subset: data
in subset: identifiers

Locus ID (MaizeGDB)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby_namespace:MaizeGDB_Locus
has definition: Identifier of locus from MaizeGDB (Maize genome database).
in subset: bio
in subset: data
in subset: identifiers

Quantitative trait locus
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence coordinates
has db xref: Moby:SO_QTL
has definition: 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).
in subset: obsolete
comment: A QTL sometimes but does not necessarily correspond to a gene.
deprecated: true

Gene ID (KOME)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has db xref: Moby_namespace:GeneId
has definition: Identifier of a gene from the KOME database.
in subset: bio
in subset: data
in subset: identifiers

Locus ID (Tropgene)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has db xref: Moby:Tropgene_locus
has definition: Identifier of a locus from the Tropgene database.
in subset: bio
in subset: data
in subset: identifiers

Alignment
type: Class
subclass of: Data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An alignment of molecular sequences, structures or profiles derived from them.
in subset: bio
in subset: data

Atomic property
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
has definition: Data for an atom (in a molecular structure).
has exact synonym: General atomic property
in subset: bio
in subset: data

UniProt keyword
type: Class
subclass of: Keyword
Created in: beta12orEarlier
has db xref: Moby_namespace:SP_KW
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW
has definition: A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.
in subset: bio
in subset: data

Ordered locus name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Locus ID
has definition: 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.
in subset: obsolete
deprecated: true

Sequence coordinates
type: Class
subclass of: Data
subclass of: Sequence position
subclass of: Sequence range
Created in: beta12orEarlier
has db xref: Moby:GCP_MapInterval
has db xref: Moby:GCP_MapPoint
has db xref: Moby:GCP_MapPosition
has db xref: Moby:GenePosition
has db xref: Moby:HitPosition
has db xref: Moby:Locus
has db xref: Moby:MapPosition
has db xref: Moby:Position
has db xref: PDBML:_atom_site.id
has definition: A position in a map (for example a genetic map), either a single position (point) or a region / interval.
has exact synonym: Locus
has exact synonym: Map position
in subset: bio
in subset: data
comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.

Amino acid property
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
has definition: Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.
has exact synonym: Amino acid data
in subset: bio
in subset: data

Annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Report
has definition: 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.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Map data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: 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.
has narrow synonym: Map attribute
has narrow synonym: Map set data
in subset: bio
in subset: data

Vienna RNA structural data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: RNA structure
has definition: Data used by the Vienna RNA analysis package.
in subset: obsolete
deprecated: true

Sequence mask parameter
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence attribute
has definition: Data used to replace (mask) characters in a molecular sequence.
in subset: obsolete
deprecated: true

Enzyme kinetics data
type: Class
subclass of: Protein property
subclass of: Reaction data
Created in: beta12orEarlier
has definition: Data concerning chemical reaction(s) catalysed by enzyme(s).
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Michaelis Menten plot
type: Class
subclass of: Enzyme kinetics data
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Hanes Woolf plot
type: Class
subclass of: Enzyme kinetics data
Created in: beta12orEarlier
has definition: 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).
in subset: bio
in subset: data

Experimental data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protocol
consider: Experimental measurement
has definition: Raw data from or annotation on laboratory experiments.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

Genome version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Genome report
has definition: Information on a genome version.
in subset: obsolete
deprecated: true

Evidence
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Sequence record lite
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Sequence
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
Created in: beta12orEarlier
has definition: One or more molecular sequences, possibly with associated annotation.
has exact synonym: Sequences
in subset: bio
in subset: data
comment: This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.

Nucleic acid sequence record (lite)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Protein sequence record (lite)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Report
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Document
has exact synonym: Record
in subset: bio
in subset: data
comment: 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.

Molecular property (general)
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
has definition: General data for a molecule.
has exact synonym: General molecular property
in subset: bio
in subset: data

Structural data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure
consider: Structure report
has definition: Data concerning molecular structural data.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Sequence motif (nucleic acid)
type: Class
subclass of: Sequence motif
Created in: beta12orEarlier
has definition: A nucleotide sequence motif.
has exact synonym: Nucleic acid sequence motif
has narrow synonym: DNA sequence motif
has narrow synonym: RNA sequence motif
in subset: bio
in subset: data

Sequence motif (protein)
type: Class
subclass of: Sequence motif
Created in: beta12orEarlier
has definition: An amino acid sequence motif.
has exact synonym: Protein sequence motif
in subset: bio
in subset: data

Search parameter
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: Some simple value controlling a search operation, typically a search of a database.
in subset: obsolete
deprecated: true

Database search results
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: A report of hits from searching a database of some type.
has exact synonym: Database hits
has exact synonym: Search results
in subset: bio
in subset: data

Secondary structure
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Structure
has definition: The secondary structure assignment (predicted or real) of a nucleic acid or protein.
in subset: obsolete
deprecated: true

Matrix
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: An array of numerical values.
has exact synonym: Array
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Alignment data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Alignment score or penalty
has definition: Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Nucleic acid report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: A human-readable collection of information about one or more specific nucleic acid molecules.
in subset: bio
in subset: data

Structure report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Structure-derived report
in subset: bio
in subset: data

Nucleic acid structure data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: operation_0912
consider: Nucleic acid property
consider: Nucleic acid structure report
has definition: 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).
in subset: obsolete
deprecated: true

Molecular property
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.
has exact synonym: Physicochemical property
has related synonym: SO:0000400
in subset: bio
in subset: data

DNA base structural data
type: Class
subclass of: Nucleic acid property
Created in: beta12orEarlier
has definition: Structural data for DNA base pairs or runs of bases, such as energy or angle data.
in subset: bio
in subset: data

Database entry version information
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Database metadata
has definition: 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.
in subset: obsolete
deprecated: true

Accession
type: Class
subclass of: Identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.
in subset: bio
in subset: data
in subset: identifiers

SNP
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: single nucleotide polymorphism (SNP) in a DNA sequence.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Data reference
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.
in subset: bio
in subset: data
comment: A list of database accessions or identifiers are usually included.

Job identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a submitted job.
in subset: bio
in subset: data
in subset: identifiers

Name
type: Class
subclass of: Identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A name of a thing, which need not necessarily uniquely identify it.
has exact synonym: Symbolic name
in subset: bio
in subset: data
in subset: identifiers
broad match: label

Axiom
annotated source: Name
annotated property: broadMatch
annotated target: label
comment: Closely related, but focusing on labeling and human readability but not on identification.

Type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).
in subset: obsolete
deprecated: true

Account authentication
type: Class
subclass of: Person identifier
Created in: beta12orEarlier
has definition: Authentication data usually used to log in into an account on an information system such as a web application or a database.
in subset: bio
in subset: data
in subset: identifiers

KEGG organism code
type: Class
subclass of: KEGG object identifier
subclass of: Organism name
Created in: beta12orEarlier
has definition: A three-letter code used in the KEGG databases to uniquely identify organisms.
in subset: bio
in subset: data
in subset: identifiers

Gene name (KEGG GENES)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of an entry (gene) from the KEGG GENES database.
in subset: obsolete
deprecated: true

BioCyc ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Identifier of an object from one of the BioCyc databases.
in subset: bio
in subset: data
in subset: identifiers

Compound ID (BioCyc)
type: Class
subclass of: Accession
subclass of: BioCyc ID
subclass of: Compound accession
Created in: beta12orEarlier
has definition: Identifier of a compound from the BioCyc chemical compounds database.
has exact synonym: BioCyc compound ID
has exact synonym: BioCyc compound identifier
in subset: bio
in subset: data
in subset: identifiers

Reaction ID (BioCyc)
type: Class
subclass of: Accession
subclass of: BioCyc ID
subclass of: Reaction ID
Created in: beta12orEarlier
has definition: Identifier of a biological reaction from the BioCyc reactions database.
in subset: bio
in subset: data
in subset: identifiers

Enzyme ID (BioCyc)
type: Class
subclass of: Accession
subclass of: BioCyc ID
subclass of: Enzyme ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme from the BioCyc enzymes database.
has exact synonym: BioCyc enzyme ID
in subset: bio
in subset: data
in subset: identifiers

Reaction ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Reaction data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a biological reaction from a database.
in subset: bio
in subset: data
in subset: identifiers

Identifier (hybrid)
type: Class
subclass of: Identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).
in subset: bio
in subset: data
in subset: identifiers
comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.

Molecular property identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Molecular property
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a molecular property.
in subset: bio
in subset: data
in subset: identifiers

Codon usage table ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Codon usage table
subclass of: Restriction
  on property: is identifier of
  some values from: Genetic code
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a codon usage table, for example a genetic code.
has exact synonym: Codon usage table identifier
in subset: bio
in subset: data
in subset: identifiers

FlyBase primary identifier
type: Class
subclass of: FlyBase ID
Created in: beta12orEarlier
has definition: Primary identifier of an object from the FlyBase database.
in subset: bio
in subset: data
in subset: identifiers

WormBase identifier
type: Class
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Identifier of an object from the WormBase database.
in subset: bio
in subset: data
in subset: identifiers

WormBase wormpep ID
type: Class
subclass of: Accession
subclass of: WormBase identifier
subclass of: Protein accession
Created in: beta12orEarlier
Regular expression: CE[0-9]{5}
has definition: Protein identifier used by WormBase database.
in subset: bio
in subset: data
in subset: identifiers

Nucleic acid features (codon)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: 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.
in subset: obsolete
deprecated: true

Map identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Map
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a map of a molecular sequence.
in subset: bio
in subset: data
in subset: identifiers

Person identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a software end-user on a website or a database (typically a person or an entity).
in subset: bio
in subset: data
in subset: identifiers

Nucleic acid identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Nucleic acid report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Name or other identifier of a nucleic acid molecule.
in subset: bio
in subset: data
in subset: identifiers

Translation frame specification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Sequence attribute
consider: Sequence attribute
has definition: Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).
in subset: obsolete
deprecated: true

Genetic code identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Genetic code
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a genetic code.
in subset: bio
in subset: data
in subset: identifiers

Genetic code name
type: Class
subclass of: Name
subclass of: Genetic code identifier
Created in: beta12orEarlier
has definition: Informal name for a genetic code, typically an organism name.
in subset: bio
in subset: data
in subset: identifiers

File format name
type: Class
subclass of: Name
subclass of: Format identifier
Created in: beta12orEarlier
has definition: Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.
in subset: bio
in subset: data
in subset: identifiers

Sequence profile type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.
in subset: obsolete
deprecated: true

Operating system name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: Name of a computer operating system such as Linux, PC or Mac.
in subset: bio
in subset: data
in subset: identifiers

Mutation type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Mutation identifier
has definition: A type of point or block mutation, including insertion, deletion, change, duplication and moves.
in subset: obsolete
deprecated: true

Logical operator
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: A logical operator such as OR, AND, XOR, and NOT.
in subset: bio
in subset: data
in subset: identifiers

Results sort order
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: A control of the order of data that is output, for example the order of sequences in an alignment.
in subset: obsolete
comment: Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.
deprecated: true

Toggle
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: A simple parameter that is a toggle (boolean value), typically a control for a modal tool.
in subset: obsolete
deprecated: true

Sequence width
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence length
has definition: The width of an output sequence or alignment.
in subset: obsolete
deprecated: true

Gap penalty
type: Class
subclass of: Alignment score or penalty
Created in: beta12orEarlier
has definition: A penalty for introducing or extending a gap in an alignment.
in subset: bio
in subset: data

Nucleic acid melting temperature
type: Class
subclass of: Nucleic acid thermodynamic data
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Melting temperature
in subset: bio
in subset: data

Concentration
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
has definition: The concentration of a chemical compound.
in subset: bio
in subset: data

Window step size
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence length
has definition: Size of the incremental 'step' a sequence window is moved over a sequence.
in subset: obsolete
deprecated: true

EMBOSS graph
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Image
has definition: An image of a graph generated by the EMBOSS suite.
in subset: obsolete
deprecated: true

EMBOSS report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: An application report generated by the EMBOSS suite.
in subset: obsolete
deprecated: true

Sequence offset
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence attribute
has definition: An offset for a single-point sequence position.
in subset: obsolete
deprecated: true

Threshold
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Score
has definition: A value that serves as a threshold for a tool (usually to control scoring or output).
in subset: obsolete
deprecated: true

Protein report (transcription factor)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein report
has definition: An informative report on a transcription factor protein.
in subset: obsolete
comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
deprecated: true

Database category name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Database metadata
has definition: The name of a category of biological or bioinformatics database.
in subset: obsolete
deprecated: true

Sequence profile name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence profile ID
has definition: Name of a sequence profile.
in subset: obsolete
deprecated: true

Color
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: Specification of one or more colors.
in subset: obsolete
deprecated: true

Rendering parameter
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: A parameter that is used to control rendering (drawing) to a device or image.
in subset: obsolete
deprecated: true

Sequence name
type: Class
subclass of: Sequence identifier
subclass of: Name
Created in: beta12orEarlier
has definition: Any arbitrary name of a molecular sequence.
in subset: bio
in subset: data
in subset: identifiers

Date
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: A temporal date.
in subset: obsolete
deprecated: true

Word composition
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Base word frequencies table
consider: Amino acid word frequencies table
has definition: Word composition data for a molecular sequence.
in subset: obsolete
deprecated: true

Fickett testcode plot
type: Class
subclass of: Plot
Created in: beta12orEarlier
has definition: A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.
in subset: bio
in subset: data

Sequence similarity plot
type: Class
subclass of: Sequence alignment report
subclass of: Plot
Created in: beta12orEarlier
has definition: A plot of sequence similarities identified from word-matching or character comparison.
has related synonym: Sequence conservation report
in subset: bio
in subset: data
comment: 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.

Helical wheel
type: Class
subclass of: Protein secondary structure image
Created in: beta12orEarlier
has definition: An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.
in subset: bio
in subset: data

Helical net
type: Class
subclass of: Protein secondary structure image
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: Useful for highlighting amphipathicity and other properties.

Protein sequence properties plot
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein property
has definition: A plot of general physicochemical properties of a protein sequence.
in subset: obsolete
deprecated: true

Protein ionisation curve
type: Class
subclass of: Protein property
subclass of: Plot
Created in: beta12orEarlier
has definition: A plot of pK versus pH for a protein.
in subset: bio
in subset: data

Sequence composition plot
type: Class
subclass of: Sequence composition report
subclass of: Plot
Created in: beta12orEarlier
has definition: A plot of character or word composition / frequency of a molecular sequence.
in subset: bio
in subset: data

Nucleic acid density plot
type: Class
subclass of: Sequence composition report
subclass of: Plot
Created in: beta12orEarlier
has definition: Density plot (of base composition) for a nucleotide sequence.
in subset: bio
in subset: data

Sequence trace image
type: Class
subclass of: Sequence image
Created in: beta12orEarlier
has definition: Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).
in subset: bio
in subset: data

Nucleic acid features (siRNA)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Nucleic acid features
has definition: A report on siRNA duplexes in mRNA.
in subset: obsolete
deprecated: true

Sequence set (stream)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence set
has definition: A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.
in subset: obsolete
comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.
deprecated: true

FlyBase secondary identifier
type: Class
subclass of: FlyBase ID
Created in: beta12orEarlier
has definition: Secondary identifier of an object from the FlyBase database.
in subset: bio
in subset: data
in subset: identifiers
comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database.

Cardinality
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data
has definition: The number of a certain thing.
in subset: obsolete
deprecated: true

Exactly 1
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: A single thing.
in subset: obsolete
deprecated: true

1 or more
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: One or more things.
in subset: obsolete
deprecated: true

Exactly 2
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: Exactly two things.
in subset: obsolete
deprecated: true

2 or more
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Resource metadata
has definition: Two or more things.
in subset: obsolete
deprecated: true

Sequence checksum
type: Class
subclass of: Sequence attribute
Created in: beta12orEarlier
has definition: A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.
has exact synonym: Hash
has exact synonym: Hash code
has exact synonym: Hash sum
has exact synonym: Hash value
in subset: bio
in subset: data

Protein features report (chemical modifications)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: chemical modification of a protein.
in subset: obsolete
replaced by: Protein features
deprecated: true

Error
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: Data on an error generated by computer system or tool.
in subset: obsolete
deprecated: true

Database entry metadata
type: Class
subclass of: Resource metadata
Created in: beta12orEarlier
has definition: Basic information on any arbitrary database entry.
in subset: bio
in subset: data

Gene cluster
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence cluster (nucleic acid)
has definition: A cluster of similar genes.
in subset: obsolete
deprecated: true

Sequence record full
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Plasmid identifier
type: Class
subclass of: Nucleic acid identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a plasmid in a database.
in subset: bio
in subset: data
in subset: identifiers

Mutation ID
type: Class
subclass of: Accession
subclass of: Mutation identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique identifier of a specific mutation catalogued in a database.
in subset: bio
in subset: data
in subset: identifiers

Mutation annotation (basic)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: 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.
in subset: obsolete
deprecated: true

Mutation annotation (prevalence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..
in subset: obsolete
deprecated: true

Mutation annotation (prognostic)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.
in subset: obsolete
deprecated: true

Mutation annotation (functional)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: 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.
in subset: obsolete
deprecated: true

Codon number
type: Class
subclass of: Sequence position
Created in: beta12orEarlier
has definition: The number of a codon, for instance, at which a mutation is located.
in subset: bio
in subset: data

Tumor annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Disease report
has definition: 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.
in subset: obsolete
deprecated: true

Server metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: System metadata
has definition: Basic information about a server on the web, such as an SRS server.
in subset: obsolete
deprecated: true

Database field name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a field in a database.
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (SYSTERS)
type: Class
subclass of: Sequence cluster ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of a sequence cluster from the SYSTERS database.
has exact synonym: SYSTERS cluster ID
in subset: bio
in subset: data
in subset: identifiers

Ontology metadata
type: Class
subclass of: Resource metadata
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
Created in: beta12orEarlier
has definition: Data concerning a biological ontology.
in subset: bio
in subset: data

Raw SCOP domain classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein family report
has definition: Raw SCOP domain classification data files.
in subset: obsolete
comment: These are the parsable data files provided by SCOP.
deprecated: true

Raw CATH domain classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein family report
has definition: Raw CATH domain classification data files.
in subset: obsolete
comment: These are the parsable data files provided by CATH.
deprecated: true

Heterogen annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files.
in subset: obsolete
deprecated: true

Phylogenetic property values
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Phylogenetic character data
has definition: Phylogenetic property values data.
in subset: obsolete
deprecated: true

Sequence set (bootstrapped)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Sequence set
has definition: A collection of sequences output from a bootstrapping (resampling) procedure.
in subset: obsolete
comment: Bootstrapping is often performed in phylogenetic analysis.
deprecated: true

Phylogenetic consensus tree
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Phylogenetic tree
has definition: A consensus phylogenetic tree derived from comparison of multiple trees.
in subset: obsolete
deprecated: true

Schema
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: A data schema for organising or transforming data of some type.
in subset: obsolete
deprecated: true

DTD
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: A DTD (document type definition).
in subset: obsolete
deprecated: true

XML Schema
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: An XML Schema.
in subset: obsolete
deprecated: true

Relax-NG schema
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: A relax-NG schema.
in subset: obsolete
deprecated: true

XSLT stylesheet
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: An XSLT stylesheet.
in subset: obsolete
deprecated: true

Data resource definition name
type: Class
subclass of: Data resource definition ID
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a data type.
in subset: bio
in subset: data
in subset: identifiers

OBO file format name
type: Class
subclass of: File format name
Created in: beta12orEarlier
has definition: Name of an OBO file format such as OBO-XML, plain and so on.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (MIPS)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier for genetic elements in MIPS database.
has exact synonym: MIPS genetic element identifier
in subset: bio
in subset: data
in subset: identifiers

Sequence identifier (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence accession (protein)
has definition: An identifier of protein sequence(s) or protein sequence database entries.
in subset: obsolete
deprecated: true

Sequence identifier (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence accession (nucleic acid)
has definition: An identifier of nucleotide sequence(s) or nucleotide sequence database entries.
in subset: obsolete
deprecated: true

EMBL accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
Created in: beta12orEarlier
has definition: An accession number of an entry from the EMBL sequence database.
has exact synonym: EMBL ID
has exact synonym: EMBL accession number
has exact synonym: EMBL identifier
in subset: bio
in subset: data
in subset: identifiers

UniProt ID
type: Class
subclass of: Sequence name
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
Created in: beta12orEarlier
has definition: An identifier of a polypeptide in the UniProt database.
has exact synonym: UniProt entry name
has exact synonym: UniProt identifier
has exact synonym: UniProtKB entry name
has exact synonym: UniProtKB identifier
in subset: bio
in subset: data
in subset: identifiers

GenBank accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
Created in: beta12orEarlier
has definition: Accession number of an entry from the GenBank sequence database.
has exact synonym: GenBank ID
has exact synonym: GenBank accession number
has exact synonym: GenBank identifier
in subset: bio
in subset: data
in subset: identifiers

Gramene secondary identifier
type: Class
subclass of: Gramene identifier
Created in: beta12orEarlier
has definition: Secondary (internal) identifier of a Gramene database entry.
has exact synonym: Gramene internal ID
has exact synonym: Gramene internal identifier
has exact synonym: Gramene secondary ID
in subset: bio
in subset: data
in subset: identifiers

Sequence variation ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of an entry from a database of molecular sequence variation.
in subset: bio
in subset: data
in subset: identifiers

Gene ID
type: Class
subclass of: Gene identifier
subclass of: Locus ID
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.
has exact synonym: Gene accession
has exact synonym: Gene code
in subset: bio
in subset: data
in subset: identifiers

Gene name (AceView)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of an entry (gene) from the AceView genes database.
in subset: obsolete
deprecated: true

Gene ID (ECK)
type: Class
subclass of: Gene ID (EcoGene)
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK
has definition: Identifier of an E. coli K-12 gene from EcoGene Database.
has exact synonym: E. coli K-12 gene identifier
has exact synonym: ECK accession
in subset: bio
in subset: data
in subset: identifiers

Gene ID (HGNC)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier for a gene approved by the HUGO Gene Nomenclature Committee.
has exact synonym: HGNC ID
in subset: bio
in subset: data
in subset: identifiers

Gene name
type: Class
subclass of: Gene identifier
subclass of: Name
Created in: beta12orEarlier
has definition: 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.
has narrow synonym: Allele name
in subset: bio
in subset: data
in subset: identifiers

Gene name (NCBI)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of an entry (gene) from the NCBI genes database.
in subset: obsolete
deprecated: true

SMILES string
type: Class
subclass of: Chemical formula
Created in: beta12orEarlier
has definition: A specification of a chemical structure in SMILES format.
in subset: bio
in subset: data

STRING ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the STRING database of protein-protein interactions.
in subset: bio
in subset: data
in subset: identifiers

Virus annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Organism report
has definition: An informative report on a specific virus.
in subset: obsolete
deprecated: true

Virus annotation (taxonomy)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Organism report
has definition: An informative report on the taxonomy of a specific virus.
in subset: obsolete
deprecated: true

Reaction ID (SABIO-RK)
type: Class
subclass of: Accession
subclass of: Reaction ID
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a biological reaction from the SABIO-RK reactions database.
in subset: bio
in subset: data
in subset: identifiers

Carbohydrate report
type: Class
subclass of: Structure report
Created in: beta12orEarlier
has definition: A human-readable collection of information about one or more specific carbohydrate 3D structure(s).
in subset: bio
in subset: data

GI number
type: Class
subclass of: Accession
subclass of: Sequence accession (hybrid)
Created in: beta12orEarlier
has definition: 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.
has exact synonym: NCBI GI number
in subset: bio
in subset: data
in subset: identifiers
comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.

NCBI version
type: Class
subclass of: Accession
subclass of: Sequence accession (hybrid)
Created in: beta12orEarlier
has definition: 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.
has exact synonym: NCBI accession.version
has exact synonym: accession.version
in subset: bio
in subset: data
in subset: identifiers
comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.

Cell line name
type: Class
subclass of: Strain name
Created in: beta12orEarlier
has definition: The name of a cell line.
in subset: bio
in subset: data
in subset: identifiers

Cell line name (exact)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The exact name of a cell line.
in subset: bio
in subset: data
in subset: identifiers

Cell line name (truncated)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The truncated name of a cell line.
in subset: bio
in subset: data
in subset: identifiers

Cell line name (no punctuation)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The name of a cell line without any punctuation.
in subset: bio
in subset: data
in subset: identifiers

Cell line name (assonant)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The assonant name of a cell line.
in subset: bio
in subset: data
in subset: identifiers

Enzyme ID
type: Class
subclass of: Enzyme identifier
subclass of: Protein accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique, persistent identifier of an enzyme.
has exact synonym: Enzyme accession
in subset: bio
in subset: data
in subset: identifiers

REBASE enzyme number
type: Class
subclass of: Accession
subclass of: Enzyme ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme from the REBASE enzymes database.
in subset: bio
in subset: data
in subset: identifiers

DrugBank ID
type: Class
subclass of: Accession
subclass of: Drug accession
Created in: beta12orEarlier
Regular expression: DB[0-9]{5}
has definition: Unique identifier of a drug from the DrugBank database.
in subset: bio
in subset: data
in subset: identifiers

GI number (protein)
type: Class
subclass of: GI number
Created in: beta12orEarlier
has definition: A unique identifier assigned to NCBI protein sequence records.
has exact synonym: protein gi
has exact synonym: protein gi number
in subset: bio
in subset: data
in subset: identifiers
comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.

Bit score
type: Class
subclass of: Sequence similarity
Created in: beta12orEarlier
has definition: A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system.
in subset: bio
in subset: data
comment: Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches.

Translation phase specification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Sequence attribute
consider: Sequence attribute
has definition: Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.
in subset: obsolete
deprecated: true

Resource metadata
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Provenance metadata
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Ontology identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Ontology
Created in: beta12orEarlier
has definition: Any arbitrary identifier of an ontology.
in subset: bio
in subset: data
in subset: identifiers

Ontology concept name
type: Class
subclass of: Name
subclass of: Ontology concept identifier
Created in: beta12orEarlier
has definition: The name of a concept in an ontology.
in subset: bio
in subset: data
in subset: identifiers

Genome build identifier
type: Class
subclass of: Genome identifier
Created in: beta12orEarlier
has definition: An identifier of a build of a particular genome.
in subset: bio
in subset: data
in subset: identifiers

Pathway or network name
type: Class
subclass of: Pathway or network identifier
Created in: beta12orEarlier
has definition: The name of a biological pathway or network.
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9]{2,3}[0-9]{5}
has definition: Identifier of a pathway from the KEGG pathway database.
has exact synonym: KEGG pathway ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (NCI-Nature)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9]+
has definition: Identifier of a pathway from the NCI-Nature pathway database.
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (ConsensusPathDB)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
subclass of: ConsensusPathDB identifier
Created in: beta12orEarlier
has definition: Identifier of a pathway from the ConsensusPathDB pathway database.
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (UniRef)
type: Class
subclass of: Sequence cluster ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the UniRef database.
has exact synonym: UniRef cluster id
has exact synonym: UniRef entry accession
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (UniRef100)
type: Class
subclass of: Sequence cluster ID (UniRef)
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the UniRef100 database.
has exact synonym: UniRef100 cluster id
has exact synonym: UniRef100 entry accession
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (UniRef90)
type: Class
subclass of: Sequence cluster ID (UniRef)
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the UniRef90 database.
has exact synonym: UniRef90 cluster id
has exact synonym: UniRef90 entry accession
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (UniRef50)
type: Class
subclass of: Sequence cluster ID (UniRef)
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the UniRef50 database.
has exact synonym: UniRef50 cluster id
has exact synonym: UniRef50 entry accession
in subset: bio
in subset: data
in subset: identifiers

Ontology data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
Created in: beta12orEarlier
has definition: Data concerning or derived from an ontology.
has exact synonym: Ontological data
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

RNA family report
type: Class
subclass of: Gene family report
Created in: beta12orEarlier
has definition: A human-readable collection of information about a specific RNA family or other group of classified RNA sequences.
has exact synonym: RNA family annotation
in subset: bio
in subset: data

RNA family identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: RNA family report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an RNA family, typically an entry from a RNA sequence classification database.
in subset: bio
in subset: data
in subset: identifiers

RFAM accession
type: Class
subclass of: Accession
subclass of: RNA family identifier
Created in: beta12orEarlier
has definition: Stable accession number of an entry (RNA family) from the RFAM database.
in subset: bio
in subset: data
in subset: identifiers

Protein signature type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.
in subset: obsolete
deprecated: true

Domain-nucleic acid interaction report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein interaction data
has definition: An informative report on protein domain-DNA/RNA interaction(s).
in subset: obsolete
deprecated: true

Domain-domain interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Protein interaction data
has definition: An informative report on protein domain-protein domain interaction(s).
in subset: obsolete
deprecated: true

Domain-domain interaction (indirect)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein interaction data
has definition: Data on indirect protein domain-protein domain interaction(s).
in subset: obsolete
deprecated: true

Sequence accession (hybrid)
type: Class
subclass of: Sequence accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession number of a nucleotide or protein sequence database entry.
in subset: bio
in subset: data
in subset: identifiers

2D PAGE data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: Data concerning two-dimensional polygel electrophoresis.
in subset: obsolete
replaced by: Protocol
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
deprecated: true

2D PAGE report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: two-dimensional gel electrophoresis experiments, gels or spots in a gel.
in subset: obsolete
replaced by: Protocol
deprecated: true

Pathway or network accession
type: Class
subclass of: Pathway or network identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A persistent, unique identifier of a biological pathway or network (typically a database entry).
in subset: bio
in subset: data
in subset: identifiers

Secondary structure alignment
type: Class
subclass of: Alignment
Created in: beta12orEarlier
has definition: Alignment of the (1D representations of) secondary structure of two or more molecules.
in subset: bio
in subset: data

ASTD ID
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Identifier of an object from the ASTD database.
in subset: bio
in subset: data
in subset: identifiers

ASTD ID (exon)
type: Class
subclass of: ASTD ID
Created in: beta12orEarlier
has definition: Identifier of an exon from the ASTD database.
in subset: bio
in subset: data
in subset: identifiers

ASTD ID (intron)
type: Class
subclass of: ASTD ID
Created in: beta12orEarlier
has definition: Identifier of an intron from the ASTD database.
in subset: bio
in subset: data
in subset: identifiers

ASTD ID (polya)
type: Class
subclass of: ASTD ID
Created in: beta12orEarlier
has definition: Identifier of a polyA signal from the ASTD database.
in subset: bio
in subset: data
in subset: identifiers

ASTD ID (tss)
type: Class
subclass of: ASTD ID
Created in: beta12orEarlier
has definition: Identifier of a transcription start site from the ASTD database.
in subset: bio
in subset: data
in subset: identifiers

2D PAGE spot report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.
in subset: obsolete
replaced by: Protocol
deprecated: true

Spot ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Unique identifier of a spot from a two-dimensional (protein) gel.
in subset: bio
in subset: data
in subset: identifiers

Spot serial number
type: Class
subclass of: Accession
subclass of: Spot ID
Created in: beta12orEarlier
has definition: Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.
in subset: bio
in subset: data
in subset: identifiers

Spot ID (HSC-2DPAGE)
type: Class
subclass of: Accession
subclass of: Spot ID
Created in: beta12orEarlier
has definition: Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.
in subset: bio
in subset: data
in subset: identifiers

Protein-motif interaction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein interaction data
has definition: Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.
in subset: obsolete
deprecated: true

Strain identifier
type: Class
subclass of: Organism identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a strain of an organism variant, typically a plant, virus or bacterium.
in subset: bio
in subset: data
in subset: identifiers

CABRI accession
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: A unique identifier of an item from the CABRI database.
in subset: bio
in subset: data
in subset: identifiers

Experiment report (genotyping)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
in subset: obsolete
replaced by: Protocol
deprecated: true

Genotype experiment ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Protocol
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of genotype experiment metadata.
in subset: bio
in subset: data
in subset: identifiers

EGA accession
type: Class
subclass of: Accession
subclass of: Genotype experiment ID
Created in: beta12orEarlier
has definition: Identifier of an entry from the EGA database.
in subset: bio
in subset: data
in subset: identifiers

IPI protein ID
type: Class
subclass of: Sequence accession (protein)
subclass of: Accession
Created in: beta12orEarlier
Regular expression: IPI[0-9]{8}
has definition: Identifier of a protein entry catalogued in the International Protein Index (IPI) database.
in subset: bio
in subset: data
in subset: identifiers

RefSeq accession (protein)
type: Class
subclass of: RefSeq accession
Created in: beta12orEarlier
has definition: Accession number of a protein from the RefSeq database.
has exact synonym: RefSeq protein ID
in subset: bio
in subset: data
in subset: identifiers

EPD ID
type: Class
subclass of: Accession
subclass of: Promoter ID
Created in: beta12orEarlier
has definition: Identifier of an entry (promoter) from the EPD database.
has exact synonym: EPD identifier
in subset: bio
in subset: data
in subset: identifiers

TAIR accession
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Identifier of an entry from the TAIR database.
in subset: bio
in subset: data
in subset: identifiers

TAIR accession (At gene)
type: Class
subclass of: TAIR accession (gene)
Created in: beta12orEarlier
has definition: Identifier of an Arabidopsis thaliana gene from the TAIR database.
in subset: bio
in subset: data
in subset: identifiers

UniSTS accession
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the UniSTS database.
in subset: bio
in subset: data
in subset: identifiers

UNITE accession
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the UNITE database.
in subset: bio
in subset: data
in subset: identifiers

UTR accession
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the UTR database.
in subset: bio
in subset: data
in subset: identifiers

UniParc accession
type: Class
subclass of: Sequence accession (protein)
subclass of: Accession
Created in: beta12orEarlier
Regular expression: UPI[A-F0-9]{10}
has definition: Accession number of a UniParc (protein sequence) database entry.
has exact synonym: UPI
has exact synonym: UniParc ID
in subset: bio
in subset: data
in subset: identifiers

mFLJ/mKIAA number
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of an entry from the Rouge or HUGE databases.
in subset: bio
in subset: data
in subset: identifiers

Fungi annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Organism report
has definition: An informative report on a specific fungus.
in subset: obsolete
deprecated: true

Fungi annotation (anamorph)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Organism report
has definition: An informative report on a specific fungus anamorph.
in subset: obsolete
deprecated: true

Ensembl protein ID
type: Class
subclass of: Accession
subclass of: Ensembl ID
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a protein from the Ensembl database.
has exact synonym: Ensembl ID (protein)
has exact synonym: Protein ID (Ensembl)
in subset: bio
in subset: data
in subset: identifiers

Toxin annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report on a specific toxin.
in subset: obsolete
deprecated: true

Protein report (membrane protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein features
has definition: An informative report on a membrane protein.
in subset: obsolete
deprecated: true

Protein-drug interaction report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: An informative report on tentative or known protein-drug interaction(s).
in subset: obsolete
replaced by: Protein-ligand interaction report
deprecated: true

Map data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Map
consider: Map data
has definition: Data concerning a map of molecular sequence(s).
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Phylogenetic data
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Protein data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein report
has definition: Data concerning one or more protein molecules.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Nucleic acid data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Nucleic acid report
has definition: Data concerning one or more nucleic acid molecules.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Text data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Literature and language
Created in: beta12orEarlier
has definition: 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.
has narrow synonym: Article data
has narrow synonym: Scientific text data
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.

Parameter
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Thing
consider: Data
has definition: Typically a simple numerical or string value that controls the operation of a tool.
in subset: obsolete
deprecated: true

Molecular data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Molecular property
has definition: Data concerning a specific type of molecule.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Molecule report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Protein report
consider: Nucleic acid report
has definition: An informative report on a specific molecule.
in subset: obsolete
deprecated: true

Organism report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: A human-readable collection of information about a specific organism.
has exact synonym: Organism annotation
in subset: bio
in subset: data

Protocol
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Experiment annotation
has exact synonym: Experiment metadata
has exact synonym: Experiment report
in subset: bio
in subset: data

Sequence attribute
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: An attribute of a molecular sequence, possibly in reference to some other sequence.
has narrow synonym: Sequence parameter
in subset: bio
in subset: data

Sequence tag profile
type: Class
subclass of: Gene expression profile
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Sequencing-based expression profile
has narrow synonym: Sequence tag profile (with gene assignment)
in subset: bio
in subset: data
comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
comment: 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.

Mass spectrometry data
type: Class
subclass of: Experimental measurement
Created in: beta12orEarlier
has definition: Data concerning a mass spectrometry measurement.
in subset: bio
in subset: data

Protein structure raw data
type: Class
subclass of: Experimental measurement
Created in: beta12orEarlier
has definition: Raw data from experimental methods for determining protein structure.
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.

Mutation identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a mutation.
in subset: bio
in subset: data
in subset: identifiers

Alignment data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Alignment
consider: Alignment data
has definition: Data concerning an alignment of two or more molecular sequences, structures or derived data.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles.
deprecated: true

Data index data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data index
has definition: Data concerning an index of data.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Amino acid name (single letter)
type: Class
subclass of: Amino acid name
Created in: beta12orEarlier
has definition: Single letter amino acid identifier, e.g. G.
in subset: bio
in subset: data
in subset: identifiers

Amino acid name (three letter)
type: Class
subclass of: Amino acid name
Created in: beta12orEarlier
has definition: Three letter amino acid identifier, e.g. GLY.
in subset: bio
in subset: data
in subset: identifiers

Amino acid name (full name)
type: Class
subclass of: Amino acid name
Created in: beta12orEarlier
has definition: Full name of an amino acid, e.g. Glycine.
in subset: bio
in subset: data
in subset: identifiers

Toxin identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Toxin structure
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a toxin.
in subset: bio
in subset: data
in subset: identifiers

ArachnoServer ID
type: Class
subclass of: Accession
subclass of: Toxin accession
Created in: beta12orEarlier
has definition: Unique identifier of a toxin from the ArachnoServer database.
in subset: bio
in subset: data
in subset: identifiers

Expressed gene list
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: ID list
has definition: A simple summary of expressed genes.
in subset: obsolete
deprecated: true

BindingDB Monomer ID
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
has definition: Unique identifier of a monomer from the BindingDB database.
in subset: bio
in subset: data
in subset: identifiers

GO concept name
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept name
has definition: The name of a concept from the GO ontology.
in subset: obsolete
deprecated: true

GO concept ID (biological process)
type: Class
subclass of: GO concept ID
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
has definition: An identifier of a 'biological process' concept from the the Gene Ontology.
in subset: bio
in subset: data
in subset: identifiers

GO concept ID (molecular function)
type: Class
subclass of: GO concept ID
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
has definition: An identifier of a 'molecular function' concept from the the Gene Ontology.
in subset: bio
in subset: data
in subset: identifiers

GO concept name (cellular component)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept name
has definition: The name of a concept for a cellular component from the GO ontology.
in subset: obsolete
deprecated: true

Northern blot image
type: Class
subclass of: Raw image
Created in: beta12orEarlier
has definition: An image arising from a Northern Blot experiment.
in subset: bio
in subset: data

Blot ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Unique identifier of a blot from a Northern Blot.
in subset: bio
in subset: data
in subset: identifiers

BlotBase blot ID
type: Class
subclass of: Accession
subclass of: Blot ID
Created in: beta12orEarlier
has definition: Unique identifier of a blot from a Northern Blot from the BlotBase database.
in subset: bio
in subset: data
in subset: identifiers

Hierarchy
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.
has exact synonym: Hierarchy annotation
in subset: bio
in subset: data

Hierarchy identifier
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Biological model accession
has definition: Identifier of an entry from a database of biological hierarchies.
in subset: obsolete
deprecated: true

Brite hierarchy ID
type: Class
subclass of: Accession
subclass of: Biological model accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the Brite database of biological hierarchies.
in subset: bio
in subset: data
in subset: identifiers

Cancer type
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Name
has definition: A type (represented as a string) of cancer.
in subset: obsolete
deprecated: true

BRENDA organism ID
type: Class
subclass of: Accession
subclass of: Organism accession
Created in: beta12orEarlier
has definition: A unique identifier for an organism used in the BRENDA database.
in subset: bio
in subset: data
in subset: identifiers

UniGene taxon
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a taxon using the controlled vocabulary of the UniGene database.
has exact synonym: UniGene organism abbreviation
in subset: bio
in subset: data
in subset: identifiers

UTRdb taxon
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a taxon using the controlled vocabulary of the UTRdb database.
in subset: bio
in subset: data
in subset: identifiers

Catalogue ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a catalogue of biological resources.
has exact synonym: Catalogue identifier
in subset: bio
in subset: data
in subset: identifiers

CABRI catalogue name
type: Class
subclass of: Name
subclass of: Catalogue ID
Created in: beta12orEarlier
has definition: The name of a catalogue of biological resources from the CABRI database.
in subset: bio
in subset: data
in subset: identifiers

Secondary structure alignment metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence alignment report
has definition: An informative report on protein secondary structure alignment-derived data or metadata.
in subset: obsolete
deprecated: true

Molecule interaction report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
Obsolete since: 1.5
Old parent: Thing
consider: Protein interaction data
has definition: An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).
in subset: obsolete
deprecated: true

Pathway or network
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).
has exact synonym: Network
has exact synonym: Pathway
in subset: bio
in subset: data

Small molecule data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Small molecule report
has definition: Data concerning one or more small molecules.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Genotype and phenotype data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Genotype/phenotype report
has definition: Data concerning a particular genotype, phenotype or a genotype / phenotype relation.
in subset: obsolete
deprecated: true

Expression data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.
has narrow synonym: Gene expression data
has narrow synonym: Gene product profile
has narrow synonym: Gene product quantification data
has narrow synonym: Gene transcription profile
has narrow synonym: Gene transcription quantification data
has narrow synonym: Metabolite expression data
has narrow synonym: Microarray data
has narrow synonym: Non-coding RNA profile
has narrow synonym: Non-coding RNA quantification data
has narrow synonym: Protein expression data
has narrow synonym: RNA profile
has narrow synonym: RNA quantification data
has narrow synonym: RNA-seq data
has narrow synonym: Transcriptome profile
has narrow synonym: Transcriptome quantification data
has narrow synonym: mRNA profile
has narrow synonym: mRNA quantification data
has related synonym: Protein profile
has related synonym: Protein quantification data
has related synonym: Proteome profile
has related synonym: Proteome quantification data
in subset: bio
in subset: data

Compound ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: C[0-9]+
has definition: Unique identifier of a chemical compound from the KEGG database.
has exact synonym: KEGG compound ID
has exact synonym: KEGG compound identifier
in subset: bio
in subset: data
in subset: identifiers

RFAM name
type: Class
subclass of: Name
subclass of: RNA family identifier
Created in: beta12orEarlier
has definition: Name (not necessarily stable) an entry (RNA family) from the RFAM database.
in subset: bio
in subset: data
in subset: identifiers

Reaction ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Reaction ID
Created in: beta12orEarlier
Regular expression: R[0-9]+
has definition: Identifier of a biological reaction from the KEGG reactions database.
in subset: bio
in subset: data
in subset: identifiers

Drug ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Accession
subclass of: Drug accession
Created in: beta12orEarlier
Regular expression: D[0-9]+
has definition: Unique identifier of a drug from the KEGG Drug database.
in subset: bio
in subset: data
in subset: identifiers

Ensembl ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
Regular expression: ENS[A-Z]*[FPTG][0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.
has exact synonym: Ensembl IDs
in subset: bio
in subset: data
in subset: identifiers

ICD identifier
type: Class
subclass of: Disease ID
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
Created in: beta12orEarlier
Regular expression: [A-Z][0-9]+(\.[-[0-9]+])?
has definition: An identifier of a disease from the International Classification of Diseases (ICD) database.
in subset: bio
in subset: data
in subset: identifiers

Sequence cluster ID (CluSTr)
type: Class
subclass of: Sequence cluster ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?
has definition: Unique identifier of a sequence cluster from the CluSTr database.
has exact synonym: CluSTr ID
has exact synonym: CluSTr cluster ID
in subset: bio
in subset: data
in subset: identifiers

KEGG Glycan ID
type: Class
subclass of: KEGG object identifier
subclass of: Accession
subclass of: Carbohydrate accession
Created in: beta12orEarlier
Regular expression: G[0-9]+
has definition: Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).
in subset: bio
in subset: data
in subset: identifiers

TCDB ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+
has definition: A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.
has exact synonym: TC number
in subset: bio
in subset: data
in subset: identifiers
comment: OBO file for regular expression.

MINT ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: MINT\-[0-9]{1,5}
has definition: Unique identifier of an entry from the MINT database of protein-protein interactions.
in subset: bio
in subset: data
in subset: identifiers

DIP ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: DIP[\:\-][0-9]{3}[EN]
has definition: Unique identifier of an entry from the DIP database of protein-protein interactions.
in subset: bio
in subset: data
in subset: identifiers

Signaling Gateway protein ID
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
Regular expression: A[0-9]{6}
has definition: Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.
in subset: bio
in subset: data
in subset: identifiers

Protein modification ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a protein modification catalogued in a database.
in subset: bio
in subset: data
in subset: identifiers

RESID ID
type: Class
subclass of: Accession
subclass of: Protein modification ID
Created in: beta12orEarlier
Regular expression: AA[0-9]{4}
has definition: Identifier of a protein modification catalogued in the RESID database.
in subset: bio
in subset: data
in subset: identifiers

RGD ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
Regular expression: [0-9]{4,7}
has definition: Identifier of an entry from the RGD database.
in subset: bio
in subset: data
in subset: identifiers

TAIR accession (protein)
type: Class
subclass of: Sequence accession (protein)
subclass of: TAIR accession
Created in: beta12orEarlier
Regular expression: AASequence:[0-9]{10}
has definition: Identifier of a protein sequence from the TAIR database.
in subset: bio
in subset: data
in subset: identifiers

Compound ID (HMDB)
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: HMDB[0-9]{5}
has definition: Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).
has exact synonym: HMDB ID
in subset: bio
in subset: data
in subset: identifiers

LIPID MAPS ID
type: Class
subclass of: Accession
subclass of: Lipid accession
Created in: beta12orEarlier
Regular expression: LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?
has definition: Identifier of an entry from the LIPID MAPS database.
has exact synonym: LM ID
in subset: bio
in subset: data
in subset: identifiers

PeptideAtlas ID
type: Class
subclass of: Accession
subclass of: Peptide ID
Created in: beta12orEarlier
Regular expression: PAp[0-9]{8}
has db xref: PDBML:pdbx_PDB_strand_id
has definition: Identifier of a peptide from the PeptideAtlas peptide databases.
in subset: bio
in subset: data
in subset: identifiers

Molecular interaction ID
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: Identifier of a report of molecular interactions from a database (typically).
in subset: obsolete
replaced by: Protein interaction ID
deprecated: true

BioGRID interaction ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: A unique identifier of an interaction from the BioGRID database.
in subset: bio
in subset: data
in subset: identifiers

Enzyme ID (MEROPS)
type: Class
subclass of: Accession
subclass of: Enzyme ID
Created in: beta12orEarlier
Regular expression: S[0-9]{2}\.[0-9]{3}
has definition: Unique identifier of a peptidase enzyme from the MEROPS database.
has exact synonym: MEROPS ID
in subset: bio
in subset: data
in subset: identifiers

Mobile genetic element ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a mobile genetic element.
in subset: bio
in subset: data
in subset: identifiers

ACLAME ID
type: Class
subclass of: Accession
subclass of: Mobile genetic element ID
Created in: beta12orEarlier
Regular expression: mge:[0-9]+
has definition: An identifier of a mobile genetic element from the Aclame database.
in subset: bio
in subset: data
in subset: identifiers

SGD ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
Regular expression: PWY[a-zA-Z_0-9]{2}\-[0-9]{3}
has definition: Identifier of an entry from the Saccharomyces genome database (SGD).
in subset: bio
in subset: data
in subset: identifiers

Book ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Unique identifier of a book.
in subset: bio
in subset: data
in subset: identifiers

ISBN
type: Class
subclass of: Accession
subclass of: Book ID
Created in: beta12orEarlier
Regular expression: (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)
has definition: The International Standard Book Number (ISBN) is for identifying printed books.
in subset: bio
in subset: data
in subset: identifiers

Compound ID (3DMET)
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: B[0-9]{5}
has definition: Identifier of a metabolite from the 3DMET database.
has exact synonym: 3DMET ID
in subset: bio
in subset: data
in subset: identifiers

MatrixDB interaction ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: ([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_.*)
has definition: A unique identifier of an interaction from the MatrixDB database.
in subset: bio
in subset: data
in subset: identifiers

cPath ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.
in subset: bio
in subset: data
in subset: identifiers
comment: These identifiers are unique within the cPath database, however, they are not stable between releases.

PubChem bioassay ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: PubChem ID
Created in: beta12orEarlier
notRecommendedForAnnotation: true
Regular expression: [0-9]+
has definition: Identifier of an assay from the PubChem database.
in subset: bio
in subset: data
in subset: identifiers

PubChem ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: Identifier of an entry from the PubChem database.
has exact synonym: PubChem identifier
in subset: bio
in subset: data
in subset: identifiers

Reaction ID (MACie)
type: Class
subclass of: Accession
subclass of: Reaction ID
Created in: beta12orEarlier
Regular expression: M[0-9]{4}
has definition: Identifier of an enzyme reaction mechanism from the MACie database.
has exact synonym: MACie entry number
in subset: bio
in subset: data
in subset: identifiers

Gene ID (miRBase)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
Regular expression: MI[0-9]{7}
has definition: Identifier for a gene from the miRBase database.
has exact synonym: miRNA ID
has exact synonym: miRNA identifier
has exact synonym: miRNA name
in subset: bio
in subset: data
in subset: identifiers

Gene ID (ZFIN)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
Regular expression: ZDB\-GENE\-[0-9]+\-[0-9]+
has definition: Identifier for a gene from the Zebrafish information network genome (ZFIN) database.
in subset: bio
in subset: data
in subset: identifiers

Reaction ID (Rhea)
type: Class
subclass of: Accession
subclass of: Reaction ID
Created in: beta12orEarlier
Regular expression: [0-9]{5}
has definition: Identifier of an enzyme-catalysed reaction from the Rhea database.
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (Unipathway)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: UPA[0-9]{5}
has definition: Identifier of a biological pathway from the Unipathway database.
has exact synonym: upaid
in subset: bio
in subset: data
in subset: identifiers

Compound ID (ChEMBL)
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a small molecular from the ChEMBL database.
has exact synonym: ChEMBL ID
in subset: bio
in subset: data
in subset: identifiers

LGICdb identifier
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9]+
has definition: Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.
in subset: bio
in subset: data
in subset: identifiers

Reaction kinetics ID (SABIO-RK)
type: Class
subclass of: Reaction ID (SABIO-RK)
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.
in subset: bio
in subset: data
in subset: identifiers

PharmGKB ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
Regular expression: PA[0-9]+
has definition: Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (PharmGKB)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
subclass of: PharmGKB ID
Created in: beta12orEarlier
Regular expression: PA[0-9]+
has definition: Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bio
in subset: data
in subset: identifiers

Disease ID (PharmGKB)
type: Class
subclass of: Disease ID
subclass of: Accession
subclass of: PharmGKB ID
Created in: beta12orEarlier
Regular expression: PA[0-9]+
has definition: Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bio
in subset: data
in subset: identifiers

Drug ID (PharmGKB)
type: Class
subclass of: Accession
subclass of: PharmGKB ID
subclass of: Drug accession
Created in: beta12orEarlier
Regular expression: PA[0-9]+
has definition: Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bio
in subset: data
in subset: identifiers

Drug ID (TTD)
type: Class
subclass of: Accession
subclass of: Drug accession
Created in: beta12orEarlier
Regular expression: DAP[0-9]+
has definition: Identifier of a drug from the Therapeutic Target Database (TTD).
in subset: bio
in subset: data
in subset: identifiers

Target ID (TTD)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
Regular expression: TTDS[0-9]+
has definition: Identifier of a target protein from the Therapeutic Target Database (TTD).
in subset: bio
in subset: data
in subset: identifiers

Cell type identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A unique identifier of a type or group of cells.
in subset: bio
in subset: data
in subset: identifiers

NeuronDB ID
type: Class
subclass of: Accession
subclass of: Cell type accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: A unique identifier of a neuron from the NeuronDB database.
in subset: bio
in subset: data
in subset: identifiers

NeuroMorpho ID
type: Class
subclass of: Accession
subclass of: Cell type accession
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9]+
has definition: A unique identifier of a neuron from the NeuroMorpho database.
in subset: bio
in subset: data
in subset: identifiers

Compound ID (ChemIDplus)
type: Class
subclass of: Accession
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a chemical from the ChemIDplus database.
has exact synonym: ChemIDplus ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (SMPDB)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: SMP[0-9]{5}
has definition: Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).
in subset: bio
in subset: data
in subset: identifiers

BioNumbers ID
type: Class
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.
in subset: bio
in subset: data
in subset: identifiers

T3DB ID
type: Class
subclass of: Accession
subclass of: Toxin accession
Created in: beta12orEarlier
Regular expression: T3D[0-9]+
has definition: Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.
in subset: bio
in subset: data
in subset: identifiers

Carbohydrate identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Carbohydrate structure
subclass of: Restriction
  on property: is identifier of
  some values from: Carbohydrate report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a carbohydrate.
in subset: bio
in subset: data
in subset: identifiers

GlycomeDB ID
type: Class
subclass of: Accession
subclass of: Carbohydrate accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of an entry from the GlycomeDB database.
in subset: bio
in subset: data
in subset: identifiers

LipidBank ID
type: Class
subclass of: Accession
subclass of: Lipid accession
Created in: beta12orEarlier
Regular expression: [a-zA-Z_0-9]+[0-9]+
has definition: Identifier of an entry from the LipidBank database.
in subset: bio
in subset: data
in subset: identifiers

CDD ID
type: Class
subclass of: Protein domain ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: cd[0-9]{5}
has definition: Identifier of a conserved domain from the Conserved Domain Database.
in subset: bio
in subset: data
in subset: identifiers

MMDB ID
type: Class
subclass of: Structure ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9]{1,5}
has definition: An identifier of an entry from the MMDB database.
has exact synonym: MMDB accession
in subset: bio
in subset: data
in subset: identifiers

iRefIndex ID
type: Class
subclass of: Protein interaction ID
subclass of: Accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Unique identifier of an entry from the iRefIndex database of protein-protein interactions.
in subset: bio
in subset: data
in subset: identifiers

ModelDB ID
type: Class
subclass of: Accession
subclass of: Biological model accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Unique identifier of an entry from the ModelDB database.
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (DQCS)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).
in subset: bio
in subset: data
in subset: identifiers

Ensembl ID (Homo sapiens)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division).
in subset: obsolete
deprecated: true

Ensembl ID ('Bos taurus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Canis familiaris')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Cavia porcellus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Ciona intestinalis')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Ciona savignyi')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Danio rerio')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Dasypus novemcinctus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Echinops telfairi')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Erinaceus europaeus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Felis catus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Gallus gallus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Gasterosteus aculeatus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Homo sapiens')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Loxodonta africana')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Macaca mulatta')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Monodelphis domestica')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Mus musculus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Myotis lucifugus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division).
in subset: obsolete
deprecated: true

Ensembl ID ("Ornithorhynchus anatinus")
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Oryctolagus cuniculus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Oryzias latipes')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Otolemur garnettii')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Pan troglodytes')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Rattus norvegicus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Spermophilus tridecemlineatus')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Takifugu rubripes')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Tupaia belangeri')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division).
in subset: obsolete
deprecated: true

Ensembl ID ('Xenopus tropicalis')
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ensembl ID
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division).
in subset: obsolete
deprecated: true

CATH identifier
type: Class
subclass of: Protein domain ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a protein domain (or other node) from the CATH database.
in subset: bio
in subset: data
in subset: identifiers

CATH node ID (family)
type: Class
subclass of: CATH node ID
Created in: beta12orEarlier
Example: 2.10.10.10
has definition: A code number identifying a family from the CATH database.
in subset: bio
in subset: data
in subset: identifiers

Enzyme ID (CAZy)
type: Class
subclass of: Accession
subclass of: Enzyme ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme from the CAZy enzymes database.
has exact synonym: CAZy ID
in subset: bio
in subset: data
in subset: identifiers

Clone ID (IMAGE)
type: Class
subclass of: Clone ID
subclass of: Accession
Created in: beta12orEarlier
has definition: A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).
has exact synonym: I.M.A.G.E. cloneID
has exact synonym: IMAGE cloneID
in subset: bio
in subset: data
in subset: identifiers

GO concept ID (cellular component)
type: Class
subclass of: GO concept ID
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
has definition: An identifier of a 'cellular component' concept from the Gene Ontology.
has exact synonym: GO concept identifier (cellular compartment)
in subset: bio
in subset: data
in subset: identifiers

Chromosome name (BioCyc)
type: Class
subclass of: Chromosome name
Created in: beta12orEarlier
has definition: Name of a chromosome as used in the BioCyc database.
in subset: bio
in subset: data
in subset: identifiers

CleanEx entry name
type: Class
subclass of: Gene expression report ID
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a gene expression profile from the CleanEx database.
in subset: bio
in subset: data
in subset: identifiers

CleanEx dataset code
type: Class
subclass of: Experiment annotation ID
Created in: beta12orEarlier
has definition: An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.
in subset: bio
in subset: data
in subset: identifiers

Genome report
type: Class
subclass of: Organism report
Created in: beta12orEarlier
has definition: A human-readable collection of information concerning a genome as a whole.
in subset: bio
in subset: data

Protein ID (CORUM)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a protein complex from the CORUM database.
has exact synonym: CORUM complex ID
in subset: bio
in subset: data
in subset: identifiers

CDD PSSM-ID
type: Class
subclass of: Sequence profile ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of a position-specific scoring matrix from the CDD database.
in subset: bio
in subset: data
in subset: identifiers

Protein ID (CuticleDB)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a protein from the CuticleDB database.
has exact synonym: CuticleDB ID
in subset: bio
in subset: data
in subset: identifiers

DBD ID
type: Class
subclass of: Accession
subclass of: Transcription factor accession
Created in: beta12orEarlier
has definition: Identifier of a predicted transcription factor from the DBD database.
in subset: bio
in subset: data
in subset: identifiers

Oligonucleotide probe annotation
type: Class
subclass of: Microarray metadata
subclass of: Restriction
  on property: has topic
  some values from: Probes and primers
Created in: beta12orEarlier
has definition: General annotation on an oligonucleotide probe, or a set of probes.
has narrow synonym: Oligonucleotide probe sets annotation
in subset: bio
in subset: data

Oligonucleotide ID
type: Class
subclass of: Nucleic acid identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of an oligonucleotide from a database.
in subset: bio
in subset: data
in subset: identifiers

dbProbe ID
type: Class
subclass of: Accession
subclass of: Oligonucleotide ID
Created in: beta12orEarlier
has definition: Identifier of an oligonucleotide probe from the dbProbe database.
in subset: bio
in subset: data
in subset: identifiers

Dinucleotide property
type: Class
subclass of: DNA base structural data
Created in: beta12orEarlier
has definition: Physicochemical property data for one or more dinucleotides.
in subset: bio
in subset: data

DiProDB ID
type: Class
subclass of: Accession
subclass of: Oligonucleotide ID
Created in: beta12orEarlier
has definition: Identifier of an dinucleotide property from the DiProDB database.
in subset: bio
in subset: data
in subset: identifiers

Protein features report (disordered structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: disordered structure in a protein.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein ID (DisProt)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a protein from the DisProt database.
has exact synonym: DisProt ID
in subset: bio
in subset: data
in subset: identifiers

Embryo report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Fate map
has definition: Annotation on an embryo or concerning embryological development.
in subset: obsolete
deprecated: true

Ensembl transcript ID
type: Class
subclass of: Accession
subclass of: Ensembl ID
subclass of: Transcript ID
Created in: beta12orEarlier
has definition: Unique identifier for a gene transcript from the Ensembl database.
has exact synonym: Transcript ID (Ensembl)
in subset: bio
in subset: data
in subset: identifiers

Inhibitor annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Small molecule report
has definition: An informative report on one or more small molecules that are enzyme inhibitors.
in subset: obsolete
deprecated: true

Promoter ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has db xref: Moby:GeneAccessionList
has definition: An identifier of a promoter of a gene that is catalogued in a database.
in subset: bio
in subset: data
in subset: identifiers

EST accession
type: Class
subclass of: Clone ID
Created in: beta12orEarlier
has definition: Identifier of an EST sequence.
in subset: bio
in subset: data
in subset: identifiers

COGEME EST ID
type: Class
subclass of: Accession
subclass of: EST accession
Created in: beta12orEarlier
has definition: Identifier of an EST sequence from the COGEME database.
in subset: bio
in subset: data
in subset: identifiers

COGEME unisequence ID
type: Class
subclass of: Accession
subclass of: EST accession
Created in: beta12orEarlier
has definition: Identifier of a unisequence from the COGEME database.
in subset: bio
in subset: data
in subset: identifiers
comment: A unisequence is a single sequence assembled from ESTs.

Protein family ID (GeneFarm)
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Accession number of an entry (protein family) from the GeneFarm database.
has exact synonym: GeneFarm family ID
in subset: bio
in subset: data
in subset: identifiers

Family name
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has definition: The name of a family of organism.
in subset: bio
in subset: data
in subset: identifiers

Genus name (virus)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Genus name
has definition: The name of a genus of viruses.
in subset: obsolete
deprecated: true

Family name (virus)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Family name
has definition: The name of a family of viruses.
in subset: obsolete
deprecated: true

Database name (SwissRegulon)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Database metadata
has definition: The name of a SwissRegulon database.
in subset: obsolete
deprecated: true

Sequence feature ID (SwissRegulon)
type: Class
subclass of: Sequence feature ID
subclass of: Accession
Created in: beta12orEarlier
has definition: A feature identifier as used in the SwissRegulon database.
in subset: bio
in subset: data
in subset: identifiers
comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".

FIG ID
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the NMPDR database.
in subset: bio
in subset: data
in subset: identifiers
comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number.

Gene ID (Xenbase)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the Xenbase database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (Genolist)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the Genolist database.
in subset: bio
in subset: data
in subset: identifiers

Gene name (Genolist)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene symbol
has definition: Name of an entry (gene) from the Genolist genes database.
in subset: obsolete
deprecated: true

ABS ID
type: Class
subclass of: Accession
subclass of: Promoter ID
Created in: beta12orEarlier
has definition: Identifier of an entry (promoter) from the ABS database.
has exact synonym: ABS identifier
in subset: bio
in subset: data
in subset: identifiers

AraC-XylS ID
type: Class
subclass of: Accession
subclass of: Transcription factor accession
Created in: beta12orEarlier
has definition: Identifier of a transcription factor from the AraC-XylS database.
in subset: bio
in subset: data
in subset: identifiers

Gene name (HUGO)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene symbol
has definition: Name of an entry (gene) from the HUGO database.
in subset: obsolete
deprecated: true

Locus ID (PseudoCAP)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a locus from the PseudoCAP database.
in subset: bio
in subset: data
in subset: identifiers

Locus ID (UTR)
type: Class
subclass of: Locus ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a locus from the UTR database.
in subset: bio
in subset: data
in subset: identifiers

MonosaccharideDB ID
type: Class
subclass of: Accession
subclass of: Monosaccharide accession
Created in: beta12orEarlier
has definition: Unique identifier of a monosaccharide from the MonosaccharideDB database.
in subset: bio
in subset: data
in subset: identifiers

Database name (CMD)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Database metadata
has definition: The name of a subdivision of the Collagen Mutation Database (CMD) database.
in subset: obsolete
deprecated: true

Database name (Osteogenesis)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Database metadata
has definition: The name of a subdivision of the Osteogenesis database.
in subset: obsolete
deprecated: true

Genome identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of a particular genome.
in subset: bio
in subset: data
in subset: identifiers

GenomeReviews ID
type: Class
Old parent: Accession
Old parent: Genome accession
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.26
has definition: An identifier of a particular genome.
in subset: obsolete
replaced by: Genome identifier
deprecated: true

GlycoMap ID
type: Class
subclass of: Accession
subclass of: Carbohydrate accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of an entry from the GlycoMapsDB (Glycosciences.de) database.
in subset: bio
in subset: data
in subset: identifiers

Carbohydrate conformational map
type: Class
subclass of: Carbohydrate property
Created in: beta12orEarlier
has definition: A conformational energy map of the glycosidic linkages in a carbohydrate molecule.
in subset: bio
in subset: data

Transcription factor name
type: Class
subclass of: Protein name
subclass of: Transcription factor identifier
Created in: beta12orEarlier
has definition: The name of a transcription factor.
in subset: bio
in subset: data
in subset: identifiers

TCID
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Identifier of a membrane transport proteins from the transport classification database (TCDB).
in subset: bio
in subset: data
in subset: identifiers

Pfam domain name
type: Class
subclass of: Protein family name
Created in: beta12orEarlier
Regular expression: PF[0-9]{5}
has definition: Name of a domain from the Pfam database.
in subset: bio
in subset: data
in subset: identifiers

Pfam clan ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
Regular expression: CL[0-9]{4}
has definition: Accession number of a Pfam clan.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (VectorBase)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier for a gene from the VectorBase database.
has exact synonym: VectorBase ID
in subset: bio
in subset: data
in subset: identifiers

UTRSite ID
type: Class
subclass of: Sequence motif identifier
Created in: beta12orEarlier
has definition: Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.
in subset: bio
in subset: data
in subset: identifiers

Sequence signature report
type: Class
subclass of: Report
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Sequence motif report
has exact synonym: Sequence profile report
in subset: bio
in subset: data

Locus annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene report
has definition: An informative report on a particular locus.
in subset: obsolete
deprecated: true

Protein name (UniProt)
type: Class
subclass of: Protein name
Created in: beta12orEarlier
has definition: Official name of a protein as used in the UniProt database.
in subset: bio
in subset: data
in subset: identifiers

Term ID list
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: ID list
has definition: One or more terms from one or more controlled vocabularies which are annotations on an entity.
in subset: obsolete
comment: The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.
deprecated: true

HAMAP ID
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Name of a protein family from the HAMAP database.
in subset: bio
in subset: data
in subset: identifiers

Identifier with metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Identifier
has definition: Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance.
in subset: obsolete
deprecated: true

Gene symbol annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Report
has definition: Annotation about a gene symbol.
in subset: obsolete
deprecated: true

Transcript ID
type: Class
subclass of: Nucleic acid identifier
subclass of: Molecule accession
subclass of: Restriction
  on property: is identifier of
  some values from: Nucleic acid features
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a RNA transcript.
in subset: bio
in subset: data
in subset: identifiers

HIT ID
type: Class
subclass of: Accession
subclass of: Transcript ID
Created in: beta12orEarlier
has definition: Identifier of an RNA transcript from the H-InvDB database.
in subset: bio
in subset: data
in subset: identifiers

HIX ID
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene cluster in the H-InvDB database.
in subset: bio
in subset: data
in subset: identifiers

HPA antibody id
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Identifier of a antibody from the HPA database.
in subset: bio
in subset: data
in subset: identifiers

IMGT/HLA ID
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (JCVI)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).
in subset: bio
in subset: data
in subset: identifiers

Kinase name
type: Class
subclass of: Protein name
Created in: beta12orEarlier
has definition: The name of a kinase protein.
in subset: bio
in subset: data
in subset: identifiers

ConsensusPathDB entity ID
type: Class
subclass of: Accession
subclass of: ConsensusPathDB identifier
Created in: beta12orEarlier
has definition: Identifier of a physical entity from the ConsensusPathDB database.
in subset: bio
in subset: data
in subset: identifiers

ConsensusPathDB entity name
type: Class
subclass of: Name
subclass of: ConsensusPathDB identifier
Created in: beta12orEarlier
has definition: Name of a physical entity from the ConsensusPathDB database.
in subset: bio
in subset: data
in subset: identifiers

CCAP strain number
type: Class
subclass of: Accession
subclass of: Strain accession
Created in: beta12orEarlier
has definition: The number of a strain of algae and protozoa from the CCAP database.
in subset: bio
in subset: data
in subset: identifiers

Stock number
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of stock from a catalogue of biological resources.
in subset: bio
in subset: data
in subset: identifiers

Stock number (TAIR)
type: Class
subclass of: Accession
subclass of: Stock number
Created in: beta12orEarlier
has definition: A stock number from The Arabidopsis information resource (TAIR).
in subset: bio
in subset: data
in subset: identifiers

REDIdb ID
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the RNA editing database (REDIdb).
in subset: bio
in subset: data
in subset: identifiers

SMART domain name
type: Class
subclass of: Protein family name
Created in: beta12orEarlier
has definition: Name of a domain from the SMART database.
in subset: bio
in subset: data
in subset: identifiers

Protein family ID (PANTHER)
type: Class
subclass of: Accession
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Accession number of an entry (family) from the PANTHER database.
has exact synonym: Panther family ID
in subset: bio
in subset: data
in subset: identifiers

RNAVirusDB ID
type: Class
subclass of: Accession
subclass of: Virus identifier
Created in: beta12orEarlier
has definition: A unique identifier for a virus from the RNAVirusDB database.
in subset: bio
in subset: data
in subset: identifiers
comment: Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.

Virus identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An accession of annotation on a (group of) viruses (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers
has exact synonym: Virus ID

NCBI Genome Project ID
type: Class
subclass of: Accession
subclass of: Genome accession
Created in: beta12orEarlier
has definition: An identifier of a genome project assigned by NCBI.
in subset: bio
in subset: data
in subset: identifiers

NCBI genome accession
type: Class
subclass of: Accession
subclass of: Genome accession
Created in: beta12orEarlier
has definition: A unique identifier of a whole genome assigned by the NCBI.
in subset: bio
in subset: data
in subset: identifiers

Sequence profile data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Sequence signature data
deprecated: true

Protein ID (TopDB)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a membrane protein from the TopDB database.
has exact synonym: TopDB ID
in subset: bio
in subset: data
in subset: identifiers

Gel ID
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a two-dimensional (protein) gel.
has exact synonym: Gel identifier
in subset: bio
in subset: data
in subset: identifiers

Reference map name (SWISS-2DPAGE)
type: Class
subclass of: Name
subclass of: Gel ID
Created in: beta12orEarlier
has definition: Name of a reference map gel from the SWISS-2DPAGE database.
in subset: bio
in subset: data
in subset: identifiers

Protein ID (PeroxiBase)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a peroxidase protein from the PeroxiBase database.
has exact synonym: PeroxiBase ID
in subset: bio
in subset: data
in subset: identifiers

SISYPHUS ID
type: Class
subclass of: Structure alignment ID
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the SISYPHUS database of tertiary structure alignments.
in subset: bio
in subset: data
in subset: identifiers

ORF ID
type: Class
subclass of: Locus ID
subclass of: Accession
subclass of: ORF identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of an open reading frame (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

ORF identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An identifier of an open reading frame.
in subset: bio
in subset: data
in subset: identifiers

LINUCS ID
type: Class
subclass of: Accession
subclass of: Carbohydrate accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the GlycosciencesDB database.
has exact synonym: LInear Notation for Unique description of Carbohydrate Sequences ID
in subset: bio
in subset: data
in subset: identifiers
Regular expression: [1-9][0-9]*

Protein ID (LGICdb)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a ligand-gated ion channel protein from the LGICdb database.
has exact synonym: LGICdb ID
in subset: bio
in subset: data
in subset: identifiers

MaizeDB ID
type: Class
subclass of: Accession
subclass of: EST accession
Created in: beta12orEarlier
has definition: Identifier of an EST sequence from the MaizeDB database.
in subset: bio
in subset: data
in subset: identifiers

Gene ID (MfunGD)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the MfunGD database.
in subset: bio
in subset: data
in subset: identifiers

Orpha number
type: Class
subclass of: Disease ID
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
Created in: beta12orEarlier
has definition: An identifier of a disease from the Orpha database.
in subset: bio
in subset: data
in subset: identifiers

Protein ID (EcID)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a protein from the EcID database.
in subset: bio
in subset: data
in subset: identifiers

Clone ID (RefSeq)
type: Class
subclass of: RefSeq accession
subclass of: Clone ID
Created in: beta12orEarlier
has definition: A unique identifier of a cDNA molecule catalogued in the RefSeq database.
in subset: bio
in subset: data
in subset: identifiers

Protein ID (ConoServer)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Unique identifier for a cone snail toxin protein from the ConoServer database.
in subset: bio
in subset: data
in subset: identifiers

GeneSNP ID
type: Class
subclass of: Accession
subclass of: Sequence variation ID
Created in: beta12orEarlier
has definition: Identifier of a GeneSNP database entry.
in subset: bio
in subset: data
in subset: identifiers

Lipid identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Lipid structure
subclass of: Restriction
  on property: is identifier of
  some values from: Lipid report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Identifier of a lipid.
in subset: bio
in subset: data
in subset: identifiers

Databank
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A flat-file (textual) data archive.
in subset: obsolete
replaced by: Database metadata
deprecated: true

Web portal
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A web site providing data (web pages) on a common theme to a HTTP client.
in subset: obsolete
replaced by: Tool metadata
deprecated: true

Gene ID (VBASE2)
type: Class
subclass of: Accession
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier for a gene from the VBASE2 database.
has exact synonym: VBASE2 ID
in subset: bio
in subset: data
in subset: identifiers

DPVweb ID
type: Class
subclass of: Accession
subclass of: Virus identifier
Created in: beta12orEarlier
has definition: A unique identifier for a virus from the DPVweb database.
has exact synonym: DPVweb virus ID
in subset: bio
in subset: data
in subset: identifiers

Pathway ID (BioSystems)
type: Class
subclass of: Accession
subclass of: Pathway or network accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of a pathway from the BioSystems pathway database.
in subset: bio
in subset: data
in subset: identifiers

Experimental data (proteomics)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protocol
has definition: Data concerning a proteomics experiment.
in subset: obsolete
deprecated: true

Abstract
type: Class
subclass of: Text data
Created in: beta12orEarlier
has definition: An abstract of a scientific article.
in subset: bio
in subset: data

Lipid structure
type: Class
subclass of: Structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a lipid structure.
in subset: bio
in subset: data

Drug structure
type: Class
subclass of: Small molecule structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for the (3D) structure of a drug.
in subset: bio
in subset: data

Toxin structure
type: Class
subclass of: Small molecule structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for the (3D) structure of a toxin.
in subset: bio
in subset: data

Position-specific scoring matrix
type: Class
subclass of: Sequence profile
subclass of: Matrix
Created in: beta12orEarlier
has definition: 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.
has exact synonym: PSSM
in subset: bio
in subset: data

Distance matrix
type: Class
subclass of: Matrix
Created in: beta12orEarlier
has definition: A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.
in subset: bio
in subset: data

Structural distance matrix
type: Class
subclass of: Distance matrix
Created in: beta12orEarlier
has definition: Distances (values representing similarity) between a group of molecular structures.
in subset: bio
in subset: data

Article metadata
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Text data
has definition: Bibliographic data concerning scientific article(s).
in subset: obsolete
deprecated: true

Ontology concept
type: Class
subclass of: Ontology data
Created in: beta12orEarlier
has definition: A concept from a biological ontology.
in subset: bio
in subset: data
comment: This includes any fields from the concept definition such as concept name, definition, comments and so on.

Codon usage bias
type: Class
subclass of: Codon usage data
Created in: beta12orEarlier
has definition: A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.
in subset: bio
in subset: data

Northern blot report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Northern Blot experiments.
in subset: obsolete
replaced by: Protocol
deprecated: true

Radiation hybrid map
type: Class
subclass of: Physical map
Created in: beta12orEarlier
has definition: A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.
has exact synonym: RH map
in subset: bio
in subset: data
comment: The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.

ID list
type: Class
subclass of: Data reference
Created in: beta12orEarlier
has definition: A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.
in subset: bio
in subset: data

Phylogenetic gene frequencies data
type: Class
subclass of: Phylogenetic continuous quantitative data
Created in: beta12orEarlier
has definition: Gene frequencies data that may be read during phylogenetic tree calculation.
in subset: bio
in subset: data

Sequence set (polymorphic)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence set (nucleic acid)
has definition: A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
in subset: obsolete
deprecated: true

DRCAT resource
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Annotated URI
has definition: An entry (resource) from the DRCAT bioinformatics resource catalogue.
in subset: obsolete
deprecated: true

Protein complex
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.
in subset: bio
in subset: data

Protein structural motif
type: Class
subclass of: Protein structure
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: data

Lipid report
type: Class
subclass of: Structure report
Created in: beta12orEarlier
has definition: A human-readable collection of information about one or more specific lipid 3D structure(s).
in subset: bio
in subset: data

Secondary structure image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Protein structure image
has definition: Image of one or more molecular secondary structures.
in subset: obsolete
deprecated: true

Secondary structure report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Structure report
has definition: An informative report on general information, properties or features of one or more molecular secondary structures.
in subset: obsolete
deprecated: true

DNA features
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid features
has definition: DNA sequence-specific feature annotation (not in a feature table).
in subset: obsolete
deprecated: true

RNA features report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Gene report
has definition: Features concerning RNA or regions of DNA that encode an RNA molecule.
in subset: obsolete
deprecated: true

Plot
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph.
has exact synonym: Graph data
in subset: bio
in subset: data

Protein sequence record
type: Class
subclass of: Sequence record
subclass of: Protein sequence
Created in: beta12orEarlier
has definition: A protein sequence and associated metadata.
has exact synonym: Sequence record (protein)
in subset: bio
in subset: data

Nucleic acid sequence record
type: Class
subclass of: Sequence record
subclass of: Nucleic acid sequence
Created in: beta12orEarlier
has definition: A nucleic acid sequence and associated metadata.
has exact synonym: Nucleotide sequence record
has exact synonym: Sequence record (nucleic acid)
has narrow synonym: DNA sequence record
has narrow synonym: RNA sequence record
in subset: bio
in subset: data

Protein sequence record (full)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Nucleic acid sequence record (full)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
in subset: obsolete
replaced by: Sequence record
deprecated: true

Biological model accession
type: Class
subclass of: Biological model ID
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a mathematical model, typically an entry from a database.
in subset: bio
in subset: data
in subset: identifiers

Cell type name
type: Class
subclass of: Name
subclass of: Cell type identifier
Created in: beta12orEarlier
has definition: The name of a type or group of cells.
in subset: bio
in subset: data
in subset: identifiers

Cell type accession
type: Class
subclass of: Cell type identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a type or group of cells (catalogued in a database).
has exact synonym: Cell type ID
in subset: bio
in subset: data
in subset: identifiers

Compound accession
type: Class
subclass of: Compound identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of an entry from a database of chemicals.
has exact synonym: Chemical compound accession
has exact synonym: Small molecule accession
in subset: bio
in subset: data
in subset: identifiers

Drug accession
type: Class
subclass of: Drug identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a drug.
in subset: bio
in subset: data
in subset: identifiers

Toxin name
type: Class
subclass of: Name
subclass of: Toxin identifier
Created in: beta12orEarlier
has definition: Name of a toxin.
in subset: bio
in subset: data
in subset: identifiers

Toxin accession
type: Class
subclass of: Toxin identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a toxin (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

Monosaccharide accession
type: Class
subclass of: Monosaccharide identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a monosaccharide (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

Drug name
type: Class
subclass of: Compound name
subclass of: Drug identifier
Created in: beta12orEarlier
has definition: Common name of a drug.
in subset: bio
in subset: data
in subset: identifiers

Carbohydrate accession
type: Class
subclass of: Carbohydrate identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of an entry from a database of carbohydrates.
in subset: bio
in subset: data
in subset: identifiers

Molecule accession
type: Class
subclass of: Molecule identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a specific molecule (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

Data resource definition accession
type: Class
subclass of: Data resource definition ID
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a data definition (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

Genome accession
type: Class
subclass of: Genome identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An accession of a particular genome (in a database).
in subset: bio
in subset: data
in subset: identifiers

Map accession
type: Class
subclass of: Map identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An accession of a map of a molecular sequence (deposited in a database).
in subset: bio
in subset: data
in subset: identifiers

Lipid accession
type: Class
subclass of: Lipid identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of an entry from a database of lipids.
in subset: bio
in subset: data
in subset: identifiers

Peptide ID
type: Class
subclass of: Peptide identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a peptide deposited in a database.
in subset: bio
in subset: data
in subset: identifiers

Protein accession
type: Class
subclass of: Protein identifier
subclass of: Molecule accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a protein deposited in a database.
has exact synonym: Protein accessions
in subset: bio
in subset: data
in subset: identifiers

Organism accession
type: Class
subclass of: Organism identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: An accession of annotation on a (group of) organisms (catalogued in a database).
in subset: bio
in subset: data
in subset: identifiers

Organism name
type: Class
subclass of: Organism identifier
subclass of: Name
Created in: beta12orEarlier
has db xref: Moby:BriefOccurrenceRecord
has db xref: Moby:FirstEpithet
has db xref: Moby:InfraspecificEpithet
has db xref: Moby:OccurrenceRecord
has db xref: Moby:Organism_Name
has db xref: Moby:OrganismsLongName
has db xref: Moby:OrganismsShortName
has definition: The name of an organism (or group of organisms).
in subset: bio
in subset: data
in subset: identifiers

Protein family accession
type: Class
subclass of: Protein family identifier
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of a protein family (that is deposited in a database).
in subset: bio
in subset: data
in subset: identifiers

Transcription factor accession
type: Class
subclass of: Transcription factor identifier
subclass of: Protein accession
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession of an entry from a database of transcription factors or binding sites.
in subset: bio
in subset: data
in subset: identifiers

Strain accession
type: Class
subclass of: Strain identifier
subclass of: Organism accession
subclass of: Restriction
  on property: is identifier of
  some values from: Cell line report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Accession number of a strain of an organism variant, typically a plant, virus or bacterium.
in subset: bio
in subset: data
in subset: identifiers

Virus identifier
type: Class
Old parent: Organism identifier
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.26
notRecommendedForAnnotation: true
has definition: An accession of annotation on a (group of) viruses (catalogued in a database).
in subset: obsolete
replaced by: Virus identifier
deprecated: true

Sequence features metadata
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Metadata on sequence features.
in subset: bio
in subset: data

Gramene identifier
type: Class
subclass of: Sequence accession (protein)
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of a Gramene database entry.
in subset: bio
in subset: data
in subset: identifiers

DDBJ accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
Created in: beta12orEarlier
has definition: An identifier of an entry from the DDBJ sequence database.
has exact synonym: DDBJ ID
has exact synonym: DDBJ accession number
has exact synonym: DDBJ identifier
in subset: bio
in subset: data
in subset: identifiers

ConsensusPathDB identifier
type: Class
subclass of: Identifier (hybrid)
Created in: beta12orEarlier
has definition: An identifier of an entity from the ConsensusPathDB database.
in subset: bio
in subset: data
in subset: identifiers

Sequence data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Sequence attribute
has definition: Data concerning, extracted from, or derived from the analysis of molecular sequence(s).
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Codon usage
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Codon usage data
has definition: Data concerning codon usage.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Article report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Text mining report
consider: Annotated text
has definition: Data derived from the analysis of a scientific text such as a full text article from a scientific journal.
in subset: obsolete
deprecated: true

Sequence report
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Sequence-derived report
in subset: bio
in subset: data

Protein secondary structure
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: Data concerning the properties or features of one or more protein secondary structures.
in subset: bio
in subset: data

Hopp and Woods plot
type: Class
subclass of: Peptide immunogenicity data
subclass of: Plot
Created in: beta12orEarlier
has definition: A Hopp and Woods plot of predicted antigenicity of a peptide or protein.
in subset: bio
in subset: data

Nucleic acid melting curve
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Nucleic acid melting profile
Old parent: Plot
has definition: A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
in subset: obsolete
replaced by: Nucleic acid melting profile
deprecated: true

Nucleic acid probability profile
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Nucleic acid melting profile
has definition: A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
in subset: obsolete
replaced by: Nucleic acid melting profile
deprecated: true

Nucleic acid temperature profile
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.21
Old parent: Nucleic acid melting profile
has definition: A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
in subset: obsolete
replaced by: Nucleic acid melting profile
deprecated: true

Gene regulatory network report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: A report typically including a map (diagram) of a gene regulatory network.
in subset: obsolete
replaced by: Pathway or network report
deprecated: true

2D PAGE gel report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: An informative report on a two-dimensional (2D PAGE) gel.
in subset: obsolete
replaced by: Protocol
deprecated: true

Oligonucleotide probe sets annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.14
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Oligonucleotide probe annotation
deprecated: true

Microarray image
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Image
has definition: An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.
in subset: obsolete
deprecated: true

Image
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen.
has exact synonym: Image data
in subset: bio
in subset: data

Sequence image
type: Class
subclass of: Sequence report
subclass of: Image
Created in: beta12orEarlier
has definition: Image of a molecular sequence, possibly with sequence features or properties shown.
in subset: bio
in subset: data

Protein hydropathy data
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: A report on protein properties concerning hydropathy.
has exact synonym: Protein hydropathy report
in subset: bio
in subset: data

Workflow data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Workflow metadata
has definition: Data concerning a computational workflow.
in subset: obsolete
deprecated: true

Workflow
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Workflow metadata
has definition: A computational workflow.
in subset: obsolete
deprecated: true

Secondary structure data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure report
has definition: Data concerning molecular secondary structure data.
in subset: obsolete
deprecated: true

Protein sequence (raw)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: 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).
Obsolete since: 1.23
Old parent: Raw sequence
has definition: A raw protein sequence (string of characters).
in subset: obsolete
replaced by: Protein sequence
deprecated: true

Nucleic acid sequence (raw)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: 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).
Obsolete since: 1.23
Old parent: Raw sequence
has definition: A raw nucleic acid sequence.
in subset: obsolete
replaced by: Nucleic acid sequence
deprecated: true

Protein sequence
type: Class
subclass of: Sequence
Created in: beta12orEarlier
Documentation: Protein primary structure
has definition: One or more protein sequences, possibly with associated annotation.
has exact synonym: Amino acid sequence
has exact synonym: Amino acid sequences
has exact synonym: Protein sequences
in subset: bio
in subset: data

Nucleic acid sequence
type: Class
subclass of: Sequence
Created in: beta12orEarlier
has definition: One or more nucleic acid sequences, possibly with associated annotation.
has exact synonym: Nucleic acid sequences
has exact synonym: Nucleotide sequence
has exact synonym: Nucleotide sequences
has narrow synonym: DNA sequence
in subset: bio
in subset: data

Reaction data
type: Class
subclass of: Data
Created in: beta12orEarlier
has definition: Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.
has exact synonym: Enzyme kinetics annotation
has exact synonym: Reaction annotation
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Peptide property
type: Class
subclass of: Molecular property
Created in: beta12orEarlier
has definition: Data concerning small peptides.
has exact synonym: Peptide data
in subset: bio
in subset: data

Protein classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: An informative report concerning the classification of protein sequences or structures.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Sequence motif data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Data concerning specific or conserved pattern in molecular sequences.
in subset: obsolete
replaced by: Sequence signature data
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Sequence profile data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence profile
has definition: Data concerning models representing a (typically multiple) sequence alignment.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Pathway or network data
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Pathway or network
consider: Pathway or network report
has definition: Data concerning a specific biological pathway or network.
in subset: obsolete
deprecated: true

Pathway or network report
type: Class
subclass of: Report
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.
in subset: bio
in subset: data

Nucleic acid thermodynamic data
type: Class
subclass of: Nucleic acid property
Created in: beta12orEarlier
has definition: A thermodynamic or kinetic property of a nucleic acid molecule.
has exact synonym: Nucleic acid property (thermodynamic or kinetic)
has exact synonym: Nucleic acid thermodynamic property
in subset: bio
in subset: data

Nucleic acid classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
Obsolete since: 1.5
Old parent: Thing
consider: Gene family report
has definition: Data concerning the classification of nucleic acid sequences or structures.
in subset: obsolete
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true

Classification report
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.5
Old parent: Thing
consider: Report
has definition: A report on a classification of molecular sequences, structures or other entities.
in subset: obsolete
comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
deprecated: true

Protein features report (key folding sites)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: key residues involved in protein folding.
in subset: obsolete
replaced by: Protein features
deprecated: true

Protein geometry data
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc.
has exact synonym: Torsion angle data
in subset: bio
in subset: data

Protein structure image
type: Class
subclass of: Structure image
subclass of: Protein image
Created in: beta12orEarlier
has definition: An image of protein structure.
has exact synonym: Structure image (protein)
in subset: bio
in subset: data

Phylogenetic character weights
type: Class
subclass of: Phylogenetic data
Created in: beta12orEarlier
has definition: Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.
in subset: bio
in subset: data

Annotation track
type: Class
subclass of: Sequence features
Created in: beta12orEarlier
has definition: Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.
has exact synonym: Genome annotation track
has exact synonym: Genome track
has exact synonym: Genome-browser track
has exact synonym: Genomic track
has exact synonym: Sequence annotation track
in subset: bio
in subset: data

UniProt accession
type: Class
subclass of: Sequence accession (protein)
subclass of: Accession
Created in: beta12orEarlier
Documentation: accession numbers
Example: P43353|Q7M1G0|Q9C199|A5A6J6
Regular expression: [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}
has definition: Accession number of a UniProt (protein sequence) database entry.
has exact synonym: UniProt accession number
has exact synonym: UniProt entry accession
has exact synonym: UniProtKB accession
has exact synonym: UniProtKB accession number
has narrow synonym: Swiss-Prot entry accession
has narrow synonym: TrEMBL entry accession
in subset: bio
in subset: data
in subset: identifiers

NCBI genetic code ID
type: Class
subclass of: Accession
subclass of: Genetic code identifier
Created in: beta12orEarlier
Example: 16
Regular expression: [1-9][0-9]?
has definition: Identifier of a genetic code in the NCBI list of genetic codes.
in subset: bio
in subset: data
in subset: identifiers

Ontology concept identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Ontology concept
Created in: beta12orEarlier
has definition: Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
in subset: bio
in subset: data
in subset: identifiers

GO concept name (biological process)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept name
has definition: The name of a concept for a biological process from the GO ontology.
in subset: obsolete
deprecated: true

GO concept name (molecular function)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Ontology concept name
has definition: The name of a concept for a molecular function from the GO ontology.
in subset: obsolete
deprecated: true

Taxonomy
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has definition: Data concerning the classification, identification and naming of organisms.
has exact synonym: Taxonomic data
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Protein ID (EMBL/GenBank/DDBJ)
type: Class
subclass of: Accession
subclass of: Protein accession
Created in: beta13
has definition: EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
in subset: bio
in subset: data
in subset: identifiers
comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.

Core data
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Data
comment: Core data entities typically have a format and may be identified by an accession number.
deprecated: true

Sequence feature identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence features
Created in: beta13
notRecommendedForAnnotation: true
has definition: Name or other identifier of molecular sequence feature(s).
in subset: bio
in subset: data
in subset: identifiers

Structure identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Structure
Created in: beta13
notRecommendedForAnnotation: true
has definition: An identifier of a molecular tertiary structure, typically an entry from a structure database.
in subset: bio
in subset: data
in subset: identifiers

Matrix identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Matrix
Created in: beta13
notRecommendedForAnnotation: true
has definition: An identifier of an array of numerical values, such as a comparison matrix.
in subset: bio
in subset: data
in subset: identifiers

Protein sequence composition
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: A report (typically a table) on character or word composition / frequency of protein sequence(s).
in subset: obsolete
replaced by: Sequence composition report
deprecated: true

Nucleic acid sequence composition (report)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).
in subset: obsolete
replaced by: Sequence composition report
deprecated: true

Protein domain classification node
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: A node from a classification of protein structural domain(s).
in subset: obsolete
deprecated: true

CAS number
type: Class
subclass of: DeprecatedClass
Created in: beta13
deprecation_comment: Duplicates http://edamontology.org/data_1002, hence deprecated.
Obsolete since: 1.23
Old parent: Drug accession
has definition: Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
in subset: obsolete
replaced by: CAS number
deprecated: true

ATC code
type: Class
subclass of: Accession
subclass of: Drug accession
Created in: beta13
has definition: 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).
in subset: bio
in subset: data
in subset: identifiers

UNII
type: Class
subclass of: Compound identifier
Created in: beta13
has definition: A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).
has exact synonym: Unique Ingredient Identifier
in subset: bio
in subset: data
in subset: identifiers

Geotemporal metadata
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Data
has definition: Basic information concerning geographical location or time.
in subset: obsolete
deprecated: true

System metadata
type: Class
subclass of: Resource metadata
Created in: beta13
has definition: Metadata concerning the software, hardware or other aspects of a computer system.
in subset: bio
in subset: data

Sequence feature name
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.15
Old parent: Thing
has definition: A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.
in subset: obsolete
replaced by: Sequence feature label
deprecated: true

Experimental measurement
type: Class
subclass of: Data
Created in: beta13
has definition: Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.
has exact synonym: Experimental measurement data
has exact synonym: Experimentally measured data
has exact synonym: Measured data
has exact synonym: Measurement
has exact synonym: Measurement data
has narrow synonym: Measurement metadata
has narrow synonym: Raw experimental data
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.

Raw microarray data
type: Class
subclass of: Experimental measurement
subclass of: Microarray hybridisation data
Created in: beta13
has definition: Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.
in subset: bio
in subset: data
comment: Such data as found in Affymetrix CEL or GPR files.

Processed microarray data
type: Class
subclass of: Microarray hybridisation data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta13
has definition: Data generated from processing and analysis of probe set data from a microarray experiment.
has exact synonym: Gene annotation (expression)
has exact synonym: Gene expression report
has exact synonym: Microarray probe set data
in subset: bio
in subset: data
comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.

Gene expression matrix
type: Class
subclass of: Matrix
subclass of: Expression data
Created in: beta13
has definition: The final processed (normalised) data for a set of hybridisations in a microarray experiment.
has exact synonym: Gene expression data matrix
has exact synonym: Normalised microarray data
in subset: bio
in subset: data
comment: This combines data from all hybridisations.

Sample annotation
type: Class
subclass of: Resource metadata
Created in: beta13
has definition: Annotation on a biological sample, for example experimental factors and their values.
in subset: bio
in subset: data
comment: This might include compound and dose in a dose response experiment.

Microarray metadata
type: Class
subclass of: Expression data
Created in: beta13
has definition: Annotation on the array itself used in a microarray experiment.
in subset: bio
in subset: data
comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.

Microarray protocol annotation
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: Annotation on laboratory and/or data processing protocols used in an microarray experiment.
in subset: obsolete
replaced by: Protocol
comment: This might describe e.g. the normalisation methods used to process the raw data.
deprecated: true

Microarray hybridisation data
type: Class
subclass of: Expression data
Created in: beta13
has definition: Data concerning the hybridisations measured during a microarray experiment.
in subset: bio
in subset: data

Sequence features (compositionally-biased regions)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Sequence composition report
has definition: A report of regions in a molecular sequence that are biased to certain characters.
in subset: obsolete
deprecated: true

Nucleic acid features (difference and change)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
has definition: A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Nucleic acid structure report
type: Class
subclass of: Nucleic acid report
subclass of: Structure report
Created in: beta13
comment: 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.
has definition: A human-readable collection of information about regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.
has exact synonym: Nucleic acid features (structure)
has narrow synonym: Quadruplexes (report)
has narrow synonym: Stem loop (report)
has narrow synonym: d-loop (report)
in subset: bio
in subset: data

Protein features report (repeats)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: short repetitive subsequences (repeat sequences) in a protein sequence.
in subset: obsolete
replaced by: Protein features
deprecated: true

Sequence motif matches (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.
in subset: obsolete
replaced by: Sequence signature matches
deprecated: true

Sequence motif matches (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.
in subset: obsolete
replaced by: Sequence signature matches
deprecated: true

Nucleic acid features (d-loop)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Nucleic acid structure report
has definition: A report on displacement loops in a mitochondrial DNA sequence.
in subset: obsolete
comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
deprecated: true

Nucleic acid features (stem loop)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Nucleic acid structure report
has definition: A report on stem loops in a DNA sequence.
in subset: obsolete
comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.
deprecated: true

Gene transcript report
type: Class
subclass of: Nucleic acid features
Created in: beta13
has definition: 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.
has exact synonym: Clone or EST (report)
has exact synonym: Gene transcript annotation
has exact synonym: Nucleic acid features (mRNA features)
has exact synonym: Transcript (report)
has exact synonym: mRNA (report)
has exact synonym: mRNA features
in subset: bio
in subset: data
comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).

Non-coding RNA
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: features of non-coding or functional RNA molecules, including tRNA and rRNA.
in subset: obsolete
replaced by: Nucleic acid features
deprecated: true

Transcriptional features (report)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Gene transcript report
has definition: Features concerning transcription of DNA into RNA including the regulation of transcription.
in subset: obsolete
comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
deprecated: true

Nucleic acid features (immunoglobulin gene structure)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Gene report
has definition: A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.
in subset: obsolete
deprecated: true

SCOP class
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'class' node from the SCOP database.
in subset: obsolete
deprecated: true

SCOP fold
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'fold' node from the SCOP database.
in subset: obsolete
deprecated: true

SCOP superfamily
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'superfamily' node from the SCOP database.
in subset: obsolete
deprecated: true

SCOP family
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'family' node from the SCOP database.
in subset: obsolete
deprecated: true

SCOP protein
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'protein' node from the SCOP database.
in subset: obsolete
deprecated: true

SCOP species
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.5
Old parent: Thing
consider: Protein family report
has definition: Information on a 'species' node from the SCOP database.
in subset: obsolete
deprecated: true

Mass spectrometry experiment
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.8
Old parent: Thing
has definition: mass spectrometry experiments.
in subset: obsolete
replaced by: Protocol
deprecated: true

Gene family report
type: Class
subclass of: Nucleic acid report
Created in: beta13
has broad synonym: Nucleic acid classification
has definition: 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.
has exact synonym: Gene annotation (homology information)
has exact synonym: Gene annotation (homology)
has exact synonym: Gene family annotation
has exact synonym: Gene homology (report)
has exact synonym: Homology information
in subset: bio
in subset: data
comment: This includes reports on on gene homologues between species.

Protein image
type: Class
subclass of: Image
Created in: beta13
has definition: An image of a protein.
in subset: bio
in subset: data

Protein alignment
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.24
Old parent: Alignment
consider: Protein secondary structure alignment
consider: Protein sequence alignment
consider: Protein structure alignment
has definition: An alignment of protein sequences and/or structures.
in subset: obsolete
deprecated: true

NGS experiment
type: Class
subclass of: DeprecatedClass
Created in: 1.0
Obsolete since: 1.8
Old parent: Thing
has definition: sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.
in subset: obsolete
replaced by: Protocol
deprecated: true

Sequence assembly report
type: Class
subclass of: Sequence alignment report
Created in: 1.1
has definition: An informative report about a DNA sequence assembly.
has exact synonym: Assembly report
in subset: bio
in subset: data
comment: 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.

Genome index
type: Class
subclass of: Data index
Created in: 1.1
has definition: An index of a genome sequence.
in subset: bio
in subset: data
comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.

GWAS report
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.8
Old parent: Thing
has definition: Report concerning genome-wide association study experiments.
in subset: obsolete
replaced by: Protocol
deprecated: true

Cytoband position
type: Class
subclass of: Sequence coordinates
Created in: 1.2
has definition: The position of a cytogenetic band in a genome.
in subset: bio
in subset: data
comment: Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.

Cell type ontology ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
subclass of: Cell type accession
Created in: 1.2
Regular expression: CL_[0-9]{7}
has definition: Cell type ontology concept ID.
has exact synonym: CL ID
in subset: bio
in subset: data
in subset: identifiers

Kinetic model
type: Class
subclass of: Mathematical model
Created in: 1.2
has definition: Mathematical model of a network, that contains biochemical kinetics.
in subset: bio
in subset: data

COSMIC ID
type: Class
subclass of: Accession
subclass of: Sequence variation ID
Created in: 1.3
has definition: Identifier of a COSMIC database entry.
has exact synonym: COSMIC identifier
in subset: bio
in subset: data
in subset: identifiers

HGMD ID
type: Class
subclass of: Accession
subclass of: Sequence variation ID
Created in: 1.3
has definition: Identifier of a HGMD database entry.
has exact synonym: HGMD identifier
in subset: bio
in subset: data
in subset: identifiers

Sequence assembly ID
type: Class
subclass of: Sequence set ID
Created in: 1.3
notRecommendedForAnnotation: true
has definition: Unique identifier of sequence assembly.
has narrow synonym: Sequence assembly version
in subset: bio
in subset: data
in subset: identifiers

Sequence feature type
type: Class
subclass of: DeprecatedClass
Created in: 1.3
Obsolete since: 1.5
Old parent: Thing
consider: Identifier
has definition: 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.
in subset: obsolete
deprecated: true

Gene homology (report)
type: Class
subclass of: DeprecatedClass
Created in: 1.3
Obsolete since: 1.5
Old parent: Thing
consider: Gene family report
has definition: An informative report on gene homologues between species.
in subset: obsolete
deprecated: true

Ensembl gene tree ID
type: Class
subclass of: Phylogenetic tree ID
subclass of: Accession
subclass of: Ensembl ID
Created in: 1.3
Example: ENSGT00390000003602
has definition: Unique identifier for a gene tree from the Ensembl database.
has exact synonym: Ensembl ID (gene tree)
in subset: bio
in subset: data
in subset: identifiers

Gene tree
type: Class
subclass of: Phylogenetic tree
Created in: 1.3
has definition: A phylogenetic tree that is an estimate of the character's phylogeny.
in subset: bio
in subset: data

Species tree
type: Class
subclass of: Phylogenetic tree
Created in: 1.3
has definition: A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.
in subset: bio
in subset: data

Sample ID
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Sample annotation
Created in: 1.3
notRecommendedForAnnotation: true
has definition: Name or other identifier of an entry from a biosample database.
has exact synonym: Sample accession
in subset: bio
in subset: data
in subset: identifiers

MGI accession
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Created in: 1.3
has definition: Identifier of an object from the MGI database.
in subset: bio
in subset: data
in subset: identifiers

Phenotype name
type: Class
subclass of: Name
Created in: 1.3
has definition: Name of a phenotype.
has exact synonym: Phenotype
has exact synonym: Phenotypes
in subset: bio
in subset: data
in subset: identifiers

Transition matrix
type: Class
subclass of: Matrix
Created in: 1.4
has definition: A HMM transition matrix contains the probabilities of switching from one HMM state to another.
has exact synonym: HMM transition matrix
in subset: bio
in subset: data
comment: 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.

Emission matrix
type: Class
subclass of: Matrix
Created in: 1.4
has definition: 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.
has exact synonym: HMM emission matrix
in subset: bio
in subset: data
comment: 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.

Hidden Markov model
type: Class
subclass of: DeprecatedClass
Created in: 1.4
Obsolete since: 1.15
Old parent: Thing
has definition: A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.
in subset: obsolete
replaced by: Hidden Markov model
deprecated: true

Format identifier
type: Class
subclass of: Identifier (by type of entity)
Created in: 1.4
notRecommendedForAnnotation: true
has definition: An identifier of a data format.
in subset: bio
in subset: data

Raw image
type: Class
subclass of: Image
Created in: 1.5
has definition: Raw biological or biomedical image generated by some experimental technique.
in subset: bio
in subset: data

Carbohydrate property
type: Class
subclass of: Molecular property
Created in: 1.5
has definition: Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates.
has exact synonym: Carbohydrate data
in subset: bio
in subset: data

Proteomics experiment report
type: Class
subclass of: DeprecatedClass
Created in: 1.5
Obsolete since: 1.8
Old parent: Thing
has definition: Report concerning proteomics experiments.
in subset: obsolete
replaced by: Protocol
deprecated: true

RNAi report
type: Class
subclass of: DeprecatedClass
Created in: 1.5
Obsolete since: 1.8
Old parent: Thing
has definition: RNAi experiments.
in subset: obsolete
replaced by: Protocol
deprecated: true

Simulation experiment report
type: Class
subclass of: DeprecatedClass
Created in: 1.5
Obsolete since: 1.8
Old parent: Thing
has definition: biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.
in subset: obsolete
replaced by: Protocol
deprecated: true

MRI image
type: Class
subclass of: Raw image
subclass of: Restriction
  on property: has topic
  some values from: Medical imaging
Created in: 1.7
has definition: An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.
has exact synonym: MRT image
has exact synonym: Magnetic resonance imaging image
has exact synonym: Magnetic resonance tomography image
has exact synonym: NMRI image
has exact synonym: Nuclear magnetic resonance imaging image
in subset: bio
in subset: data

Cell migration track image
type: Class
subclass of: Image
subclass of: Restriction
  on property: has topic
  some values from: Cell biology
Created in: 1.7
has definition: An image from a cell migration track assay.
in subset: bio
in subset: data

Rate of association
type: Class
subclass of: Protein property
Created in: 1.7
has definition: Rate of association of a protein with another protein or some other molecule.
has exact synonym: kon
in subset: bio
in subset: data

Gene order
type: Class
subclass of: Matrix
Created in: 1.7
has definition: Multiple gene identifiers in a specific order.
in subset: bio
in subset: data
comment: Such data are often used for genome rearrangement tools and phylogenetic tree labeling.

Spectrum
type: Class
subclass of: Data
Created in: 1.7
has definition: The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.
has exact synonym: Spectra
in subset: bio
in subset: data

NMR spectrum
type: Class
subclass of: Spectrum
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.7
has definition: Spectral information for a molecule from a nuclear magnetic resonance experiment.
has exact synonym: NMR spectra
in subset: bio
in subset: data

Chemical structure sketch
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.21
Old parent: Chemical structure image
has definition: A sketch of a small molecule made with some specialised drawing package.
in subset: obsolete
replaced by: Chemical structure image
comment: Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.
deprecated: true

Nucleic acid signature
type: Class
subclass of: Sequence signature report
Created in: 1.8
has definition: An informative report about a specific or conserved nucleic acid sequence pattern.
in subset: bio
in subset: data

DNA sequence
type: Class
subclass of: Nucleic acid sequence
Created in: 1.8
has definition: A DNA sequence.
has exact synonym: DNA sequences
in subset: bio
in subset: data

RNA sequence
type: Class
subclass of: Nucleic acid sequence
Created in: 1.8
has definition: An RNA sequence.
has exact synonym: RNA sequences
in subset: bio
in subset: data

RNA sequence (raw)
type: Class
subclass of: DeprecatedClass
Created in: 1.8
deprecation_comment: 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).
Obsolete since: 1.23
Old parent: Nucleic acid sequence (raw)
has definition: A raw RNA sequence.
in subset: obsolete
replaced by: RNA sequence
deprecated: true

DNA sequence (raw)
type: Class
subclass of: DeprecatedClass
Created in: 1.8
deprecation_comment: 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).
Obsolete since: 1.23
Old parent: Nucleic acid sequence (raw)
has definition: A raw DNA sequence.
in subset: obsolete
replaced by: DNA sequence
deprecated: true

Sequence variations
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Genetic variation
Created in: 1.8
has definition: Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.
has exact synonym: Gene sequence variations
in subset: bio
in subset: data
comment: Variations are stored along with a reference genome.

Bibliography
type: Class
subclass of: Text data
Created in: 1.8
has definition: A list of publications such as scientic papers or books.
in subset: bio
in subset: data

Ontology mapping
type: Class
subclass of: Data reference
Created in: 1.8
has definition: A mapping of supplied textual terms or phrases to ontology concepts (URIs).
in subset: bio
in subset: data

Image metadata
type: Class
subclass of: Report
Created in: 1.9
has definition: Any data concerning a specific biological or biomedical image.
has exact synonym: Image-associated data
has exact synonym: Image-related data
in subset: bio
in subset: data
comment: This can include basic provenance and technical information about the image, scientific annotation and so on.

Clinical trial report
type: Class
subclass of: Report
Created in: 1.9
has definition: A human-readable collection of information concerning a clinical trial.
has exact synonym: Clinical trial information
in subset: bio
in subset: data

Reference sample report
type: Class
subclass of: Report
Created in: 1.10
has definition: A report about a biosample.
has exact synonym: Biosample report
in subset: bio
in subset: data

Gene Expression Atlas Experiment ID
type: Class
subclass of: Experiment annotation ID
Created in: 1.10
has definition: Accession number of an entry from the Gene Expression Atlas.
in subset: bio
in subset: data
in subset: identifiers

Disease identifier
type: Class
subclass of: Identifier (by type of entity)
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
Created in: 1.12
notRecommendedForAnnotation: true
has definition: Identifier of an entry from a database of disease.
in subset: bio
in subset: data
in subset: identifiers

Disease name
type: Class
subclass of: Name
subclass of: Disease identifier
Created in: 1.12
has definition: The name of some disease.
in subset: bio
in subset: data
in subset: identifiers

Learning material
type: Class
subclass of: Data
Created in: 1.12
has broad synonym: Learning resource
has definition: Learning material is a document or another digital object that is designed for learning (educational, training) purposes.
has narrow synonym: Educational material
has narrow synonym: Open educational resource (OER)
has narrow synonym: Teaching material
has narrow synonym: Training material
in subset: bio
in subset: data

Online course
type: Class
subclass of: Learning material
Created in: 1.12
has definition: A training course available for use on the Web.
has exact synonym: On-line course
has narrow synonym: MOOC
has narrow synonym: Massive open online course
in subset: bio
in subset: data

Text
type: Class
subclass of: Text data
Created in: 1.12
has definition: Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.
has exact synonym: Free text
has narrow synonym: Plain text
has narrow synonym: Textual search query
in subset: bio
in subset: data

Biodiversity data
type: Class
subclass of: Data
subclass of: Ecological data
Created in: 1.14
has definition: Machine-readable biodiversity data.
has exact synonym: Biodiversity information
has narrow synonym: OTU table
in subset: bio
in subset: data

Biosafety report
type: Class
subclass of: Report
Created in: 1.14
has definition: A human-readable collection of information concerning biosafety data.
has exact synonym: Biosafety information
in subset: bio
in subset: data

Isolation report
type: Class
subclass of: Report
Created in: 1.14
has definition: A report about any kind of isolation of biological material.
has narrow synonym: Geographic location
has narrow synonym: Isolation source
in subset: bio
in subset: data

Pathogenicity report
type: Class
subclass of: Biosafety report
Created in: 1.14
has definition: Information about the ability of an organism to cause disease in a corresponding host.
has exact synonym: Pathogenicity
in subset: bio
in subset: data

Biosafety classification
type: Class
subclass of: Biosafety report
Created in: 1.14
has definition: Information about the biosafety classification of an organism according to corresponding law.
has exact synonym: Biosafety level
in subset: bio
in subset: data

Geographic location
type: Class
subclass of: Isolation report
Created in: 1.14
has definition: A report about localisation of the isolaton of biological material e.g. country or coordinates.
in subset: bio
in subset: data

Isolation source
type: Class
subclass of: Isolation report
Created in: 1.14
has definition: A report about any kind of isolation source of biological material e.g. blood, water, soil.
in subset: bio
in subset: data

Physiology parameter
type: Class
subclass of: Experimental measurement
Created in: 1.14
has definition: Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum.
in subset: bio
in subset: data

Morphology parameter
type: Class
subclass of: Experimental measurement
Created in: 1.14
has definition: Experimentally determined parameter of the morphology of an organism, e.g. size & shape.
in subset: bio
in subset: data

Cultivation parameter
type: Class
subclass of: Experimental measurement
Created in: 1.14
has definition: Experimental determined parameter for the cultivation of an organism.
has exact synonym: Cultivation conditions
has narrow synonym: Carbon source
has narrow synonym: Culture media composition
has narrow synonym: Nitrogen source
has narrow synonym: Salinity
has narrow synonym: Temperature
has narrow synonym: pH value
in subset: bio
in subset: data

Sequencing metadata name
type: Class
subclass of: Name
Created in: 1.15
has definition: Data concerning a sequencing experiment, that may be specified as an input to some tool.
in subset: bio
in subset: data

Flow cell identifier
type: Class
subclass of: Sequencing metadata name
Created in: 1.15
has definition: An identifier of a flow cell of a sequencing machine.
in subset: bio
in subset: data
comment: 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.

Lane identifier
type: Class
subclass of: Sequencing metadata name
Created in: 1.15
has definition: An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced.
in subset: bio
in subset: data

Run number
type: Class
subclass of: Sequencing metadata name
Created in: 1.15
has definition: 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.
in subset: bio
in subset: data

Ecological data
type: Class
subclass of: Data
Created in: 1.15
has definition: Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment.
in subset: bio
in subset: data
comment: This is a broad data type and is used a placeholder for other, more specific types.

Alpha diversity data
type: Class
subclass of: Biodiversity data
Created in: 1.15
has definition: The mean species diversity in sites or habitats at a local scale.
has exact synonym: α-diversity
in subset: bio
in subset: data

Beta diversity data
type: Class
subclass of: Biodiversity data
Created in: 1.15
has definition: The ratio between regional and local species diversity.
has exact synonym: True beta diversity
has exact synonym: β-diversity
in subset: bio
in subset: data

Gamma diversity data
type: Class
subclass of: Biodiversity data
Created in: 1.15
has definition: The total species diversity in a landscape.
has exact synonym: ɣ-diversity
in subset: bio
in subset: data

Ordination plot
type: Class
subclass of: Protein property
subclass of: Plot
Created in: 1.15
has definition: 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.
in subset: bio
in subset: data

Over-representation data
type: Class
subclass of: Data
Created in: 1.16
has definition: A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data.
has exact synonym: Enrichment report
has exact synonym: Over-representation report
has narrow synonym: Functional enrichment report
in subset: bio
in subset: data

GO-term enrichment data
type: Class
subclass of: Over-representation data
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: 1.16
has broad synonym: GO-term report
has definition: 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.
has exact synonym: GO-term enrichment report
has exact synonym: Gene ontology concept over-representation report
has exact synonym: Gene ontology enrichment report
has exact synonym: Gene ontology term enrichment report
in subset: bio
in subset: data

Localisation score
type: Class
subclass of: Score
Created in: 1.16
has definition: Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry.
has narrow synonym: False localisation rate
has narrow synonym: PTM localisation
has narrow synonym: PTM score
in subset: bio
in subset: data

Unimod ID
type: Class
subclass of: Accession
subclass of: Protein modification ID
Created in: 1.16
has definition: Identifier of a protein modification catalogued in the Unimod database.
in subset: bio
in subset: data
in subset: identifiers

ProteomeXchange ID
type: Class
subclass of: Experiment annotation ID
Created in: 1.16
has definition: Identifier for mass spectrometry proteomics data in the proteomexchange.org repository.
in subset: bio
in subset: data
in subset: identifiers

Clustered expression profiles
type: Class
subclass of: Expression data
Created in: 1.16
has definition: Groupings of expression profiles according to a clustering algorithm.
has narrow synonym: Clustered gene expression profiles
in subset: bio
in subset: data

BRENDA ontology concept ID
type: Class
subclass of: Ontology concept ID
subclass of: Accession
Created in: 1.16
has definition: An identifier of a concept from the BRENDA ontology.
in subset: bio
in subset: data
in subset: identifiers

Annotated text
type: Class
subclass of: Text data
subclass of: Text
Created in: 1.16
has definition: A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations.
in subset: bio
in subset: data

Query script
type: Class
subclass of: Data
Created in: 1.16
has definition: A structured query, in form of a script, that defines a database search task.
in subset: bio
in subset: data

3D EM Map
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.19
has definition: Structural 3D model (volume map) from electron microscopy.
in subset: bio
in subset: data

3D EM Mask
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.19
has definition: 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.
in subset: bio
in subset: data

EM Movie
type: Class
subclass of: Raw image
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.19
has definition: Raw DDD movie acquisition from electron microscopy.
in subset: bio
in subset: data

EM Micrograph
type: Class
subclass of: Raw image
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.19
has definition: Raw acquisition from electron microscopy or average of an aligned DDD movie.
in subset: bio
in subset: data

Molecular simulation data
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: 1.21
has definition: Data coming from molecular simulations, computer "experiments" on model molecules.
in subset: bio
in subset: data
comment: Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).

RNA central ID
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Accession
Created in: 1.21
has definition: Identifier of an entry from the RNA central database of annotated human miRNAs.
in subset: bio
in subset: data
in subset: identifiers
comment: 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).

Electronic health record
type: Class
subclass of: Report
Created in: 1.21
has definition: A human-readable systematic collection of patient (or population) health information in a digital format.
has exact synonym: EHR
has exact synonym: EMR
has exact synonym: Electronic medical record
in subset: bio
in subset: data

Simulation
type: Class
subclass of: Data
Created in: 1.22
has definition: 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).
in subset: bio
in subset: data

Trajectory data
type: Class
subclass of: Simulation
Created in: 1.22
has definition: 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.
in subset: bio
in subset: data

Forcefield parameters
type: Class
subclass of: Simulation
Created in: 1.22
has definition: 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.
in subset: bio
in subset: data

Topology data
type: Class
subclass of: Simulation
Created in: 1.22
has definition: 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.
in subset: bio
in subset: data

Histogram
type: Class
subclass of: Plot
Created in: 1.22
has definition: Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots.
has exact synonym: Density plot
in subset: bio
in subset: data

Quality control report
type: Class
subclass of: Report
Created in: 1.23
has definition: Report of the quality control review that was made of factors involved in a procedure.
has exact synonym: QC metrics
has exact synonym: QC report
has exact synonym: Quality control metrics

Count matrix
type: Class
subclass of: Matrix
Created in: 1.23
has definition: A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak).
has exact synonym: Read count matrix
in subset: bio
in subset: data

DNA structure alignment
type: Class
subclass of: Nucleic acid structure alignment
Created in: 1.24
has definition: Alignment (superimposition) of DNA tertiary (3D) structures.
has exact synonym: Structure alignment (DNA)
in subset: bio
in subset: data

Q-value
type: Class
subclass of: Statistical estimate score
Created in: 1.24
has definition: 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).
has exact synonym: Adjusted P-value
has exact synonym: FDR
has exact synonym: Padj
has exact synonym: pFDR
in subset: bio
in subset: data
comment: Q-values are widely used in high-throughput data analysis (e.g. detection of differentially expressed genes from transcriptome data).

Profile HMM
type: Class
subclass of: Sequence profile
subclass of: Hidden Markov model
Created in: 1.24
has definition: 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.
in subset: bio
in subset: data

Pathway ID (WikiPathways)
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
subclass of: Pathway or network accession
Created in: 1.24
Documentation: www.wikipathways.org
Regular expression: WP[0-9]+
has definition: Identifier of a pathway from the WikiPathways pathway database.
has exact synonym: WikiPathways ID
has exact synonym: WikiPathways pathway ID
in subset: bio
in subset: data
in subset: identifiers

Pathway overrepresentation data
type: Class
subclass of: Over-representation data
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: 1.24
has definition: 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.
has exact synonym: Pathway analysis results
has exact synonym: Pathway enrichment report
has exact synonym: Pathway over-representation report
has exact synonym: Pathway report
has exact synonym: Pathway term enrichment report
in subset: bio
in subset: data

ORCID Identifier
type: Class
subclass of: Author ID
Created in: 1.26
Documentation: orcid.org
Documentation: orcid
Regular expression: \d{4}-\d{4}-\d{4}-\d{3}(\d|X)
has definition: Identifier of a researcher registered with the ORCID database. Used to identify author IDs.
in subset: bio
in subset: data
in subset: identifiers

Data management plan
type: Class
subclass of: Data
subclass of: Restriction
  on property: has topic
  some values from: Data management
Created in: 1.26
has definition: 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.
has exact synonym: DMP
in subset: bio
in subset: data

SMILES
type: Class
subclass of: Chemical formula format
subclass of: Textual format
Created in: beta12orEarlier
Documentation: Simplified molecular input line entry specification
Documentation: theory.smiles.html
has db xref: theory.smiles.html
has definition: Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.
in subset: bio
in subset: formats

InChI
type: Class
subclass of: Chemical formula format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.
in subset: bio
in subset: formats

mf
type: Class
subclass of: Chemical formula format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.
in subset: bio
in subset: formats
comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range.

InChIKey
type: Class
subclass of: Chemical formula format
subclass of: Textual format
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: formats
comment: An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification.

smarts
type: Class
subclass of: SMILES
Created in: beta12orEarlier
has definition: SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.
in subset: bio
in subset: formats

unambiguous pure
type: Class
subclass of: pure
subclass of: unambiguous sequence
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.
in subset: bio
in subset: formats

nucleotide
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.
in subset: bio
in subset: formats
comment: Non-sequence characters may be used for example for gaps.

protein
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.
in subset: bio
in subset: formats
comment: Non-sequence characters may be used for gaps and translation stop.

consensus
type: Class
subclass of: unpure
subclass of: ambiguous
Created in: beta12orEarlier
has definition: Alphabet for the consensus of two or more molecular sequences.
in subset: bio
in subset: formats

pure nucleotide
type: Class
subclass of: nucleotide
subclass of: pure
Created in: beta12orEarlier
has definition: Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.
in subset: bio
in subset: formats

unambiguous pure nucleotide
type: Class
subclass of: unambiguous pure
subclass of: nucleotide
Created in: beta12orEarlier
has definition: Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .
in subset: bio
in subset: formats

dna
type: Class
subclass of: nucleotide
Created in: beta12orEarlier
has definition: Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.
in subset: bio
in subset: formats

rna
type: Class
subclass of: nucleotide
Created in: beta12orEarlier
has definition: Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.
in subset: bio
in subset: formats

unambiguous pure dna
type: Class
subclass of: unambiguous pure
subclass of: dna
Created in: beta12orEarlier
has definition: Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.
in subset: bio
in subset: formats

pure dna
type: Class
subclass of: pure nucleotide
subclass of: dna
Created in: beta12orEarlier
has definition: Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
in subset: bio
in subset: formats

unambiguous pure rna sequence
type: Class
subclass of: unambiguous pure
subclass of: rna
Created in: beta12orEarlier
has definition: Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.
in subset: bio
in subset: formats

pure rna
type: Class
subclass of: pure nucleotide
subclass of: rna
Created in: beta12orEarlier
has definition: Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
in subset: bio
in subset: formats

unambiguous pure protein
type: Class
subclass of: unambiguous pure
subclass of: protein
Created in: beta12orEarlier
has definition: Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.
in subset: bio
in subset: formats

pure protein
type: Class
subclass of: protein
subclass of: pure
Created in: beta12orEarlier
has definition: Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.
in subset: bio
in subset: formats

UniGene entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from UniGene.
in subset: obsolete
comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
deprecated: true

COG sequence cluster format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the COG database of clusters of (related) protein sequences.
in subset: obsolete
deprecated: true

EMBL feature location
type: Class
subclass of: Sequence range format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.
has exact synonym: Feature location
in subset: bio
in subset: formats

quicktandem
type: Class
subclass of: Sequence features (repeats) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).
in subset: bio
in subset: formats

Sanger inverted repeats
type: Class
subclass of: Sequence features (repeats) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).
in subset: bio
in subset: formats

EMBOSS repeat
type: Class
subclass of: Sequence features (repeats) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for tandem repeats in a sequence (an EMBOSS report format).
in subset: bio
in subset: formats

est2genome format
type: Class
subclass of: Gene annotation format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of a report on exon-intron structure generated by EMBOSS est2genome.
in subset: bio
in subset: formats

restrict format
type: Class
subclass of: Nucleic acid features (restriction sites) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for restriction enzyme recognition sites used by EMBOSS restrict program.
in subset: bio
in subset: formats

restover format
type: Class
subclass of: Nucleic acid features (restriction sites) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for restriction enzyme recognition sites used by EMBOSS restover program.
in subset: bio
in subset: formats

REBASE restriction sites
type: Class
subclass of: Nucleic acid features (restriction sites) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format for restriction enzyme recognition sites used by REBASE database.
in subset: bio
in subset: formats

FASTA search results format
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using FASTA.
in subset: bio
in subset: formats
comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)

BLAST results
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using some variant of BLAST.
in subset: bio
in subset: formats
comment: This includes score data, alignment data and summary table.

mspcrunch
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using some variant of MSPCrunch.
in subset: bio
in subset: formats

Smith-Waterman format
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using some variant of Smith Waterman.
in subset: bio
in subset: formats

dhf
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.
in subset: bio
in subset: formats
comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.

lhf
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.
in subset: bio
in subset: formats
comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database.

InterPro hits format
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Results format for searches of the InterPro database.
in subset: bio
in subset: formats

InterPro protein view report format
type: Class
subclass of: InterPro hits format
Created in: beta12orEarlier
has definition: Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.
in subset: bio
in subset: formats
comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.

InterPro match table format
type: Class
subclass of: InterPro hits format
Created in: beta12orEarlier
has definition: Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.
in subset: bio
in subset: formats
comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.

HMMER Dirichlet prior
type: Class
subclass of: Dirichlet distribution format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Dirichlet distribution HMMER format.
in subset: bio
in subset: formats

MEME Dirichlet prior
type: Class
subclass of: Dirichlet distribution format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Dirichlet distribution MEME format.
in subset: bio
in subset: formats

HMMER emission and transition
type: Class
subclass of: HMM emission and transition counts format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.
in subset: bio
in subset: formats

prosite-pattern
type: Class
subclass of: Sequence motif format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of a regular expression pattern from the Prosite database.
in subset: bio
in subset: formats

EMBOSS sequence pattern
type: Class
subclass of: Sequence motif format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of an EMBOSS sequence pattern.
in subset: bio
in subset: formats

meme-motif
type: Class
subclass of: Sequence motif format
subclass of: Textual format
Created in: beta12orEarlier
has definition: A motif in the format generated by the MEME program.
in subset: bio
in subset: formats

prosite-profile
type: Class
subclass of: Sequence profile format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Sequence profile (sequence classifier) format used in the PROSITE database.
in subset: bio
in subset: formats

JASPAR format
type: Class
subclass of: Sequence profile format
subclass of: Textual format
Created in: beta12orEarlier
has definition: A profile (sequence classifier) in the format used in the JASPAR database.
in subset: bio
in subset: formats

MEME background Markov model
type: Class
subclass of: Hidden Markov model format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of the model of random sequences used by MEME.
in subset: bio
in subset: formats

HMMER format
type: Class
subclass of: Hidden Markov model format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of a hidden Markov model representation used by the HMMER package.
in subset: bio
in subset: formats

HMMER-aln
type: Class
subclass of: FASTA-like (text)
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
in subset: bio
in subset: formats

DIALIGN format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Format of multiple sequences aligned by DIALIGN package.
in subset: bio
in subset: formats

daf
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.
in subset: bio
in subset: formats
comment: The format is clustal-like and includes annotation of domain family classification information.

Sequence-MEME profile alignment
type: Class
subclass of: Sequence-profile alignment format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.
in subset: bio
in subset: formats

HMMER profile alignment (sequences versus HMMs)
type: Class
subclass of: Sequence-profile alignment format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.
in subset: bio
in subset: formats

HMMER profile alignment (HMM versus sequences)
type: Class
subclass of: Sequence-profile alignment format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.
in subset: bio
in subset: formats

Phylip distance matrix
type: Class
subclass of: Sequence distance matrix format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of PHYLIP phylogenetic distance matrix data.
in subset: bio
in subset: formats
comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).

ClustalW dendrogram
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Dendrogram (tree file) format generated by ClustalW.
in subset: bio
in subset: formats

Phylip tree raw
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.
in subset: bio
in subset: formats

Phylip continuous quantitative characters
type: Class
subclass of: Phylogenetic continuous quantitative character format
subclass of: Textual format
Created in: beta12orEarlier
has definition: PHYLIP file format for continuous quantitative character data.
in subset: bio
in subset: formats

Phylogenetic property values format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Phylogenetic character data format
has definition: Format of phylogenetic property data.
in subset: obsolete
deprecated: true

Phylip character frequencies format
type: Class
subclass of: Phylogenetic continuous quantitative character format
subclass of: Textual format
Created in: beta12orEarlier
has definition: PHYLIP file format for phylogenetics character frequency data.
in subset: bio
in subset: formats

Phylip discrete states format
type: Class
subclass of: Phylogenetic discrete states format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of PHYLIP discrete states data.
in subset: bio
in subset: formats

Phylip cliques format
type: Class
subclass of: Phylogenetic tree report (cliques) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of PHYLIP cliques data.
in subset: bio
in subset: formats

Phylip tree format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Phylogenetic tree data format used by the PHYLIP program.
in subset: bio
in subset: formats

TreeBASE format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: The format of an entry from the TreeBASE database of phylogenetic data.
in subset: bio
in subset: formats

TreeFam format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: The format of an entry from the TreeFam database of phylogenetic data.
in subset: bio
in subset: formats

Phylip tree distance format
type: Class
subclass of: Phylogenetic tree report (tree distances) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.
in subset: bio
in subset: formats

dssp
type: Class
subclass of: Protein secondary structure format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).
in subset: bio
in subset: formats
comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.

hssp
type: Class
subclass of: Protein secondary structure format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).
in subset: bio
in subset: formats

Dot-bracket format
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.
has exact synonym: Vienna RNA format
has exact synonym: Vienna RNA secondary structure format
in subset: bio
in subset: formats

Vienna local RNA secondary structure format
type: Class
subclass of: Dot-bracket format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.
in subset: bio
in subset: formats

PDB database entry format
type: Class
subclass of: Tertiary structure format
subclass of: Restriction
  on property: is format of
  some values from: Structure
subclass of: Restriction
  on property: is format of
  some values from: Trajectory data
Created in: beta12orEarlier
has definition: Format of an entry (or part of an entry) from the PDB database.
has exact synonym: PDB entry format
in subset: bio
in subset: formats

PDB
type: Class
subclass of: PDB database entry format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Entry format of PDB database in PDB format.
has exact synonym: PDB format
in subset: bio
in subset: formats

mmCIF
type: Class
subclass of: PDB database entry format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Entry format of PDB database in mmCIF format.
in subset: bio
in subset: formats

PDBML
type: Class
subclass of: PDB database entry format
subclass of: XML
Created in: beta12orEarlier
has definition: Entry format of PDB database in PDBML (XML) format.
in subset: bio
in subset: formats

Domainatrix 3D-1D scoring matrix format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.
in subset: obsolete
replaced by: 3D-1D scoring matrix format
deprecated: true

aaindex
type: Class
subclass of: Amino acid index format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Amino acid index format used by the AAindex database.
in subset: bio
in subset: formats

IntEnz enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from IntEnz (The Integrated Relational Enzyme Database).
in subset: obsolete
comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
deprecated: true

BRENDA enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the BRENDA enzyme database.
in subset: obsolete
deprecated: true

KEGG REACTION enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the KEGG REACTION database of biochemical reactions.
in subset: obsolete
deprecated: true

KEGG ENZYME enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the KEGG ENZYME database.
in subset: obsolete
deprecated: true

REBASE proto enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the proto section of the REBASE enzyme database.
in subset: obsolete
deprecated: true

REBASE withrefm enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the withrefm section of the REBASE enzyme database.
in subset: obsolete
deprecated: true

Pcons report format
type: Class
subclass of: Protein structure report (quality evaluation) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of output of the Pcons Model Quality Assessment Program (MQAP).
in subset: bio
in subset: formats
comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.

ProQ report format
type: Class
subclass of: Protein structure report (quality evaluation) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of output of the ProQ protein model quality predictor.
in subset: bio
in subset: formats
comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.

SMART domain assignment report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of SMART domain assignment data.
in subset: obsolete
comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.
deprecated: true

BIND entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the BIND database of protein interaction.
in subset: obsolete
deprecated: true

IntAct entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the IntAct database of protein interaction.
in subset: obsolete
deprecated: true

InterPro entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.
in subset: obsolete
comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
deprecated: true

InterPro entry abstract format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.
in subset: obsolete
comment: References are included and a functional inference is made where possible.
deprecated: true

Gene3D entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the Gene3D protein secondary database.
in subset: obsolete
deprecated: true

PIRSF entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the PIRSF protein secondary database.
in subset: obsolete
deprecated: true

PRINTS entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the PRINTS protein secondary database.
in subset: obsolete
deprecated: true

Panther Families and HMMs entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the Panther library of protein families and subfamilies.
in subset: obsolete
deprecated: true

Pfam entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the Pfam protein secondary database.
in subset: obsolete
deprecated: true

SMART entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the SMART protein secondary database.
in subset: obsolete
deprecated: true

Superfamily entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the Superfamily protein secondary database.
in subset: obsolete
deprecated: true

TIGRFam entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the TIGRFam protein secondary database.
in subset: obsolete
deprecated: true

ProDom entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the ProDom protein domain classification database.
in subset: obsolete
deprecated: true

FSSP entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the FSSP database.
in subset: obsolete
deprecated: true

findkm
type: Class
subclass of: Enzyme kinetics report format
subclass of: Textual format
Created in: beta12orEarlier
has definition: 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).
in subset: bio
in subset: formats

Ensembl gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of Ensembl genome database.
in subset: obsolete
deprecated: true

DictyBase gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of DictyBase genome database.
in subset: obsolete
deprecated: true

CGD gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of Candida Genome database.
in subset: obsolete
deprecated: true

DragonDB gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of DragonDB genome database.
in subset: obsolete
deprecated: true

EcoCyc gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of EcoCyc genome database.
in subset: obsolete
deprecated: true

FlyBase gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of FlyBase genome database.
in subset: obsolete
deprecated: true

Gramene gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of Gramene genome database.
in subset: obsolete
deprecated: true

KEGG GENES gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of KEGG GENES genome database.
in subset: obsolete
deprecated: true

MaizeGDB gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Maize genetics and genomics database (MaizeGDB).
in subset: obsolete
deprecated: true

MGD gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Mouse Genome Database (MGD).
in subset: obsolete
deprecated: true

RGD gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Rat Genome Database (RGD).
in subset: obsolete
deprecated: true

SGD gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Saccharomyces Genome Database (SGD).
in subset: obsolete
deprecated: true

GeneDB gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Sanger GeneDB genome database.
in subset: obsolete
deprecated: true

TAIR gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of The Arabidopsis Information Resource (TAIR) genome database.
in subset: obsolete
deprecated: true

WormBase gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the WormBase genomes database.
in subset: obsolete
deprecated: true

ZFIN gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the Zebrafish Information Network (ZFIN) genome database.
in subset: obsolete
deprecated: true

TIGR gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format of the TIGR genome database.
in subset: obsolete
deprecated: true

dbSNP polymorphism report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the dbSNP database.
in subset: obsolete
deprecated: true

OMIM entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the OMIM database of genotypes and phenotypes.
in subset: obsolete
deprecated: true

HGVbase entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of a record from the HGVbase database of genotypes and phenotypes.
in subset: obsolete
deprecated: true

HIVDB entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of a record from the HIVDB database of genotypes and phenotypes.
in subset: obsolete
deprecated: true

KEGG DISEASE entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the KEGG DISEASE database.
in subset: obsolete
deprecated: true

Primer3 primer
type: Class
subclass of: Nucleic acid features (primers) format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program.
in subset: bio
in subset: formats

ABI
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
has definition: A format of raw sequence read data from an Applied Biosystems sequencing machine.
in subset: bio
in subset: formats

mira
type: Class
subclass of: Sequence trace format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of MIRA sequence trace information file.
in subset: bio
in subset: formats

CAF
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: beta12orEarlier
Documentation: caf
File extension: caf
has db xref: caf
has definition: Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.
in subset: bio
in subset: formats

EXP
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: beta12orEarlier
Documentation: exp.html
has definition: Sequence assembly project file EXP format.
has exact synonym: Affymetrix EXP format
in subset: bio
in subset: formats

SCF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
Documentation: formats unix 2.html
has db xref: formats unix 2.html
has definition: Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.
in subset: bio
in subset: formats

PHD
type: Class
subclass of: Sequence trace format
subclass of: Textual format
Created in: beta12orEarlier
Documentation: PHD sequence format
has db xref: PHD sequence format
has definition: PHD sequence trace format to store serialised chromatogram data (reads).
in subset: bio
in subset: formats

dat
type: Class
subclass of: Gene expression report format
subclass of: Textual format
subclass of: Restriction
  on property: is format of
  some values from: Microarray spots image
Created in: beta12orEarlier
has definition: Format of Affymetrix data file of raw image data.
has exact synonym: Affymetrix image data file format
in subset: bio
in subset: formats

cel
type: Class
subclass of: Gene expression report format
subclass of: Textual format
subclass of: Restriction
  on property: is format of
  some values from: Raw microarray data
Created in: beta12orEarlier
has definition: Format of Affymetrix data file of information about (raw) expression levels of the individual probes.
has exact synonym: Affymetrix probe raw data format
in subset: bio
in subset: formats

affymetrix
type: Class
subclass of: Sequence cluster format (nucleic acid)
subclass of: Textual format
Created in: beta12orEarlier
has definition: Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.
in subset: bio
in subset: formats

ArrayExpress entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the ArrayExpress microarrays database.
in subset: obsolete
deprecated: true

affymetrix-exp
type: Class
subclass of: Microarray experiment data format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Affymetrix data file format for information about experimental conditions and protocols.
has exact synonym: Affymetrix experimental conditions data file format
in subset: bio
in subset: formats

CHP
type: Class
subclass of: Gene expression report format
subclass of: Textual format
subclass of: Restriction
  on property: is format of
  some values from: Processed microarray data
Created in: beta12orEarlier
Documentation: http://dept.stat.lsa.umich.edu/~kshedden/Courses/Stat545/Notes/AffxFileFormats/chp.html
File extension: chp
has definition: Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.
has exact synonym: Affymetrix probe normalised data format
in subset: bio
in subset: formats

EMDB entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the Electron Microscopy DataBase (EMDB).
in subset: obsolete
deprecated: true

KEGG PATHWAY entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.
in subset: obsolete
deprecated: true

MetaCyc entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the MetaCyc metabolic pathways database.
in subset: obsolete
deprecated: true

HumanCyc entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of a report from the HumanCyc metabolic pathways database.
in subset: obsolete
deprecated: true

INOH entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the INOH signal transduction pathways database.
in subset: obsolete
deprecated: true

PATIKA entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the PATIKA biological pathways database.
in subset: obsolete
deprecated: true

Reactome entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the reactome biological pathways database.
in subset: obsolete
deprecated: true

aMAZE entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the aMAZE biological pathways and molecular interactions database.
in subset: obsolete
deprecated: true

CPDB entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the CPDB database.
in subset: obsolete
deprecated: true

Panther Pathways entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the Panther Pathways database.
in subset: obsolete
deprecated: true

Taverna workflow format
type: Class
subclass of: Workflow format
subclass of: XML
Created in: beta12orEarlier
has definition: Format of Taverna workflows.
in subset: bio
in subset: formats

BioModel mathematical model format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of mathematical models from the BioModel database.
in subset: obsolete
comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
deprecated: true

KEGG LIGAND entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG LIGAND chemical database.
in subset: obsolete
deprecated: true

KEGG COMPOUND entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG COMPOUND database.
in subset: obsolete
deprecated: true

KEGG PLANT entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG PLANT database.
in subset: obsolete
deprecated: true

KEGG GLYCAN entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG GLYCAN database.
in subset: obsolete
deprecated: true

PubChem entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from PubChem.
in subset: obsolete
deprecated: true

ChemSpider entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from a database of chemical structures and property predictions.
in subset: obsolete
deprecated: true

ChEBI entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from Chemical Entities of Biological Interest (ChEBI).
in subset: obsolete
comment: ChEBI includes an ontological classification defining relations between entities or classes of entities.
deprecated: true

MSDchem ligand dictionary entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the MSDchem ligand dictionary.
in subset: obsolete
deprecated: true

HET group dictionary entry format
type: Class
subclass of: Chemical data format
subclass of: Textual format
Created in: beta12orEarlier
has definition: The format of an entry from the HET group dictionary (HET groups from PDB files).
in subset: bio
in subset: formats

KEGG DRUG entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the KEGG DRUG database.
in subset: obsolete
deprecated: true

PubMed citation
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
Created in: beta12orEarlier
has definition: Format of bibliographic reference as used by the PubMed database.
in subset: bio
in subset: formats

Medline Display Format
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
Created in: beta12orEarlier
has definition: Format for abstracts of scientific articles from the Medline database.
in subset: bio
in subset: formats
comment: Bibliographic reference information including citation information is included

CiteXplore-core
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
Created in: beta12orEarlier
has definition: CiteXplore 'core' citation format including title, journal, authors and abstract.
in subset: bio
in subset: formats

CiteXplore-all
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
Created in: beta12orEarlier
has definition: CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references.
in subset: bio
in subset: formats

pmc
type: Class
subclass of: Article format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Article format of the PubMed Central database.
in subset: bio
in subset: formats

iHOP format
type: Class
subclass of: Text mining report format
subclass of: HTML
subclass of: XML
Created in: beta12orEarlier
has definition: The format of iHOP (Information Hyperlinked over Proteins) text-mining result.
in subset: bio
in subset: formats

OSCAR format
type: Class
subclass of: Textual format
subclass of: XML
subclass of: Annotated text format
Citation: http://doi.org/10.1186/1758-2946-3-41
Created in: beta12orEarlier
has definition: OSCAR format of annotated chemical text.
in subset: bio
in subset: formats
comment: 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.

PDB atom record format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: PDB
has definition: Format of an ATOM record (describing data for an individual atom) from a PDB file.
in subset: obsolete
deprecated: true

CATH chain report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of CATH domain classification information for a polypeptide chain.
in subset: obsolete
comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.
deprecated: true

CATH PDB report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of CATH domain classification information for a protein PDB file.
in subset: obsolete
comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.
deprecated: true

NCBI gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry (gene) format of the NCBI database.
in subset: obsolete
deprecated: true

GeneIlluminator gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has db xref: Moby:GI_Gene
has definition: Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.
in subset: obsolete
comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.
deprecated: true

BacMap gene card format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has db xref: Moby:BacMapGeneCard
has definition: Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.
in subset: obsolete
deprecated: true

ColiCard report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).
in subset: obsolete
deprecated: true

PlasMapper TextMap
type: Class
subclass of: Map format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Map of a plasmid (circular DNA) in PlasMapper TextMap format.
in subset: bio
in subset: formats

newick
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Phylogenetic tree Newick (text) format.
has exact synonym: nh
in subset: bio
in subset: formats

TreeCon format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Phylogenetic tree TreeCon (text) format.
in subset: bio
in subset: formats

Nexus format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
Created in: beta12orEarlier
has definition: Phylogenetic tree Nexus (text) format.
in subset: bio
in subset: formats

Format
type: Class
disjoint with: Operation
disjoint with: Topic
disjoint with: DeprecatedClass
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
has exact synonym: Data format
has exact synonym: Data model
has exact synonym: Exchange format
has exact synonym: File format
in subset: bio
in subset: formats
comment: The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
related match: IAO_0000098
broad match: format
related match: MachineLanguage
broad match: Quality
broad match: SIO_000612
related match: SIO_000618
related match: compression_004
broad match: BFO_0000002
related match: BFO_0000019
related match: quality
broad match: Perpetuant
broad match: Symbol structure

Axiom
annotated source: Format
annotated property: hasExactSynonym
annotated target: Data model
comment: 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'.)

Axiom
annotated source: Format
annotated property: hasExactSynonym
annotated target: File format
comment: File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.

Atomic data format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: PDB database entry format
has definition: Data format for an individual atom.
in subset: obsolete
deprecated: true

Sequence record format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence record
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a molecular sequence record.
in subset: bio
in subset: formats

Sequence feature annotation format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for molecular sequence feature information.
in subset: bio
in subset: formats

Alignment format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for molecular sequence alignment information.
in subset: bio
in subset: formats

acedb
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: ACEDB sequence format.
in subset: bio
in subset: formats

clustal sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: ClustalW format
has definition: Clustalw output format.
in subset: obsolete
deprecated: true

codata
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Codata entry format.
in subset: bio
in subset: formats

dbid
type: Class
subclass of: FASTA-like (text)
Created in: beta12orEarlier
has definition: Fasta format variant with database name before ID.
in subset: bio
in subset: formats

EMBL format
type: Class
subclass of: EMBL-like (text)
subclass of: Sequence feature table format (text)
Created in: beta12orEarlier
has definition: EMBL entry format.
has exact synonym: EMBL
has exact synonym: EMBL sequence format
in subset: bio
in subset: formats

Staden experiment format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Staden experiment file format.
in subset: bio
in subset: formats

FASTA
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: FASTA format including NCBI-style IDs.
has exact synonym: FASTA format
has exact synonym: FASTA sequence format
in subset: bio
in subset: formats

FASTQ
type: Class
subclass of: FASTQ-like format (text)
Created in: beta12orEarlier
File extension: fastq
File extension: fq
has definition: FASTQ short read format ignoring quality scores.
has exact synonym: FASTAQ
has exact synonym: fq
in subset: bio
in subset: formats

FASTQ-illumina
type: Class
subclass of: FASTQ-like format (text)
Created in: beta12orEarlier
has definition: FASTQ Illumina 1.3 short read format.
in subset: bio
in subset: formats

FASTQ-sanger
type: Class
subclass of: FASTQ-like format (text)
Created in: beta12orEarlier
has definition: FASTQ short read format with phred quality.
in subset: bio
in subset: formats

FASTQ-solexa
type: Class
subclass of: FASTQ-like format (text)
Created in: beta12orEarlier
has definition: FASTQ Solexa/Illumina 1.0 short read format.
in subset: bio
in subset: formats

fitch program
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Fitch program format.
in subset: bio
in subset: formats

GCG
type: Class
subclass of: Textual format
subclass of: GCG format variant
Created in: beta12orEarlier
has definition: GCG sequence file format.
has exact synonym: GCG SSF
in subset: bio
in subset: formats
comment: GCG SSF (single sequence file) file format.

GenBank format
type: Class
subclass of: GenBank-like format (text)
subclass of: Sequence feature table format (text)
Created in: beta12orEarlier
has definition: Genbank entry format.
has exact synonym: GenBank
in subset: bio
in subset: formats

genpept
type: Class
subclass of: GenBank-like format (text)
Created in: beta12orEarlier
has definition: Genpept protein entry format.
in subset: bio
in subset: formats
comment: Currently identical to refseqp format

GFF2-seq
type: Class
subclass of: GFF2
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: GFF feature file format with sequence in the header.
in subset: bio
in subset: formats

GFF3-seq
type: Class
subclass of: GFF3
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: GFF3 feature file format with sequence.
in subset: bio
in subset: formats

giFASTA format
type: Class
subclass of: FASTA-like (text)
Created in: beta12orEarlier
has definition: FASTA sequence format including NCBI-style GIs.
in subset: bio
in subset: formats

hennig86
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Hennig86 output sequence format.
in subset: bio
in subset: formats

ig
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Intelligenetics sequence format.
in subset: bio
in subset: formats

igstrict
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Intelligenetics sequence format (strict version).
in subset: bio
in subset: formats

jackknifer
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Jackknifer interleaved and non-interleaved sequence format.
in subset: bio
in subset: formats

mase format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Mase program sequence format.
in subset: bio
in subset: formats

mega-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Mega interleaved and non-interleaved sequence format.
in subset: bio
in subset: formats

GCG MSF
type: Class
subclass of: GCG format variant
Created in: beta12orEarlier
has definition: GCG MSF (multiple sequence file) file format.
in subset: bio
in subset: formats

nbrf/pir
type: Class
subclass of: Textual format
Created in: beta12orEarlier
File extension: pir
has definition: NBRF/PIR entry sequence format.
has exact synonym: nbrf
has exact synonym: pir
in subset: bio
in subset: formats

nexus-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Nexus/paup interleaved sequence format.
in subset: bio
in subset: formats

pdbatom
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: PDB sequence format (ATOM lines).
in subset: bio
in subset: formats
comment: pdb format in EMBOSS.

pdbatomnuc
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: PDB nucleotide sequence format (ATOM lines).
in subset: bio
in subset: formats
comment: pdbnuc format in EMBOSS.

pdbseqresnuc
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: PDB nucleotide sequence format (SEQRES lines).
in subset: bio
in subset: formats
comment: pdbnucseq format in EMBOSS.

pdbseqres
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: PDB sequence format (SEQRES lines).
in subset: bio
in subset: formats
comment: pdbseq format in EMBOSS.

Pearson format
type: Class
subclass of: FASTA-like (text)
Created in: beta12orEarlier
has definition: Plain old FASTA sequence format (unspecified format for IDs).
in subset: bio
in subset: formats

phylip sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: PHYLIP format
has definition: Phylip interleaved sequence format.
in subset: obsolete
deprecated: true

phylipnon sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: PHYLIP sequential
has definition: PHYLIP non-interleaved sequence format.
in subset: obsolete
deprecated: true

raw
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Raw sequence format with no non-sequence characters.
in subset: bio
in subset: formats

refseqp
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Refseq protein entry sequence format.
in subset: bio
in subset: formats
comment: Currently identical to genpept format

selex sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: selex
has definition: Selex sequence format.
in subset: obsolete
deprecated: true

Staden format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
Documentation: 003063.html
Documentation: staden
has db xref: 003063.html
has db xref: staden
has definition: Staden suite sequence format.
in subset: bio
in subset: formats

Stockholm format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
Documentation: Stockholm format
has definition: Stockholm multiple sequence alignment format (used by Pfam and Rfam).
in subset: bio
in subset: formats

strider format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: DNA strider output sequence format.
in subset: bio
in subset: formats

UniProtKB format
type: Class
subclass of: UniProt-like (text)
Created in: beta12orEarlier
has definition: UniProtKB entry sequence format.
has exact synonym: SwissProt format
has exact synonym: UniProt format
in subset: bio
in subset: formats

plain text format (unformatted)
type: Class
subclass of: Textual format
Created in: beta12orEarlier
File extension: txt
has definition: Plain text sequence format (essentially unformatted).
in subset: bio
in subset: formats

treecon sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: TreeCon-seq
has definition: Treecon output sequence format.
in subset: obsolete
deprecated: true

ASN.1 sequence format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: NCBI ASN.1-based sequence format.
in subset: bio
in subset: formats

DAS format
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: beta12orEarlier
has definition: DAS sequence (XML) format (any type).
has exact synonym: das sequence format
in subset: bio
in subset: formats

dasdna
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: beta12orEarlier
has definition: DAS sequence (XML) format (nucleotide-only).
in subset: bio
in subset: formats
comment: The use of this format is deprecated.

debug-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: EMBOSS debugging trace sequence format of full internal data content.
in subset: bio
in subset: formats

jackknifernon
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Jackknifer output sequence non-interleaved format.
in subset: bio
in subset: formats

meganon sequence format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: meganon
has definition: Mega non-interleaved output sequence format.
in subset: obsolete
deprecated: true

NCBI format
type: Class
subclass of: FASTA-like (text)
Created in: beta12orEarlier
has definition: NCBI FASTA sequence format with NCBI-style IDs.
in subset: bio
in subset: formats
comment: There are several variants of this.

nexusnon
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Nexus/paup non-interleaved sequence format.
in subset: bio
in subset: formats

GFF2
type: Class
subclass of: GFF
Created in: beta12orEarlier
Documentation: spec.html
has db xref: spec.html
has definition: General Feature Format (GFF) of sequence features.
in subset: bio
in subset: formats

GFF3
type: Class
subclass of: GFF
Created in: beta12orEarlier
Documentation: gff3.md
Ontology used: www.sequenceontology.org
has db xref: gff3.md
has definition: Generic Feature Format version 3 (GFF3) of sequence features.
in subset: bio
in subset: formats

pir
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: PIR feature format.
in subset: obsolete
replaced by: nbrf/pir
deprecated: true

swiss feature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: UniProtKB format
has definition: Swiss-Prot feature format.
in subset: obsolete
deprecated: true

DASGFF
type: Class
subclass of: XML
subclass of: Sequence feature table format (XML)
Created in: beta12orEarlier
has definition: DAS GFF (XML) feature format.
has exact synonym: DASGFF feature
has exact synonym: das feature
in subset: bio
in subset: formats

debug-feat
type: Class
subclass of: Sequence feature annotation format
subclass of: Textual format
Created in: beta12orEarlier
has definition: EMBOSS debugging trace feature format of full internal data content.
in subset: bio
in subset: formats

EMBL feature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: EMBL format
has definition: EMBL feature format.
in subset: obsolete
deprecated: true

GenBank feature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: GenBank format
has definition: Genbank feature format.
in subset: obsolete
deprecated: true

ClustalW format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: ClustalW format for (aligned) sequences.
has exact synonym: clustal
in subset: bio
in subset: formats

debug
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: EMBOSS alignment format for debugging trace of full internal data content.
in subset: bio
in subset: formats

FASTA-aln
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Fasta format for (aligned) sequences.
in subset: bio
in subset: formats

markx0
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX0 alignment format.
in subset: bio
in subset: formats

markx1
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX1 alignment format.
in subset: bio
in subset: formats

markx10
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX10 alignment format.
in subset: bio
in subset: formats

markx2
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX2 alignment format.
in subset: bio
in subset: formats

markx3
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX3 alignment format.
in subset: bio
in subset: formats

match
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Alignment format for start and end of matches between sequence pairs.
in subset: bio
in subset: formats

mega
type: Class
subclass of: mega variant
Created in: beta12orEarlier
has definition: Mega format for (typically aligned) sequences.
in subset: bio
in subset: formats

meganon
type: Class
subclass of: mega variant
Created in: beta12orEarlier
has definition: Mega non-interleaved format for (typically aligned) sequences.
in subset: bio
in subset: formats

msf alignment format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: GCG MSF
has definition: MSF format for (aligned) sequences.
in subset: obsolete
deprecated: true

nexus alignment format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: nexus-seq
has definition: Nexus/paup format for (aligned) sequences.
in subset: obsolete
deprecated: true

nexusnon alignment format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: nexusnon
has definition: Nexus/paup non-interleaved format for (aligned) sequences.
in subset: obsolete
deprecated: true

pair
type: Class
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: EMBOSS simple sequence pairwise alignment format.
in subset: bio
in subset: formats

PHYLIP format
type: Class
subclass of: Phylip format variant
Created in: beta12orEarlier
Documentation: http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format
has definition: Phylip format for (aligned) sequences.
has exact synonym: PHYLIP
has exact synonym: PHYLIP interleaved format
has exact synonym: ph
has exact synonym: phy
in subset: bio
in subset: formats

PHYLIP sequential
type: Class
subclass of: Phylip format variant
Created in: beta12orEarlier
Documentation: http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format
has definition: Phylip non-interleaved format for (aligned) sequences.
has exact synonym: PHYLIP sequential format
has exact synonym: phylipnon
in subset: bio
in subset: formats

scores format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Alignment format for score values for pairs of sequences.
in subset: bio
in subset: formats

selex
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: SELEX format for (aligned) sequences.
in subset: bio
in subset: formats

EMBOSS simple format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: EMBOSS simple multiple alignment format.
in subset: bio
in subset: formats

srs format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Simple multiple sequence (alignment) format for SRS.
in subset: bio
in subset: formats

srspair
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
has definition: Simple sequence pair (alignment) format for SRS.
in subset: bio
in subset: formats

T-Coffee format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: T-Coffee program alignment format.
in subset: bio
in subset: formats

TreeCon-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Treecon format for (aligned) sequences.
in subset: bio
in subset: formats

Phylogenetic tree format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic tree
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a phylogenetic tree.
in subset: bio
in subset: formats

Biological pathway or network format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Pathway or network
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a biological pathway or network.
in subset: bio
in subset: formats

Sequence-profile alignment format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence signature matches
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a sequence-profile alignment.
in subset: bio
in subset: formats

Sequence-profile alignment (HMM) format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence-profile alignment format
has definition: Data format for a sequence-HMM profile alignment.
in subset: obsolete
deprecated: true

Amino acid index format
type: Class
subclass of: Matrix format
subclass of: Restriction
  on property: is format of
  some values from: Amino acid index
Created in: beta12orEarlier
has definition: Data format for an amino acid index.
in subset: bio
in subset: formats

Article format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Article
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a full-text scientific article.
has exact synonym: Literature format
in subset: bio
in subset: formats

Text mining report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Text mining report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format of a report from text mining.
in subset: bio
in subset: formats

Enzyme kinetics report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Enzyme kinetics data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for reports on enzyme kinetics.
in subset: bio
in subset: formats

Chemical data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Small molecule report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report on a chemical compound.
has exact synonym: Chemical compound annotation format
has exact synonym: Chemical structure format
has exact synonym: Small molecule report format
has exact synonym: Small molecule structure format
in subset: bio
in subset: formats

Gene annotation format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Gene report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report on a particular locus, gene, gene system or groups of genes.
has exact synonym: Gene features format
in subset: bio
in subset: formats

Workflow format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a workflow.
has exact synonym: Programming language
has exact synonym: Script format
in subset: bio
in subset: formats

Tertiary structure format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for a molecular tertiary structure.
in subset: bio
in subset: formats

Biological model format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.2
Old parent: Thing
consider: Biological pathway or network format
has definition: Data format for a biological model.
in subset: obsolete
deprecated: true

Chemical formula format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Chemical formula
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Text format of a chemical formula.
in subset: bio
in subset: formats

Phylogenetic character data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic character data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of raw (unplotted) phylogenetic data.
in subset: bio
in subset: formats

Phylogenetic continuous quantitative character format
type: Class
subclass of: Phylogenetic character data format
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic continuous quantitative data
Created in: beta12orEarlier
has definition: Format of phylogenetic continuous quantitative character data.
in subset: bio
in subset: formats

Phylogenetic discrete states format
type: Class
subclass of: Phylogenetic character data format
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic discrete data
Created in: beta12orEarlier
has definition: Format of phylogenetic discrete states data.
in subset: bio
in subset: formats

Phylogenetic tree report (cliques) format
type: Class
subclass of: Phylogenetic character data format
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic character cliques
Created in: beta12orEarlier
has definition: Format of phylogenetic cliques data.
in subset: bio
in subset: formats

Phylogenetic tree report (invariants) format
type: Class
subclass of: Phylogenetic character data format
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic invariants
Created in: beta12orEarlier
has definition: Format of phylogenetic invariants data.
in subset: bio
in subset: formats

Electron microscopy model format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Format (by type of data)
has definition: Annotation format for electron microscopy models.
in subset: obsolete
deprecated: true

Phylogenetic tree report (tree distances) format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic tree distances
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for phylogenetic tree distance data.
in subset: bio
in subset: formats

Polymorphism report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: Sequence variation annotation format
has definition: Format for sequence polymorphism data.
in subset: obsolete
deprecated: true

Protein family report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protein family report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for reports on a protein family.
in subset: bio
in subset: formats

Protein interaction format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protein interaction data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for molecular interaction data.
has exact synonym: Molecular interaction format
in subset: bio
in subset: formats

Sequence assembly format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence assembly
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for sequence assembly data.
in subset: bio
in subset: formats

Microarray experiment data format
type: Class
subclass of: Experiment annotation format
Created in: beta12orEarlier
has definition: Format for information about a microarray experimental per se (not the data generated from that experiment).
in subset: bio
in subset: formats

Sequence trace format
type: Class
subclass of: Sequence record format
subclass of: Restriction
  on property: is format of
  some values from: Sequence trace
Created in: beta12orEarlier
has definition: Format for sequence trace data (i.e. including base call information).
in subset: bio
in subset: formats

Gene expression report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Expression data
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a file of gene expression data, e.g. a gene expression matrix or profile.
has exact synonym: Gene expression data format
in subset: bio
in subset: formats

Genotype and phenotype annotation format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Format (by type of data)
has definition: Format of a report on genotype / phenotype information.
in subset: obsolete
deprecated: true

Map format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Map
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a map of (typically one) molecular sequence annotated with features.
in subset: bio
in subset: formats

Nucleic acid features (primers) format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence.
in subset: bio
in subset: formats

Protein report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protein report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report of general information about a specific protein.
in subset: bio
in subset: formats

Protein report (enzyme) format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Format (by type of data)
has definition: Format of a report of general information about a specific enzyme.
in subset: obsolete
deprecated: true

3D-1D scoring matrix format
type: Class
subclass of: Matrix format
subclass of: Restriction
  on property: is format of
  some values from: 3D-1D scoring matrix
Created in: beta12orEarlier
has definition: Format of a matrix of 3D-1D scores (amino acid environment probabilities).
in subset: bio
in subset: formats

Protein structure report (quality evaluation) format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protein structural quality report
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report on the quality of a protein three-dimensional model.
in subset: bio
in subset: formats

Database hits (sequence) format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence search results
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a report on sequence hits and associated data from searching a sequence database.
in subset: bio
in subset: formats

Sequence distance matrix format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence distance matrix
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a matrix of genetic distances between molecular sequences.
in subset: bio
in subset: formats

Sequence motif format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence motif
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a sequence motif.
in subset: bio
in subset: formats

Sequence profile format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence profile
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a sequence profile.
in subset: bio
in subset: formats

Hidden Markov model format
type: Class
subclass of: Sequence profile format
subclass of: Restriction
  on property: is format of
  some values from: Hidden Markov model
Created in: beta12orEarlier
has definition: Format of a hidden Markov model.
in subset: bio
in subset: formats

Dirichlet distribution format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Dirichlet distribution
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format of a dirichlet distribution.
in subset: bio
in subset: formats

HMM emission and transition counts format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Transition matrix
subclass of: Restriction
  on property: is format of
  some values from: Emission matrix
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Data format for the emission and transition counts of a hidden Markov model.
in subset: bio
in subset: formats

RNA secondary structure format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: RNA secondary structure
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for secondary structure (predicted or real) of an RNA molecule.
in subset: bio
in subset: formats

Protein secondary structure format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format for secondary structure (predicted or real) of a protein molecule.
in subset: bio
in subset: formats

Sequence range format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence range
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format used to specify range(s) of sequence positions.
in subset: bio
in subset: formats

pure
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.
in subset: bio
in subset: formats

unpure
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.
in subset: bio
in subset: formats

unambiguous sequence
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.
in subset: bio
in subset: formats

ambiguous
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.
in subset: bio
in subset: formats

Sequence features (repeats) format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format used for map of repeats in molecular (typically nucleotide) sequences.
in subset: bio
in subset: formats

Nucleic acid features (restriction sites) format
type: Class
subclass of: Format (by type of data)
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format used for report on restriction enzyme recognition sites in nucleotide sequences.
in subset: bio
in subset: formats

Gene features (coding region) format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.10
Old parent: Thing
has definition: Format used for report on coding regions in nucleotide sequences.
in subset: obsolete
replaced by: Gene annotation format
deprecated: true

Sequence cluster format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence cluster
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format used for clusters of molecular sequences.
in subset: bio
in subset: formats

Sequence cluster format (protein)
type: Class
subclass of: Sequence cluster format
Created in: beta12orEarlier
has definition: Format used for clusters of protein sequences.
in subset: bio
in subset: formats

Sequence cluster format (nucleic acid)
type: Class
subclass of: Sequence cluster format
Created in: beta12orEarlier
has definition: Format used for clusters of nucleotide sequences.
in subset: bio
in subset: formats

Gene cluster format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence cluster format (nucleic acid)
has definition: Format used for clusters of genes.
in subset: obsolete
deprecated: true

EMBL-like (text)
type: Class
subclass of: Textual format
subclass of: EMBL-like format
Created in: beta12orEarlier
has definition: A text format resembling EMBL entry format.
in subset: bio
in subset: formats
comment: This concept may be used for the many non-standard EMBL-like text formats.

FASTQ-like format (text)
type: Class
subclass of: Textual format
subclass of: FASTQ-like format
Created in: beta12orEarlier
has definition: A text format resembling FASTQ short read format.
in subset: bio
in subset: formats
comment: This concept may be used for non-standard FASTQ short read-like formats.

EMBLXML
type: Class
subclass of: EMBL format (XML)
Created in: beta12orEarlier
has definition: XML format for EMBL entries.
Documentation: ENA.embl.xsd
in subset: bio
in subset: formats
deprecation_candidate: true

cdsxml
type: Class
subclass of: EMBL format (XML)
Created in: beta12orEarlier
has definition: Specific XML format for EMBL entries (only uses certain sections).
Documentation: ENA.embl.xsd
in subset: bio
in subset: formats
deprecation_candidate: true

INSDSeq
type: Class
subclass of: EMBL format (XML)
Created in: beta12orEarlier
has definition: INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/DDBJ-style flatfile formats, with a small amount of additional structure.
in subset: bio
in subset: formats
has exact synonym: INSD XML
has exact synonym: INSDC XML
Documentation: INSD v1.5.dtd.docx

geneseq
type: Class
subclass of: EMBL-like (text)
Created in: beta12orEarlier
has definition: Geneseq sequence format.
in subset: bio
in subset: formats

UniProt-like (text)
type: Class
subclass of: Textual format
subclass of: uniprotkb-like format
Created in: beta12orEarlier
has definition: A text sequence format resembling uniprotkb entry format.
in subset: bio
in subset: formats

UniProt format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: UniProt entry sequence format.
in subset: obsolete
replaced by: UniProtKB format
deprecated: true

ipi
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: UniProtKB format
has definition: ipi sequence format.
in subset: obsolete
deprecated: true

medline
type: Class
subclass of: Article format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Abstract format used by MedLine database.
in subset: bio
in subset: formats

Ontology format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Ontology
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format used for ontologies.
in subset: bio
in subset: formats

OBO format
type: Class
subclass of: Ontology format
Created in: beta12orEarlier
has definition: A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.
in subset: bio
in subset: formats

OWL format
type: Class
subclass of: Ontology format
subclass of: RDF format
Created in: beta12orEarlier
has definition: A serialisation format conforming to the Web Ontology Language (OWL) model.
in subset: bio
in subset: formats

FASTA-like (text)
type: Class
subclass of: Textual format
subclass of: FASTA-like
Created in: beta12orEarlier
has definition: A text format resembling FASTA format.
in subset: bio
in subset: formats
comment: This concept may also be used for the many non-standard FASTA-like formats.

Sequence record full format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
in subset: obsolete
replaced by: Sequence record format
deprecated: true

Sequence record lite format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Sequence record format
deprecated: true

EMBL format (XML)
type: Class
subclass of: EMBL-like (XML)
Created in: beta12orEarlier
has definition: An XML format for EMBL entries.
in subset: bio
in subset: formats
comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation.

GenBank-like format (text)
type: Class
subclass of: Textual format
subclass of: GenBank-like format
Created in: beta12orEarlier
has definition: A text format resembling GenBank entry (plain text) format.
in subset: bio
in subset: formats
comment: This concept may be used for the non-standard GenBank-like text formats.

Sequence feature table format (text)
type: Class
subclass of: Sequence feature table format
Created in: beta12orEarlier
has definition: Text format for a sequence feature table.
in subset: bio
in subset: formats

Strain data format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: Format
has definition: Format of a report on organism strain data / cell line.
in subset: obsolete
deprecated: true

CIP strain data format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format for a report of strain data as used for CIP database entries.
in subset: obsolete
deprecated: true

phylip property values
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Phylogenetic character data format
has definition: PHYLIP file format for phylogenetic property data.
in subset: obsolete
deprecated: true

STRING entry format (HTML)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format (HTML) for the STRING database of protein interaction.
in subset: obsolete
deprecated: true

STRING entry format (XML)
type: Class
subclass of: Protein interaction format
subclass of: XML
Created in: beta12orEarlier
has definition: Entry format (XML) for the STRING database of protein interaction.
in subset: bio
in subset: formats

GFF
type: Class
subclass of: Sequence feature table format (text)
subclass of: Textual format
Created in: beta12orEarlier
has definition: GFF feature format (of indeterminate version).
in subset: bio
in subset: formats

GTF
type: Class
subclass of: GFF
Created in: beta12orEarlier
Documentation: GTF22.html
has db xref: format4
has db xref: GTF22.html
has definition: Gene Transfer Format (GTF), a restricted version of GFF.
in subset: bio
in subset: formats

FASTA-HTML
type: Class
subclass of: HTML
subclass of: FASTA-like
Created in: beta12orEarlier
has definition: FASTA format wrapped in HTML elements.
in subset: bio
in subset: formats

EMBL-HTML
type: Class
subclass of: HTML
subclass of: EMBL-like format
Created in: beta12orEarlier
has definition: EMBL entry format wrapped in HTML elements.
in subset: bio
in subset: formats

BioCyc enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the BioCyc enzyme database.
in subset: obsolete
deprecated: true

ENZYME enzyme report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of an entry from the Enzyme nomenclature database (ENZYME).
in subset: obsolete
deprecated: true

PseudoCAP gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of a report on a gene from the PseudoCAP database.
in subset: obsolete
deprecated: true

GeneCards gene report format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Format of a report on a gene from the GeneCards database.
in subset: obsolete
deprecated: true

Textual format
type: Class
subclass of: Format
disjoint with: Binary format
Created in: beta12orEarlier
has definition: Textual format.
has exact synonym: Plain text format
has exact synonym: txt
in subset: bio
in subset: formats
comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).

HTML
type: Class
subclass of: Format
subclass of: Restriction
  on property: is format of
  some values from: Report
disjoint with: Binary format
Created in: beta12orEarlier
has definition: HTML format.
has exact synonym: Hypertext Markup Language
in subset: bio
in subset: formats

XML
type: Class
subclass of: Format
disjoint with: Binary format
Created in: beta12orEarlier
File extension: xml
Media type: http://www.iana.org/assignments/media-types/application/xml
has db xref: XML
has db xref: http://www.iana.org/assignments/media-types/application/xml
has definition: eXtensible Markup Language (XML) format.
has exact synonym: eXtensible Markup Language
in subset: bio
in subset: formats
comment: Data in XML format can be serialised into text, or binary format.

Binary format
type: Class
subclass of: Format
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Binary format.
in subset: bio
in subset: formats
comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.

URI format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: URI
has definition: Typical textual representation of a URI.
in subset: obsolete
deprecated: true

NCI-Nature pathway entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: The format of an entry from the NCI-Nature pathways database.
in subset: obsolete
deprecated: true

Format (by type of data)
type: Class
subclass of: Format
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented.
has exact synonym: Format (typed)
in subset: bio
in subset: formats
comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.

BioXSD (XML)
type: Class
subclass of: Sequence record format
subclass of: Sequence feature annotation format
subclass of: XML
subclass of: Alignment format (XML)
subclass of: Raw sequence format
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
subclass of: Restriction
  on property: is format of
  some values from: Score
subclass of: Restriction
  on property: is format of
  some values from: Sequence
subclass of: Restriction
  on property: is format of
  some values from: Experimental measurement
Citation: btq391
Citation: http://doi.org/10.1186/1471-2105-12-494
Citation: f1000research.1113048.1
Created in: beta12orEarlier
Documentation: bioxsd.org
Documentation: BioXSD-1.1.xsd
Example: accession.xml
Example: exampleFeatureRecords.html
Example: sequenceRecord.xml
Example: sequenceRecord.xml+json+yaml.xml
Ontology used: 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.
Repository: bioxsd
comment: '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'.
has db xref: bioxsd.org
has db xref: BioXSD-1.1.xsd
has definition: 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.
has exact synonym: BioJSON
has exact synonym: BioXSD
has exact synonym: BioXSD XML
has exact synonym: BioXSD XML format
has exact synonym: BioXSD data model
has exact synonym: BioXSD format
has exact synonym: BioXSD in XML
has exact synonym: BioXSD in XML format
has exact synonym: BioXSD+XML
has exact synonym: BioXSD/GTrack
has exact synonym: BioXSD|GTrack
has exact synonym: BioYAML
in subset: bio
in subset: formats

RDF format
type: Class
subclass of: Format
subclass of: Ontology format
subclass of: Linked data format
Created in: beta12orEarlier
has definition: A serialisation format conforming to the Resource Description Framework (RDF) model.
has exact synonym: Resource Description Framework format
has related synonym: RDF
has related synonym: Resource Description Framework
in subset: bio
in subset: formats

GenBank-HTML
type: Class
subclass of: HTML
subclass of: GenBank-like format
Created in: beta12orEarlier
has definition: Genbank entry format wrapped in HTML elements.
in subset: bio
in subset: formats

Protein features (domains) format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Format (by type of data)
has definition: Format of a report on protein features (domain composition).
in subset: obsolete
deprecated: true

EMBL-like format
type: Class
subclass of: Sequence record format
Created in: beta12orEarlier
has definition: A format resembling EMBL entry (plain text) format.
in subset: bio
in subset: formats
comment: This concept may be used for the many non-standard EMBL-like formats.

FASTQ-like format
type: Class
subclass of: Sequence trace format
Created in: beta12orEarlier
has definition: A format resembling FASTQ short read format.
in subset: bio
in subset: formats
comment: This concept may be used for non-standard FASTQ short read-like formats.

FASTA-like
type: Class
subclass of: Sequence record format
Created in: beta12orEarlier
has definition: A format resembling FASTA format.
in subset: bio
in subset: formats
comment: This concept may be used for the many non-standard FASTA-like formats.

uniprotkb-like format
type: Class
subclass of: Sequence record format
subclass of: Sequence feature table format
Created in: beta12orEarlier
has definition: A sequence format resembling uniprotkb entry format.
in subset: bio
in subset: formats

Sequence feature table format
type: Class
subclass of: Sequence feature annotation format
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
Created in: beta12orEarlier
has definition: Format for a sequence feature table.
in subset: bio
in subset: formats

OBO
type: Class
subclass of: OBO format
subclass of: Textual format
Created in: beta12orEarlier
has definition: OBO ontology text format.
in subset: bio
in subset: formats

OBO-XML
type: Class
subclass of: OBO format
subclass of: XML
Created in: beta12orEarlier
has definition: OBO ontology XML format.
in subset: bio
in subset: formats

Sequence record format (text)
type: Class
subclass of: Sequence record format
Created in: beta12orEarlier
has definition: Data format for a molecular sequence record (text).
in subset: bio
in subset: formats

Sequence record format (XML)
type: Class
subclass of: Sequence record format
Created in: beta12orEarlier
has definition: Data format for a molecular sequence record (XML).
in subset: bio
in subset: formats

Sequence feature table format (XML)
type: Class
subclass of: Sequence feature table format
Created in: beta12orEarlier
has definition: XML format for a sequence feature table.
in subset: bio
in subset: formats

Alignment format (text)
type: Class
subclass of: Alignment format
Created in: beta12orEarlier
has definition: Text format for molecular sequence alignment information.
in subset: bio
in subset: formats

Alignment format (XML)
type: Class
subclass of: Alignment format
Created in: beta12orEarlier
has definition: XML format for molecular sequence alignment information.
in subset: bio
in subset: formats

Phylogenetic tree format (text)
type: Class
subclass of: Phylogenetic tree format
Created in: beta12orEarlier
has definition: Text format for a phylogenetic tree.
in subset: bio
in subset: formats

Phylogenetic tree format (XML)
type: Class
subclass of: Phylogenetic tree format
Created in: beta12orEarlier
has definition: XML format for a phylogenetic tree.
in subset: bio
in subset: formats

EMBL-like (XML)
type: Class
subclass of: XML
subclass of: EMBL-like format
Created in: beta12orEarlier
has definition: An XML format resembling EMBL entry format.
in subset: bio
in subset: formats
comment: This concept may be used for the any non-standard EMBL-like XML formats.

GenBank-like format
type: Class
subclass of: Sequence record format
Created in: beta12orEarlier
has definition: A format resembling GenBank entry (plain text) format.
in subset: bio
in subset: formats
comment: This concept may be used for the non-standard GenBank-like formats.

STRING entry format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: HTML
has definition: Entry format for the STRING database of protein interaction.
in subset: obsolete
deprecated: true

Sequence assembly format (text)
type: Class
subclass of: Sequence assembly format
Created in: beta12orEarlier
has definition: Text format for sequence assembly data.
in subset: bio
in subset: formats

Amino acid identifier format
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Amino acid identifier
has definition: Text format (representation) of amino acid residues.
in subset: obsolete
deprecated: true

completely unambiguous
type: Class
subclass of: Textual format
subclass of: Raw sequence format
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence without any unknown positions or ambiguity characters.
in subset: bio
in subset: formats

completely unambiguous pure
type: Class
subclass of: pure
subclass of: completely unambiguous
Created in: beta12orEarlier
has definition: Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.
in subset: bio
in subset: formats

completely unambiguous pure nucleotide
type: Class
subclass of: nucleotide
subclass of: completely unambiguous pure
Created in: beta12orEarlier
has definition: Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .
in subset: bio
in subset: formats

completely unambiguous pure dna
type: Class
subclass of: dna
subclass of: completely unambiguous pure
Created in: beta12orEarlier
has definition: Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.
in subset: bio
in subset: formats

completely unambiguous pure rna sequence
type: Class
subclass of: rna
subclass of: completely unambiguous pure
Created in: beta12orEarlier
has definition: Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.
in subset: bio
in subset: formats

Raw sequence format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a raw molecular sequence (i.e. the alphabet used).
in subset: bio
in subset: formats

BAM
type: Class
subclass of: Sequence trace format
subclass of: Binary format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: SAMv1.pdf
has db xref: SAMv1.pdf
has definition: 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.
in subset: bio
in subset: formats

SAM
type: Class
subclass of: Sequence trace format
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: SAMv1.pdf
has db xref: SAMv1.pdf
has definition: 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.
in subset: bio
in subset: formats
comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.

SBML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: beta12orEarlier
Documentation: sbml.org
has db xref: sbml.org
has definition: Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
in subset: bio
in subset: formats

completely unambiguous pure protein
type: Class
subclass of: protein
subclass of: completely unambiguous pure
Created in: beta12orEarlier
has definition: Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.
in subset: bio
in subset: formats

Bibliographic reference format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Citation
subclass of: Restriction
  on property: is format of
  some values from: Abstract
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of a bibliographic reference.
in subset: bio
in subset: formats

Sequence annotation track format
type: Class
subclass of: Sequence feature annotation format
subclass of: Restriction
  on property: is format of
  some values from: Annotation track
Created in: beta12orEarlier
has definition: Format of a sequence annotation track.
in subset: bio
in subset: formats

Alignment format (pair only)
type: Class
subclass of: Alignment format
subclass of: Restriction
  on property: is format of
  some values from: Pair sequence alignment
Created in: beta12orEarlier
has definition: Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
in subset: bio
in subset: formats

Sequence variation annotation format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Sequence variations
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Format of sequence variation annotation.
in subset: bio
in subset: formats

markx0 variant
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Some variant of Pearson MARKX alignment format.
in subset: bio
in subset: formats

mega variant
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Some variant of Mega format for (typically aligned) sequences.
in subset: bio
in subset: formats

Phylip format variant
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Some variant of Phylip format for (aligned) sequences.
in subset: bio
in subset: formats

AB1
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
has definition: AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.
in subset: bio
in subset: formats
comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).

ACE
type: Class
subclass of: Sequence assembly format
subclass of: Textual format
Created in: beta12orEarlier
Documentation: README.14.0.txt
has db xref: README.14.0.txt
has definition: ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).
in subset: bio
in subset: formats

BED
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format1
has db xref: format1
has definition: Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.
in subset: bio
in subset: formats
comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).

bigBed
type: Class
subclass of: Binary format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format1.5
has db xref: format1.5
has definition: bigBed format for large sequence annotation tracks, similar to textual BED format.
in subset: bio
in subset: formats

WIG
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: wiggle.html
File extension: wig
has db xref: wiggle.html
has definition: 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.
in subset: bio
in subset: formats

bigWig
type: Class
subclass of: Binary format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format6.1
has db xref: format6.1
has definition: bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.
in subset: bio
in subset: formats

PSL
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: format2
has db xref: format2
has definition: PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.
in subset: bio
in subset: formats

MAF
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format5
has db xref: format5
has definition: Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.
in subset: bio
in subset: formats
comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.

2bit
type: Class
subclass of: Binary format
subclass of: Raw sequence format
Created in: beta12orEarlier
Documentation: 2bitformat.html
has db xref: http://genome-source.cse.ucsc.edu/gitweb/
has db xref: 2bitformat.html
has definition: 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'.
in subset: bio
in subset: formats

.nib
type: Class
subclass of: Binary format
subclass of: Raw sequence format
Created in: beta12orEarlier
Documentation: format8
has db xref: format8
has definition: .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'.
in subset: bio
in subset: formats

genePred
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format9
File extension: gp
has db xref: format9
has definition: genePred table format for gene prediction tracks.
in subset: bio
in subset: formats
comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.

pgSnp
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
Documentation: format10
has db xref: format10
has definition: Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.
in subset: bio
in subset: formats

axt
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: axt.html
has db xref: axt.html
has definition: axt format of alignments, typically produced from BLASTZ.
in subset: bio
in subset: formats

LAV
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: lav format.html
File extension: lav
has db xref: lav format.html
has definition: LAV format of alignments generated by BLASTZ and LASTZ.
in subset: bio
in subset: formats

Pileup
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
Documentation: pileup.shtml
has db xref: pileup.shtml
has definition: 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).
in subset: bio
in subset: formats

VCF
type: Class
subclass of: Textual format
subclass of: Sequence variation annotation format
Created in: beta12orEarlier
Documentation: VCFv4.3.pdf
has definition: Variant Call Format (VCF) is tabular format for storing genomic sequence variations.
comment: 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.
File extension: vcf
File extension: vcf.gz
in subset: bio
in subset: formats

SRF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
Documentation: srf.sourceforge.net
has db xref: srf.sourceforge.net
has definition: Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
in subset: bio
in subset: formats

ZTR
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
Documentation: formats unix 12.html
has db xref: formats unix 12.html
has definition: ZTR format for storing chromatogram data from DNA sequencing instruments.
in subset: bio
in subset: formats

GVF
type: Class
subclass of: GFF3
subclass of: Sequence variation annotation format
Created in: beta12orEarlier
Documentation: gvf.html
has db xref: gvf.html
has definition: Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.
in subset: bio
in subset: formats

BCF
type: Class
subclass of: Binary format
subclass of: Sequence variation annotation format
Created in: beta12orEarlier
has db xref: mpileup.shtml
Documentation: VCFv4.3.pdf
File extension: bcf
File extension: bcf.gz
has definition: BCF is the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
in subset: bio
in subset: formats

Matrix format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Matrix
Created in: beta13
notRecommendedForAnnotation: true
has definition: Format of a matrix (array) of numerical values.
in subset: bio
in subset: formats

Protein domain classification format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protein family report
Created in: beta13
notRecommendedForAnnotation: true
has definition: Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).
in subset: bio
in subset: formats

Raw SCOP domain classification format
type: Class
subclass of: Protein domain classification format
Created in: beta13
has definition: Format of raw SCOP domain classification data files.
in subset: bio
in subset: formats
comment: These are the parsable data files provided by SCOP.

Raw CATH domain classification format
type: Class
subclass of: Protein domain classification format
Created in: beta13
has definition: Format of raw CATH domain classification data files.
in subset: bio
in subset: formats
comment: These are the parsable data files provided by CATH.

CATH domain report format
type: Class
subclass of: Protein domain classification format
Created in: beta13
has definition: Format of summary of domain classification information for a CATH domain.
in subset: bio
in subset: formats
comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.

SBRML
type: Class
subclass of: XML
subclass of: Biological pathway or network report format
Created in: 1.0
Documentation: http://www.comp-sys-bio.org/tiki-index.php
has db xref: http://www.comp-sys-bio.org/tiki-index.php
has definition: Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.
in subset: bio
in subset: formats

BioPAX
type: Class
subclass of: Biological pathway or network format
Created in: 1.0
Documentation: www.biopax.org
has db xref: www.biopax.org
has definition: BioPAX is an exchange format for pathway data, with its data model defined in OWL.
in subset: bio
in subset: formats

EBI Application Result XML
type: Class
subclass of: Database hits (sequence) format
subclass of: XML
subclass of: Alignment format (pair only)
Created in: 1.0
Documentation: ApplicationResult.xsd
has db xref: ApplicationResult.xsd
has definition: EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.
in subset: bio
in subset: formats

PSI MI XML (MIF)
type: Class
subclass of: Protein interaction format
subclass of: XML
Created in: 1.0
Documentation: mif
has db xref: mif
has definition: XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.
has exact synonym: MIF
in subset: bio
in subset: formats

phyloXML
type: Class
subclass of: XML
subclass of: Phylogenetic tree format (XML)
Created in: 1.0
Documentation: www.phyloxml.org
has db xref: www.phyloxml.org
has definition: phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.
in subset: bio
in subset: formats

NeXML
type: Class
subclass of: XML
subclass of: Phylogenetic tree format (XML)
Created in: 1.0
Documentation: www.nexml.org
has db xref: www.nexml.org
has definition: NeXML is a standardised XML format for rich phyloinformatic data.
in subset: bio
in subset: formats

MAGE-ML
type: Class
subclass of: Gene expression report format
subclass of: XML
subclass of: Restriction
  on property: is format of
  some values from: Processed microarray data
Created in: 1.0
Documentation: mage-ml.html
has db xref: mage-ml.html
has definition: MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).
in subset: bio
in subset: formats

MAGE-TAB
type: Class
subclass of: Gene expression report format
subclass of: TSV
subclass of: Restriction
  on property: is format of
  some values from: Processed microarray data
Created in: 1.0
Documentation: mage-tab
has db xref: mage-tab
has definition: MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).
in subset: bio
in subset: formats

GCDML
type: Class
subclass of: XML
subclass of: Experiment annotation format
Created in: 1.0
Documentation: gcdml.gensc.org
has db xref: gcdml.gensc.org
has definition: GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).
in subset: bio
in subset: formats

GTrack
type: Class
subclass of: Sequence feature table format (text)
subclass of: Textual format
subclass of: Sequence annotation track format
Citation: http://doi.org/10.1186/1471-2105-12-494
Created in: 1.0
Documentation: www.gtrack.no
Documentation: GTrack specification.html
Documentation: GTrack specification.txt
Example: examples
Example: gtrack-examples-from-the-specification
Repository: gtrack
comment: '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.
has db xref: www.gtrack.no
has db xref: GTrack specification.html
has db xref: GTrack specification.txt
has definition: 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").
has exact synonym: BioXSD/GTrack GTrack
has exact synonym: BioXSD|GTrack GTrack
has exact synonym: GTrack ecosystem of formats
has exact synonym: GTrack format
has exact synonym: GTrack|BTrack|GSuite GTrack
has exact synonym: GTrack|GSuite|BTrack GTrack
in subset: bio
in subset: formats

Biological pathway or network report format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Pathway or network report
Created in: 1.0
notRecommendedForAnnotation: true
has definition: Data format for a report of information derived from a biological pathway or network.
in subset: bio
in subset: formats

Experiment annotation format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Protocol
Created in: 1.0
notRecommendedForAnnotation: true
has definition: Data format for annotation on a laboratory experiment.
in subset: bio
in subset: formats

Cytoband format
type: Class
subclass of: Sequence range format
subclass of: Textual format
subclass of: Restriction
  on property: is format of
  some values from: Cytoband position
Created in: 1.2
Documentation: Cytoband
has db xref: Cytoband
has definition: Cytoband format for chromosome cytobands.
in subset: bio
in subset: formats
comment: Reflects a UCSC Browser DB table.

CopasiML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
subclass of: Biological pathway or network report format
Created in: 1.2
Documentation: http://www.copasi.org/tiki-index.php
has db xref: http://www.copasi.org/tiki-index.php
has definition: CopasiML, the native format of COPASI.
in subset: bio
in subset: formats

CellML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.2
Documentation: www.cellml.org
Media type: cellml+xml
has db xref: www.cellml.org
has db xref: cellml+xml
has definition: CellML, the format for mathematical models of biological and other networks.
in subset: bio
in subset: formats

PSI MI TAB (MITAB)
type: Class
subclass of: Protein interaction format
subclass of: Textual format
Created in: 1.2
Documentation: README
Documentation: MITAB27Format.html
Documentation: PSI-MITAB interactions
Documentation: psi mitab file
has db xref: README
has definition: Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.
in subset: bio
in subset: formats

PSI-PAR
type: Class
subclass of: PSI MI XML (MIF)
Created in: 1.2
Documentation: psi-par
has db xref: psi-par
has definition: Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.
in subset: bio
in subset: formats

mzML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
Documentation: mzml
has db xref: mzml
has definition: mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.
in subset: bio
in subset: formats
comment: mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.

Mass spectrometry data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Mass spectrometry data
Created in: 1.2
notRecommendedForAnnotation: true
has definition: Format for mass pectra and derived data, include peptide sequences etc.
in subset: bio
in subset: formats

TraML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
Documentation: traml
has db xref: traml
has definition: TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.
in subset: bio
in subset: formats

mzIdentML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
Documentation: mzidentml
has db xref: mzidentml
has definition: 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.
in subset: bio
in subset: formats

mzQuantML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
Documentation: mzquantml
has db xref: mzquantml
has definition: 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.
in subset: bio
in subset: formats

GelML
type: Class
subclass of: XML
subclass of: Experiment annotation format
Created in: 1.2
Documentation: gelml
has db xref: gelml
has definition: GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.
in subset: bio
in subset: formats

spML
type: Class
subclass of: XML
subclass of: Experiment annotation format
Created in: 1.2
Documentation: psidev.info
has db xref: psidev.info
has definition: 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.
in subset: bio
in subset: formats

OWL Functional Syntax
type: Class
subclass of: OWL format
subclass of: Textual format
Created in: 1.2
has definition: A human-readable encoding for the Web Ontology Language (OWL).
in subset: bio
in subset: formats

Manchester OWL Syntax
type: Class
subclass of: OWL format
subclass of: Textual format
Created in: 1.2
has definition: A syntax for writing OWL class expressions.
in subset: bio
in subset: formats
comment: This format was influenced by the OWL Abstract Syntax and the DL style syntax.

KRSS2 Syntax
type: Class
subclass of: Ontology format
subclass of: Textual format
Created in: 1.2
has definition: A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort".
in subset: bio
in subset: formats
comment: This format is used in Protege 4.

Turtle
type: Class
subclass of: Textual format
subclass of: RDF format
Created in: 1.2
has definition: The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs.
in subset: bio
in subset: formats
comment: The SPARQL Query Language incorporates a very similar syntax.

N-Triples
type: Class
subclass of: Textual format
subclass of: RDF format
Created in: 1.2
File extension: nt
has definition: A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.
in subset: bio
in subset: formats
comment: N-Triples should not be confused with Notation 3 which is a superset of Turtle.

Notation3
type: Class
subclass of: Textual format
subclass of: RDF format
Created in: 1.2
File extension: n3
has definition: A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind.
has exact synonym: N3
in subset: bio
in subset: formats

RDF/XML
type: Class
subclass of: XML
subclass of: RDF format
Created in: 1.2
File extension: rdf
Media type: rdf+xml
has definition: Resource Description Framework (RDF) XML format.
in subset: bio
in subset: formats
comment: RDF/XML can be used as a standard serialisation syntax for OWL DL, but not for OWL Full.

OWL/XML
type: Class
subclass of: OWL format
subclass of: XML
Created in: 1.2
has definition: OWL ontology XML serialisation format.
has exact synonym: OWL
in subset: bio
in subset: formats

A2M
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: 1.3
Documentation: a2m-desc.html
has db xref: a2m-desc.html
has definition: 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.
in subset: bio
in subset: formats

SFF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: 1.3
Documentation: sff
has db xref: sff
has definition: 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.
has exact synonym: Standard flowgram format
in subset: bio
in subset: formats

MAP
type: Class
subclass of: PED/MAP
Created in: 1.3
Documentation: ped
has definition: The MAP file describes SNPs and is used by the Plink package.
has exact synonym: Plink MAP
in subset: bio
in subset: formats

PED
type: Class
subclass of: PED/MAP
Created in: 1.3
Documentation: ped
has definition: The PED file describes individuals and genetic data and is used by the Plink package.
has exact synonym: Plink PED
in subset: bio
in subset: formats

Individual genetic data format
type: Class
subclass of: Format (by type of data)
Created in: 1.3
notRecommendedForAnnotation: true
has definition: Data format for a metadata on an individual and their genetic data.
in subset: bio
in subset: formats

PED/MAP
type: Class
subclass of: Textual format
subclass of: Individual genetic data format
Created in: 1.3
Documentation: ped
has definition: The PED/MAP file describes data used by the Plink package.
has exact synonym: Plink PED/MAP
in subset: bio
in subset: formats

CT
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
Created in: 1.3
Documentation: File Formats.html
Documentation: data formats.html
has definition: File format of a CT (Connectivity Table) file from the RNAstructure package.
has exact synonym: Connect format
has exact synonym: Connectivity Table file format
in subset: bio
in subset: formats

SS
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
Created in: 1.3
Documentation: xrna faq.html
has definition: XRNA old input style format.
in subset: bio
in subset: formats

RNAML
type: Class
subclass of: Alignment format
subclass of: RNA secondary structure format
subclass of: XML
Created in: 1.3
Documentation: rnaml
has definition: RNA Markup Language.
in subset: bio
in subset: formats

GDE
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: 1.3
Documentation: GDE2.2 manual.pdf
has definition: Format for the Genetic Data Environment (GDE).
in subset: bio
in subset: formats

BLC
type: Class
subclass of: Alignment format (text)
Created in: 1.3
Documentation: SECTION00018250000000000000
has definition: A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) package.
has exact synonym: Block file format
in subset: bio
in subset: formats

Data index format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Data index
Created in: 1.3
notRecommendedForAnnotation: true
has definition: Format of a data index of some type.
in subset: bio
in subset: formats

BAI
type: Class
subclass of: Binary format
subclass of: Data index format
subclass of: Restriction
  on property: is format of
  some values from: Data index
Created in: 1.3
Documentation: SAMv1.pdf
has definition: BAM indexing format.
in subset: bio
in subset: formats

HMMER2
type: Class
subclass of: HMMER format
Created in: 1.3
Documentation: Userguide.pdf
has definition: HMMER profile HMM file for HMMER versions 2.x.
in subset: bio
in subset: formats

HMMER3
type: Class
subclass of: HMMER format
Created in: 1.3
Documentation: Userguide.pdf
has definition: HMMER profile HMM file for HMMER versions 3.x.
in subset: bio
in subset: formats

PO
type: Class
subclass of: Alignment format (text)
Created in: 1.3
Documentation: http://sourceforge.net/projects/poamsa/files/latest/download
has definition: PO is the output format of Partial Order Alignment program (POA) performing Multiple Sequence Alignment (MSA).
in subset: bio
in subset: formats

BLAST XML results format
type: Class
subclass of: BLAST results
subclass of: XML
Created in: 1.3
has definition: XML format as produced by the NCBI Blast package.
in subset: bio
in subset: formats

CRAM
type: Class
subclass of: Binary format
subclass of: Alignment format (pair only)
Created in: 1.7
Documentation: http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf
has db xref: http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf
has definition: Reference-based compression of alignment format.
in subset: bio
in subset: formats

JSON
type: Class
subclass of: Format
subclass of: YAML
Created in: 1.7
File extension: json
Media type: http://www.iana.org/assignments/media-types/application/json
has db xref: JSON
has db xref: http://www.iana.org/assignments/media-types/application/json
has definition: JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.
has exact synonym: JavaScript Object Notation
in subset: bio
in subset: formats

EPS
type: Class
subclass of: PS
Created in: 1.7
has definition: Encapsulated PostScript format.
in subset: bio
in subset: formats

GIF
type: Class
subclass of: Binary format
Created in: 1.7
has definition: Graphics Interchange Format.
in subset: bio
in subset: formats

xls
type: Class
subclass of: XML
subclass of: Document format
Created in: 1.7
has definition: Microsoft Excel spreadsheet format.
has exact synonym: Microsoft Excel format
in subset: bio
in subset: formats

TSV
type: Class
subclass of: DSV
Created in: 1.7
File extension: tab
File extension: tsv
Media type: tab-separated-values
has db xref: TSV
has db xref: tab-separated-values
has definition: Tabular data represented as tab-separated values in a text file.
has exact synonym: Tab-delimited
has exact synonym: Tab-separated values
has exact synonym: tab
in subset: bio
in subset: formats

Gene expression data format
type: Class
subclass of: DeprecatedClass
Created in: 1.7
Obsolete since: 1.10
Old parent: Thing
has definition: Format of a file of gene expression data, e.g. a gene expression matrix or profile.
in subset: obsolete
replaced by: Gene expression report format
deprecated: true

Cytoscape input file format
type: Class
subclass of: Gene expression report format
subclass of: Textual format
Created in: 1.7
has definition: Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.
in subset: bio
in subset: formats

ebwt
type: Class
subclass of: Binary format
subclass of: Data index format
subclass of: Restriction
  on property: is format of
  some values from: Genome index
Created in: 1.7
Documentation: https://github.com/BenLangmead/bowtie/blob/master/MANUAL
has definition: Bowtie format for indexed reference genome for "small" genomes.
has exact synonym: Bowtie index format
in subset: bio
in subset: formats

RSF
type: Class
subclass of: GCG format variant
Created in: 1.7
Documentation: http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf
has definition: Rich sequence format.
has exact synonym: GCG RSF
in subset: bio
in subset: formats
comment: 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).

GCG format variant
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
Created in: 1.7
has definition: Some format based on the GCG format.
in subset: bio
in subset: formats

BSML
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: 1.7
Documentation: http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc
has definition: Bioinformatics Sequence Markup Language format.
in subset: bio
in subset: formats

ebwtl
type: Class
subclass of: Binary format
subclass of: Data index format
subclass of: Restriction
  on property: is format of
  some values from: Genome index
Created in: 1.7
Documentation: https://github.com/BenLangmead/bowtie/blob/master/MANUAL
has definition: Bowtie format for indexed reference genome for "large" genomes.
has exact synonym: Bowtie long index format
in subset: bio
in subset: formats

Ensembl variation file format
type: Class
subclass of: Textual format
subclass of: Sequence variation annotation format
Created in: 1.8
has db xref: var.html
has definition: Ensembl standard format for variation data.
in subset: bio
in subset: formats

docx
type: Class
subclass of: XML
subclass of: Document format
Created in: 1.8
has definition: Microsoft Word format.
has exact synonym: Microsoft Word format
has exact synonym: doc
in subset: bio
in subset: formats

Document format
type: Class
subclass of: Format (by type of data)
Created in: 1.8
notRecommendedForAnnotation: true
has definition: Format of documents including word processor, spreadsheet and presentation.
in subset: bio
in subset: formats

PDF
type: Class
subclass of: Binary format
subclass of: Document format
Created in: 1.8
has definition: Portable Document Format.
in subset: bio
in subset: formats

Image format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Image
Created in: 1.9
notRecommendedForAnnotation: true
has definition: Format used for images and image metadata.
in subset: bio
in subset: formats

DICOM format
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.9
Documentation: dicom.nema.org
has definition: Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
in subset: bio
in subset: formats

nii
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.9
Documentation: nifti-1
File extension: nii
has definition: 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.
has exact synonym: NIFTI format
has exact synonym: NIfTI-1 format
in subset: bio
in subset: formats

mhd
type: Class
subclass of: Textual format
subclass of: Image format
Created in: 1.9
Documentation: Documentation
has definition: Text-based tagged file format for medical images generated using the MetaImage software package.
has exact synonym: Metalmage format
in subset: bio
in subset: formats

nrrd
type: Class
subclass of: Textual format
subclass of: Image format
Created in: 1.9
Documentation: format.html
has definition: Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data.
in subset: bio
in subset: formats

R file format
type: Class
subclass of: Textual format
Created in: 1.9
has definition: File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.
in subset: bio
in subset: formats

SPSS
type: Class
subclass of: Textual format
Created in: 1.9
has definition: File format used for scripts for the Statistical Package for the Social Sciences.
in subset: bio
in subset: formats

MHTML
type: Class
subclass of: HTML
Created in: 1.9
Documentation: rfc2557
File extension: eml
File extension: mht
File extension: mhtml
Media type: related
comment: 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'.
has db xref: related
has db xref: rfc2557
has definition: MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on.
has exact synonym: HTML email format
has exact synonym: HTML email message format
has exact synonym: MHT
has exact synonym: MHT format
has exact synonym: MHTML format
has exact synonym: MIME HTML
has exact synonym: MIME HTML format
has exact synonym: eml
has related synonym: MIME multipart
has related synonym: MIME multipart format
has related synonym: MIME multipart message
has related synonym: MIME multipart message format
in subset: bio
in subset: formats

IDAT
type: Class
subclass of: Gene expression report format
subclass of: Binary format
subclass of: Restriction
  on property: is format of
  some values from: Raw microarray data
Created in: 1.10
has definition: 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.
in subset: bio
in subset: formats

JPG
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.10
Documentation: egff.htm
has definition: Joint Picture Group file format for lossy graphics file.
has exact synonym: JPEG
has exact synonym: jpeg
in subset: bio
in subset: formats
comment: Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.

rcc
type: Class
subclass of: Gene expression report format
subclass of: Textual format
Created in: 1.10
has definition: Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.
in subset: bio
in subset: formats

arff
type: Class
subclass of: Textual format
Created in: 1.11
Documentation: arff.html
has db xref: arff.html
has definition: ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.
in subset: bio
in subset: formats
comment: This file format is for machine learning.

afg
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: 1.11
Documentation: AFG
has db xref: AFG
has definition: AFG is a single text-based file assembly format that holds read and consensus information together.
in subset: bio
in subset: formats

bedgraph
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: 1.11
Documentation: format1.8
has db xref: format1.8
has definition: The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data.
in subset: bio
in subset: formats
comment: Holds a tab-delimited chromosome /start /end / datavalue dataset.

bedstrict
type: Class
subclass of: BED
Created in: 1.11
Documentation: format1
has db xref: format1
has definition: Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.
in subset: bio
in subset: formats
comment: Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.

bed6
type: Class
subclass of: bedstrict
Created in: 1.11
Documentation: general-usage.html
has db xref: general-usage.html
has definition: BED file format where each feature is described by chromosome, start, end, name, score, and strand.
in subset: bio
in subset: formats
comment: Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6

bed12
type: Class
subclass of: bedstrict
Created in: 1.11
Documentation: general-usage.html
has db xref: general-usage.html
has definition: A BED file where each feature is described by all twelve columns.
in subset: bio
in subset: formats
comment: Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12

chrominfo
type: Class
subclass of: Textual format
subclass of: BED
Created in: 1.11
Documentation: http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables
has db xref: http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables
has definition: Tabular format of chromosome names and sizes used by Galaxy.
in subset: bio
in subset: formats
comment: Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.

customtrack
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: 1.11
Documentation: customTrack.html
has db xref: customTrack.html
has definition: Custom Sequence annotation track format used by Galaxy.
in subset: bio
in subset: formats
comment: Used for tracks/track views within galaxy.

csfasta
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: 1.11
Documentation: http://www.clcsupport.com/clcassemblycell/420/index.php
has db xref: http://www.clcsupport.com/clcassemblycell/420/index.php
has definition: Color space FASTA format sequence variant.
in subset: bio
in subset: formats
comment: FASTA format extended for color space information.

HDF5
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.11
Documentation: H5.format.html
has db xref: H5.format.html
has definition: HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).
has exact synonym: h5
in subset: bio
in subset: formats
comment: 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.
comment: HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF.

TIFF
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: A versatile bitmap format.
in subset: bio
in subset: formats
comment: 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.

BMP
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: Standard bitmap storage format in the Microsoft Windows environment.
in subset: bio
in subset: formats
comment: Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.

im
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: image-file-formats.html
has definition: IM is a format used by LabEye and other applications based on the IFUNC image processing library.
in subset: bio
in subset: formats
comment: IFUNC library reads and writes most uncompressed interchange versions of this format.

pcd
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: PCD
File extension: pcd
has definition: Photo CD format, which is the highest resolution format for images on a CD.
in subset: bio
in subset: formats
comment: 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.

pcx
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: PCX
has definition: PCX is an image file format that uses a simple form of run-length encoding. It is lossless.
in subset: bio
in subset: formats

ppm
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: ppm.html
has definition: The PPM format is a lowest common denominator color image file format.
in subset: bio
in subset: formats

psd
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: 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.
in subset: bio
in subset: formats

xbm
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: 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.
in subset: bio
in subset: formats
comment: The XBM format was replaced by XPM for X11 in 1989.

xpm
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: 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.
in subset: bio
in subset: formats
comment: Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.

rgb
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: egff.htm
has definition: RGB file format is the native raster graphics file format for Silicon Graphics workstations.
in subset: bio
in subset: formats

pbm
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: pbm.html
has definition: 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.
in subset: bio
in subset: formats

pgm
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: pgm.html
has definition: The PGM format is a lowest common denominator grayscale file format.
in subset: bio
in subset: formats
comment: It is designed to be extremely easy to learn and write programs for.

PNG
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: PNG
File extension: png
has definition: PNG is a file format for image compression.
in subset: bio
in subset: formats
comment: It iis expected to replace the Graphics Interchange Format (GIF).

SVG
type: Class
subclass of: XML
subclass of: Image format
Created in: 1.11
Documentation: SVG
has definition: Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.
has exact synonym: Scalable Vector Graphics
in subset: bio
in subset: formats
comment: The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.

rast
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: Sun Raster
has definition: Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems.
in subset: bio
in subset: formats
comment: The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.

Sequence quality report format (text)
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Report
Created in: 1.11
notRecommendedForAnnotation: true
has definition: Textual report format for sequence quality for reports from sequencing machines.
in subset: bio
in subset: formats

qual
type: Class
subclass of: FASTQ-like format (text)
subclass of: Textual format
subclass of: Sequence quality report format (text)
Created in: 1.11
Documentation: http://en.wikipedia.org/wiki/Phred_quality_score
has definition: FASTQ format subset for Phred sequencing quality score data only (no sequences).
in subset: bio
in subset: formats
comment: Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities.

qualsolexa
type: Class
subclass of: FASTQ-solexa
subclass of: qual
Created in: 1.11
has definition: FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.
in subset: bio
in subset: formats
comment: 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)

qualillumina
type: Class
subclass of: FASTQ-illumina
subclass of: qual
Created in: 1.11
Documentation: http://en.wikipedia.org/wiki/Phred_quality_score
has definition: FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.
in subset: bio
in subset: formats
comment: 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.

qualsolid
type: Class
subclass of: qual
Created in: 1.11
Documentation: http://en.wikipedia.org/wiki/Phred_quality_score
has definition: FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.
in subset: bio
in subset: formats
comment: For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.

qual454
type: Class
subclass of: qual
Created in: 1.11
Documentation: http://en.wikipedia.org/wiki/Phred_quality_score
has definition: FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.
in subset: bio
in subset: formats

ENCODE peak format
type: Class
subclass of: bed6
Created in: 1.11
Documentation: format13
has db xref: format13
has definition: Human ENCODE peak format.
in subset: bio
in subset: formats
comment: Format that covers both the broad peak format and narrow peak format from ENCODE.

ENCODE narrow peak format
type: Class
subclass of: ENCODE peak format
Created in: 1.11
Documentation: http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html
has db xref: http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html
has definition: Human ENCODE narrow peak format.
in subset: bio
in subset: formats
comment: Format that covers both the broad peak format and narrow peak format from ENCODE.

ENCODE broad peak format
type: Class
subclass of: ENCODE peak format
Created in: 1.11
Documentation: format12
has db xref: format12
has definition: Human ENCODE broad peak format.
in subset: bio
in subset: formats

bgzip
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: tabix.html
File extension: bgz
has definition: Blocked GNU Zip format.
in subset: bio
in subset: formats
comment: BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).

tabix
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.11
Documentation: tabix.html
has db xref: tabix.html
has definition: TAB-delimited genome position file index format.
in subset: bio
in subset: formats

Graph format
type: Class
subclass of: Format (by type of data)
Created in: 1.11
notRecommendedForAnnotation: true
has definition: Data format for graph data.
in subset: bio
in subset: formats

xgmml
type: Class
subclass of: Graph format
Created in: 1.11
Documentation: module-galaxy.datatypes.graph
has definition: XML-based format used to store graph descriptions within Galaxy.
in subset: bio
in subset: formats

sif
type: Class
subclass of: Biological pathway or network format
Created in: 1.11
Documentation: module-galaxy.datatypes.graph
has definition: SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.
in subset: bio
in subset: formats

xlsx
type: Class
subclass of: Binary format
subclass of: Document format
Created in: 1.11
has definition: MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.
in subset: bio
in subset: formats

SQLite format
type: Class
subclass of: Binary format
Created in: 1.11
Documentation: fileformat2.html
has definition: Data format used by the SQLite database.
in subset: bio
in subset: formats

Gemini SQLite format
type: Class
subclass of: Sequence variation annotation format
subclass of: SQLite format
Created in: 1.11
Documentation: quick start.html
has definition: Data format used by the SQLite database conformant to the Gemini schema.
in subset: bio
in subset: formats

Index format
type: Class
subclass of: DeprecatedClass
Created in: 1.11
deprecation_comment: Duplicate of http://edamontology.org/format_3326
Obsolete since: 1.20
Old parent: Binary format
Old parent: Format (by type of data)
has definition: Format of a data index of some type.
in subset: obsolete
replaced by: Data index format
deprecated: true

snpeffdb
type: Class
subclass of: Binary format
subclass of: Data index format
Created in: 1.11
has definition: An index of a genome database, indexed for use by the snpeff tool.
in subset: bio
in subset: formats

MAT
type: Class
subclass of: Matrix format
subclass of: Restriction
  on property: is format of
  some values from: 3D-1D scoring matrix
Created in: 1.12
Documentation: mat-file-versions.html
has definition: Binary format used by MATLAB files to store workspace variables.
has exact synonym: .mat file format
has exact synonym: MAT file format
has exact synonym: MATLAB file format
in subset: bio
in subset: formats

NetCDF
type: Class
subclass of: Binary format
subclass of: Mass spectrometry data format
subclass of: Trajectory format (binary)
Created in: 1.12
Documentation: E1947.htm
comment: Network Common Data Form (NetCDF) library is supported by AMBER MD package from version 9.
has definition: 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.
has exact synonym: ANDI-MS
in subset: bio
in subset: formats

MGF
type: Class
subclass of: Mass spectrometry data format
Created in: 1.12
File extension: mgf
has definition: Mascot Generic Format. Encodes multiple MS/MS spectra in a single file.
in subset: bio
in subset: formats
comment: Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions.

dta
type: Class
subclass of: Mass spectrometry data format
Created in: 1.12
has definition: Spectral data format file where each spectrum is written to a separate file.
in subset: bio
in subset: formats
comment: 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.

pkl
type: Class
subclass of: Mass spectrometry data format
Created in: 1.12
has definition: Spectral data file similar to dta.
in subset: bio
in subset: formats
comment: Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to.

mzXML
type: Class
subclass of: Mass spectrometry data format
Created in: 1.12
Documentation: https://dx.doi.org/10.1038%2Fnbt1031
has definition: Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology.
in subset: bio
in subset: formats

pepXML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.12
Documentation: http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd
has definition: 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.
in subset: bio
in subset: formats

GPML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.12
Documentation: gpml
has definition: Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways.
in subset: bio
in subset: formats

K-mer countgraph
type: Class
subclass of: Binary format
subclass of: Graph format
Created in: 1.12
Documentation: countgraph
File extension: oxlicg
Media type: vnd.oxli.countgraph
has db xref: countgraph
has db xref: vnd.oxli.countgraph
has definition: A list of k-mers and their occurrences in a dataset. Can also be used as an implicit De Bruijn graph.

mzTab
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Citation: mcp.O113.036681
Created in: 1.13
Documentation: mztab
has db xref: mztab
has definition: mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results.
in subset: bio
in subset: formats

imzML metadata file
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Citation: j.jprot.2012.07.026
Created in: 1.13
Documentation: http://www.imzml.org/index.php
File extension: imzml
has db xref: http://www.imzml.org/index.php
has definition: imzML metadata is a data format for mass spectrometry imaging metadata.
in subset: bio
in subset: formats
comment: 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

qcML
type: Class
subclass of: XML
subclass of: Experiment annotation format
subclass of: Mass spectrometry data format
Created in: 1.13
Documentation: qcml
has db xref: qcml
has definition: qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements.
in subset: bio
in subset: formats
comment: The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well.

PRIDE XML
type: Class
subclass of: XML
subclass of: Experiment annotation format
subclass of: Mass spectrometry data format
Created in: 1.13
Documentation: pridexml
has db xref: pridexml
has definition: PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment.
in subset: bio
in subset: formats

SED-ML
type: Class
subclass of: XML
subclass of: Experiment annotation format
Citation: 978-3-540-88562-7 15
Citation: http://doi.org/10.1186/1752-0509-5-198
Created in: 1.13
Documentation: sed-ml.org
has db xref: sed-ml.org
has definition: 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.
in subset: bio
in subset: formats

COMBINE OMEX
type: Class
subclass of: Biological pathway or network format
subclass of: Binary format
subclass of: Experiment annotation format
Citation: s12859-014-0369-z
Created in: 1.13
Documentation: archive
has db xref: archive
has definition: Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology.
in subset: bio
in subset: formats
comment: 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).

ISA-TAB
type: Class
subclass of: Gene expression report format
subclass of: Textual format
subclass of: Experiment annotation format
Created in: 1.13
Documentation: specification
has db xref: specification
has definition: The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from experiments employing a combination of technologies.
in subset: bio
in subset: formats
comment: 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).

SBtab
type: Class
subclass of: Biological pathway or network format
subclass of: Textual format
Citation: http://arxiv.org/abs/1502.01463
Created in: 1.13
Documentation: sbtab.net
has db xref: sbtab.net
has definition: SBtab is a tabular format for biochemical network models.
in subset: bio
in subset: formats

BCML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.13
Documentation: BCMLdocs
has db xref: BCMLdocs
has definition: Biological Connection Markup Language (BCML) is an XML format for biological pathways.
in subset: bio
in subset: formats

BDML
type: Class
subclass of: XML
Citation: btu767
Created in: 1.13
Documentation: bdml
has db xref: bdml
has definition: Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics.
in subset: bio
in subset: formats

BEL
type: Class
subclass of: Textual format
Created in: 1.13
Documentation: www.openbel.org
has db xref: www.openbel.org
has definition: Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form.
in subset: bio
in subset: formats

SBGN-ML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.13
Documentation: The SBGN-ML format
has db xref: The SBGN-ML format
has definition: SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks.
in subset: bio
in subset: formats

AGP
type: Class
subclass of: Sequence assembly format
subclass of: Textual format
Created in: 1.13
Documentation: AGP Specification
File extension: agp
has db xref: AGP Specification
has definition: AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome).
in subset: bio
in subset: formats

PS
type: Class
subclass of: Textual format
Created in: 1.13
has definition: PostScript format.
has exact synonym: PostScript
in subset: bio
in subset: formats

SRA format
type: Class
subclass of: Binary format
Created in: 1.13
Documentation: NBK242622
File extension: sra
has definition: SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive.
has exact synonym: SRA
has exact synonym: SRA archive format
in subset: bio
in subset: formats

VDB
type: Class
subclass of: Binary format
Created in: 1.13
Documentation: NBK242622
has definition: VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive.
has exact synonym: SRA native format
in subset: bio
in subset: formats

Tabix index file format
type: Class
subclass of: Binary format
subclass of: Data index format
subclass of: Restriction
  on property: is format of
  some values from: Data index
Created in: 1.13
Documentation: tabix.pdf
has definition: Index file format used by the samtools package to index TAB-delimited genome position files.
in subset: bio
in subset: formats

Sequin format
type: Class
subclass of: Sequence feature table format (text)
Created in: 1.13
has definition: 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).
in subset: bio
in subset: formats

MSF
type: Class
subclass of: Mass spectrometry data format
Created in: 1.14
has definition: Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software.
has exact synonym: Magellan storage file format
in subset: bio
in subset: formats
comment: 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.

Biodiversity data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Biodiversity data
Created in: 1.14
notRecommendedForAnnotation: true
has definition: Data format for biodiversity data.
in subset: bio
in subset: formats

ABCD format
type: Class
subclass of: Biodiversity data format
subclass of: Restriction
  on property: is format of
  some values from: Biodiversity data
Created in: 1.14
Documentation: abcd
has definition: 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).
has exact synonym: ABCD
in subset: bio
in subset: formats

GCT/Res format
type: Class
subclass of: Gene expression report format
subclass of: Textual format
Created in: 1.14
has definition: 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.
has exact synonym: GCT format
has exact synonym: Res format
in subset: bio
in subset: formats

WIFF format
type: Class
subclass of: Binary format
subclass of: Mass spectrometry data format
Created in: 1.14
File extension: wiff
has definition: Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex).
has exact synonym: wiff
in subset: bio
in subset: formats

X!Tandem XML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.14
Documentation: X series output form.pdf
has definition: Output format used by X! series search engines that is based on the XML language BIOML.
in subset: bio
in subset: formats

Thermo RAW
type: Class
subclass of: Binary format
subclass of: Mass spectrometry data format
Created in: 1.14
has definition: Proprietary file format for mass spectrometry data from Thermo Scientific.
in subset: bio
in subset: formats
comment: Proprietary format for which documentation is not available.

Mascot .dat file
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Created in: 1.14
Documentation: mascotdatfile
has definition: "Raw" result file from Mascot database search.
in subset: bio
in subset: formats

MaxQuant APL peaklist format
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Created in: 1.14
Documentation: pr101065j
has definition: Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra.
has exact synonym: MaxQuant APL
in subset: bio
in subset: formats

SBOL
type: Class
subclass of: XML
Created in: 1.14
Documentation: specification-data-model-2-0
has definition: Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology.
in subset: bio
in subset: formats
comment: SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs.

PMML
type: Class
subclass of: XML
Created in: 1.14
Documentation: GeneralStructure.html
has definition: PMML uses XML to represent mining models. The structure of the models is described by an XML Schema.
in subset: bio
in subset: formats
comment: One or more mining models can be contained in a PMML document.

OME-TIFF
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.14
Documentation: specification.html
has definition: Image file format used by the Open Microscopy Environment (OME).
in subset: bio
in subset: formats
comment: 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.
comment: 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.

LocARNA PP
type: Class
subclass of: Textual format
Created in: 1.14
Documentation: PP
has definition: The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record.
in subset: bio
in subset: formats
comment: 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.

dbGaP format
type: Class
subclass of: Textual format
Created in: 1.14
Documentation: NBK154410
has definition: Input format used by the Database of Genotypes and Phenotypes (dbGaP).
in subset: bio
in subset: formats
comment: 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.

BIOM format
type: Class
subclass of: Textual format
subclass of: Biodiversity data format
Citation: 2047-217X-1-7
Created in: 1.15
Documentation: biom-format.org
File extension: biom
has definition: 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.
has exact synonym: BIological Observation Matrix format
has exact synonym: biom
in subset: bio
in subset: formats
comment: 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.

protXML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.15
Documentation: protXML xmlspy docs.html
has db xref: MS_1001422
has definition: A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data.
in subset: bio
in subset: formats
comment: No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML).

Linked data format
type: Class
subclass of: Format (by type of data)
Citation: jswis.2009081901
Citation: LinkedData.html
Created in: 1.15
notRecommendedForAnnotation: true
has definition: 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.
has related synonym: Semantic Web format
in subset: bio
in subset: formats

JSON-LD
type: Class
subclass of: RDF format
subclass of: JSON
subclass of: Linked data format
Created in: 1.15
Documentation: json-ld
File extension: jsonld
Media type: ld+json
has db xref: ld+json
has definition: JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON.
has exact synonym: JavaScript Object Notation for Linked Data
has exact synonym: jsonld
in subset: bio
in subset: formats

YAML
type: Class
subclass of: Format
Created in: 1.15
Documentation: yaml.org
File extension: yaml
File extension: yml
has db xref: YML
has definition: YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language.
has exact synonym: YAML Ain't Markup Language
has exact synonym: yml
in subset: bio
in subset: formats
comment: Data in YAML format can be serialised into text, or binary format.
comment: YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible".

DSV
type: Class
subclass of: Textual format
Created in: 1.16
has definition: Tabular data represented as values in a text file delimited by some character.
has exact synonym: Delimiter-separated values
has exact synonym: Tabular format
in subset: bio
in subset: formats

CSV
type: Class
subclass of: DSV
Created in: 1.16
File extension: csv
Media type: http://www.iana.org/assignments/media-types/text/csv
has db xref: CSV
has db xref: http://www.iana.org/assignments/media-types/text/csv
has definition: Tabular data represented as comma-separated values in a text file.
has exact synonym: Comma-separated values
in subset: bio
in subset: formats

SEQUEST .out file
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Created in: 1.16
File extension: out
has definition: "Raw" result file from SEQUEST database search.
in subset: bio
in subset: formats

idXML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.16
Documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1IdXMLFile.html
Documentation: http://open-ms.sourceforge.net/schemas/
has definition: XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS.
in subset: bio
in subset: formats

KNIME datatable format
type: Class
subclass of: Workflow format
Created in: 1.16
has definition: Data table formatted such that it can be passed/streamed within the KNIME platform.
in subset: bio
in subset: formats

UniProtKB XML
type: Class
subclass of: XML
subclass of: uniprotkb-like format
subclass of: Sequence record format (XML)
Created in: 1.16
Documentation: uniprot.xsd
has definition: UniProtKB XML sequence features format is an XML format available for downloading UniProt entries.
has exact synonym: UniProt XML
has exact synonym: UniProt XML format
has exact synonym: UniProtKB XML format
in subset: bio
in subset: formats

UniProtKB RDF
type: Class
subclass of: RDF format
subclass of: uniprotkb-like format
Created in: 1.16
Documentation: uniprot rdf
has definition: UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML).
has exact synonym: UniProt RDF
has exact synonym: UniProt RDF format
has exact synonym: UniProt RDF/XML
has exact synonym: UniProt RDF/XML format
has exact synonym: UniProtKB RDF format
has exact synonym: UniProtKB RDF/XML
has exact synonym: UniProtKB RDF/XML format
in subset: bio
in subset: formats

BioJSON (BioXSD)
type: Class
subclass of: Sequence record format
subclass of: Sequence feature annotation format
subclass of: Alignment format
subclass of: Raw sequence format
subclass of: JSON
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
subclass of: Restriction
  on property: is format of
  some values from: Score
subclass of: Restriction
  on property: is format of
  some values from: Sequence
subclass of: Restriction
  on property: is format of
  some values from: Experimental measurement
Citation: f1000research.1113048.1
Created in: 1.16
Documentation: bioxsd.org
Example: sequenceRecord.json
Example: sequenceRecord.xml+json+yaml.xml
Repository: bioxsd
comment: 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'.
has db xref: bioxsd.org
has definition: 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.
has exact synonym: BioJSON (BioXSD data model)
has exact synonym: BioJSON format (BioXSD)
has exact synonym: BioXSD BioJSON
has exact synonym: BioXSD BioJSON format
has exact synonym: BioXSD JSON
has exact synonym: BioXSD JSON format
has exact synonym: BioXSD in JSON
has exact synonym: BioXSD in JSON format
has exact synonym: BioXSD+JSON
has exact synonym: BioXSD/GTrack BioJSON
has exact synonym: BioXSD|BioJSON|BioYAML BioJSON
has exact synonym: BioXSD|GTrack BioJSON
in subset: bio
in subset: formats

BioYAML
type: Class
subclass of: Sequence record format
subclass of: Sequence feature annotation format
subclass of: Alignment format
subclass of: Raw sequence format
subclass of: YAML
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
subclass of: Restriction
  on property: is format of
  some values from: Score
subclass of: Restriction
  on property: is format of
  some values from: Sequence
subclass of: Restriction
  on property: is format of
  some values from: Experimental measurement
Citation: f1000research.1113048.1
Created in: 1.16
Documentation: bioxsd.org
Example: sequenceRecord.yaml
Example: sequenceRecord.xml+json+yaml.xml
Repository: bioxsd
comment: 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'.
has db xref: bioxsd.org
has definition: 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.
has exact synonym: BioXSD BioYAML
has exact synonym: BioXSD BioYAML format
has exact synonym: BioXSD YAML
has exact synonym: BioXSD YAML format
has exact synonym: BioXSD in YAML
has exact synonym: BioXSD in YAML format
has exact synonym: BioXSD+YAML
has exact synonym: BioXSD/GTrack BioYAML
has exact synonym: BioXSD|BioJSON|BioYAML BioYAML
has exact synonym: BioXSD|GTrack BioYAML
has exact synonym: BioYAML (BioXSD data model)
has exact synonym: BioYAML (BioXSD)
has exact synonym: BioYAML format
has exact synonym: BioYAML format (BioXSD)
in subset: bio
in subset: formats

BioJSON (Jalview)
type: Class
subclass of: Sequence feature annotation format
subclass of: Alignment format
subclass of: JSON
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
Created in: 1.16
Documentation: biojson
has db xref: biojson
has definition: BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench.
has exact synonym: BioJSON format (Jalview)
has exact synonym: JSON (Jalview)
has exact synonym: JSON format (Jalview)
has exact synonym: Jalview BioJSON
has exact synonym: Jalview BioJSON format
has exact synonym: Jalview JSON
has exact synonym: Jalview JSON format
in subset: bio
in subset: formats

GSuite
type: Class
subclass of: Sequence feature annotation format
subclass of: Textual format
Citation: f1000research.1112716.1
Citation: http://dx.doi.org/10.1101/067561
Created in: 1.16
Documentation: GSuite specification.html
Documentation: GSuite specification.txt
Example: examples
Repository: gtrack
comment: '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.
has db xref: GSuite specification.html
has db xref: GSuite specification.txt
has definition: 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.
has exact synonym: BioXSD/GTrack GSuite
has exact synonym: BioXSD|GTrack GSuite
has exact synonym: GSuite (GTrack ecosystem of formats)
has exact synonym: GSuite format
has exact synonym: GTrack|BTrack|GSuite GSuite
has exact synonym: GTrack|GSuite|BTrack GSuite
in subset: bio
in subset: formats

BTrack
type: Class
subclass of: Sequence feature annotation format
subclass of: Binary format
subclass of: Sequence feature table format
subclass of: Sequence annotation track format
Created in: 1.16
Repository: gtrack
comment: '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.
has definition: 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.
has exact synonym: BTrack (GTrack ecosystem of formats)
has exact synonym: BTrack format
has exact synonym: BioXSD/GTrack BTrack
has exact synonym: BioXSD|GTrack BTrack
has exact synonym: GTrack|BTrack|GSuite BTrack
has exact synonym: GTrack|GSuite|BTrack BTrack
in subset: bio
in subset: formats

MCPD
type: Class
subclass of: Textual format
subclass of: Biodiversity data format
subclass of: Restriction
  on property: is format of
  some values from: Organism report
subclass of: Restriction
  on property: is format of
  some values from: Sample annotation
subclass of: Restriction
  on property: is format of
  some values from: Reference sample report
Created in: 1.16
Documentation: faobioversity-multi-crop-passport-descriptors-v2-mcpd-v2
Documentation: faoipgri-multi-crop-passport-descriptors-mcpd
Documentation: FAO IPGRI Multi-Crop Passport Descriptors MCPD 124 01.pdf
Documentation: FAO-Bioversity multi crop passport descriptors V 2 Final rev 1526.pdf
Organisation: www.fao.org
Organisation: www.bioversityinternational.org
comment: Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012).
has db xref: faobioversity-multi-crop-passport-descriptors-v2-mcpd-v2
has db xref: faoipgri-multi-crop-passport-descriptors-mcpd
has db xref: FAO IPGRI Multi-Crop Passport Descriptors MCPD 124 01.pdf
has db xref: FAO-Bioversity multi crop passport descriptors V 2 Final rev 1526.pdf
has definition: The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information.
has exact synonym: Bioversity MCPD
has exact synonym: FAO MCPD
has exact synonym: IPGRI MCPD
has exact synonym: MCPD V.1
has exact synonym: MCPD V.2
has exact synonym: MCPD format
has exact synonym: Multi-Crop Passport Descriptors
has exact synonym: Multi-Crop Passport Descriptors format
in subset: bio
in subset: formats

Annotated text format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Annotated text
Created in: 1.16
notRecommendedForAnnotation: true
has definition: Data format of an annotated text, e.g. with recognised entities, concepts, and relations.
in subset: bio
in subset: formats

PubAnnotation format
type: Class
subclass of: JSON
subclass of: Annotated text format
Citation: http://dl.acm.org/citation.cfm
Created in: 1.16
Documentation: annotation-format
has db xref: annotation-format
has definition: JSON format of annotated scientific text used by PubAnnotations and other tools.
in subset: bio
in subset: formats

BioC
type: Class
subclass of: XML
subclass of: Annotated text format
Citation: bat064
Created in: 1.16
Documentation: bioc.sourceforge.net
has db xref: bioc.sourceforge.net
has definition: BioC is a standardised XML format for sharing and integrating text data and annotations.
in subset: bio
in subset: formats

PubTator format
type: Class
subclass of: Textual format
subclass of: Annotated text format
Citation: bas041
Citation: gkt441
Created in: 1.16
Documentation: tutorial
has db xref: tutorial
has definition: Native textual export format of annotated scientific text from PubTator.
in subset: bio
in subset: formats

Open Annotation format
type: Class
subclass of: RDF format
subclass of: JSON-LD
subclass of: Annotated text format
Created in: 1.16
Documentation: core.html
has db xref: core.html
has definition: A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD.
in subset: bio
in subset: formats

BioNLP Shared Task format
type: Class
subclass of: Textual format
subclass of: Annotated text format
Created in: 1.16
Documentation: file-formats
Documentation: standoff.html
Documentation: format
Documentation: Annotation-Data-Format
Example: examples.html
Example: format
has db xref: file-formats
has db xref: standoff.html
has db xref: format
has db xref: Annotation-Data-Format
has definition: 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.
has exact synonym: BRAT format
has exact synonym: BRAT standoff format
in subset: bio
in subset: formats

Query language
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Query script
Created in: 1.16
notRecommendedForAnnotation: true
has definition: A query language (format) for structured database queries.
has exact synonym: Query format
in subset: bio
in subset: formats

SQL
type: Class
subclass of: Textual format
Created in: 1.16
File extension: sql
Media type: sql
has db xref: SQL
has db xref: sql
has definition: SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases.
has exact synonym: Structured Query Language
in subset: bio
in subset: formats

XQuery
type: Class
subclass of: Textual format
Created in: 1.16
Documentation: Query
File extension: xq
File extension: xquery
File extension: xqy
has db xref: Query
has definition: 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.).
has exact synonym: XML Query
has exact synonym: xq
has exact synonym: xqy
in subset: bio
in subset: formats

SPARQL
type: Class
subclass of: Textual format
Created in: 1.16
Documentation: sparql11-query
has db xref: sparql11-query
has definition: SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format.
has exact synonym: SPARQL Protocol and RDF Query Language
in subset: bio
in subset: formats

xsd
type: Class
subclass of: XML
Created in: 1.17
has definition: XML format for XML Schema.
in subset: bio
in subset: formats

XMFA
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: 1.20
Documentation: files.html
has definition: XMFA format stands for eXtended Multi-FastA format and is used to store collinear sub-alignments that constitute a single genome alignment.
has exact synonym: eXtended Multi-FastA format
in subset: bio
in subset: formats

GEN
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: 1.20
Documentation: file format.html
has definition: The GEN file format contains genetic data and describes SNPs.
has exact synonym: Genotype file format
in subset: bio
in subset: formats

SAMPLE file format
type: Class
subclass of: Textual format
Created in: 1.20
Documentation: file format.html
has definition: The SAMPLE file format contains information about each individual i.e. individual IDs, covariates, phenotypes and missing data proportions, from a GWAS study.
in subset: bio
in subset: formats

SDF
type: Class
subclass of: Chemical data format
subclass of: Textual format
Created in: 1.20
Documentation: SDF
has definition: SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information.
in subset: bio
in subset: formats

Molfile
type: Class
subclass of: Chemical data format
subclass of: Textual format
Created in: 1.20
Documentation: Molfile
has definition: An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule.
in subset: bio
in subset: formats

Mol2
type: Class
subclass of: Chemical data format
subclass of: Textual format
Created in: 1.20
Documentation: Tripos+Mol2+format
has definition: Complete, portable representation of a SYBYL molecule. ASCII file which contains all the information needed to reconstruct a SYBYL molecule.
in subset: bio
in subset: formats

latex
type: Class
subclass of: Textual format
subclass of: Document format
Created in: 1.20
Documentation: documentation
has definition: format for the LaTeX document preparation system.
has exact synonym: LaTeX format
in subset: bio
in subset: formats
comment: uses the TeX typesetting program format

ELAND format
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: 1.20
Documentation: elandformat.php
has definition: 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.
has exact synonym: ELAND
has exact synonym: eland
in subset: bio
in subset: formats

Relaxed PHYLIP Interleaved
type: Class
subclass of: Phylip format variant
Created in: 1.20
Documentation: Bio.AlignIO.PhylipIO-module.html
Documentation: relaxed phylip
has definition: Phylip multiple alignment sequence format, less stringent than PHYLIP format.
has exact synonym: PHYLIP Interleaved format
in subset: bio
in subset: formats
comment: 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 Sequential
type: Class
subclass of: Phylip format variant
Created in: 1.20
Documentation: Bio.AlignIO.PhylipIO-module.html
Documentation: relaxed phylip
has definition: Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998).
has exact synonym: Relaxed PHYLIP non-interleaved
has exact synonym: Relaxed PHYLIP non-interleaved format
has exact synonym: Relaxed PHYLIP sequential format
in subset: bio
in subset: formats
comment: 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.

VisML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.20
Documentation: visML.htm
has definition: Default XML format of VisANT, containing all the network information.
has exact synonym: VisANT xml
has exact synonym: VisANT xml format
in subset: bio
in subset: formats

GML
type: Class
subclass of: Biological pathway or network format
subclass of: Textual format
Created in: 1.20
Documentation: gml-format
has definition: 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.
has exact synonym: GML format
in subset: bio
in subset: formats

FASTG
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: 1.20
Documentation: fastg.sourceforge.net
Documentation: FASTG Spec v1.00.pdf
has definition: FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty.
has exact synonym: FASTG assembly graph format
in subset: bio
in subset: formats
comment: It is called FASTG, like FASTA, but the G stands for "graph".

NMR data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: NMR spectrum
Created in: 1.20
notRecommendedForAnnotation: true
has definition: Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment.
has exact synonym: NMR peak assignment data format
has exact synonym: NMR processed data format
has exact synonym: NMR raw data format
has exact synonym: Nuclear magnetic resonance spectroscopy data format
has exact synonym: Processed NMR data format
has exact synonym: Raw NMR data format
in subset: bio
in subset: formats

nmrML
type: Class
subclass of: XML
subclass of: NMR data format
Created in: 1.20
Documentation: www.nmrML.org
Documentation: nmrML
has definition: 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.
in subset: bio
in subset: formats

proBAM
type: Class
subclass of: Sequence trace format
subclass of: Binary format
subclass of: Alignment format (pair only)
Created in: 1.20
Documentation: probam
has definition: . proBAM is an adaptation of BAM (format_2572), which was extended to meet specific requirements entailed by proteomics data.
in subset: bio
in subset: formats

proBED
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: 1.20
Documentation: probed
has definition: . proBED is an adaptation of BED (format_3003), which was extended to meet specific requirements entailed by proteomics data.
in subset: bio
in subset: formats

Raw microarray data format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Raw microarray data
Created in: 1.20
notRecommendedForAnnotation: true
has definition: Data format for raw microarray data.
has exact synonym: Microarray data format
in subset: bio
in subset: formats

GPR
type: Class
subclass of: Textual format
subclass of: Raw microarray data format
Created in: 1.20
Documentation: http://mdc.custhelp.com/app/answers/detail/a_id/17120/related/1
has definition: GenePix Results (GPR) text file format developed by Axon Instruments that is used to save GenePix Results data.
in subset: bio
in subset: formats

ARB
type: Class
subclass of: Alignment format
subclass of: Binary format
Created in: 1.20
has definition: Binary format used by the ARB software suite.
has exact synonym: ARB binary format
in subset: bio
in subset: formats

consensusXML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.20
Documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1ConsensusXMLFile.html
has definition: OpenMS format for grouping features in one map or across several maps.
in subset: bio
in subset: formats

featureXML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.20
Documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1FeatureXMLFile.html
has definition: OpenMS format for quantitation results (LC/MS features).
in subset: bio
in subset: formats

mzData
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.20
Documentation: http://www.psidev.info/mzdata-1_0_5-docs
has definition: Now deprecated data format of the HUPO Proteomics Standards Initiative. Replaced by mzML (format_3244).
in subset: bio
in subset: formats

TIDE TXT
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.20
Documentation: http://cruxtoolkit.sourceforge.net/tide-search.html
has definition: Format supported by the Tide tool for identifying peptides from tandem mass spectra.
in subset: bio
in subset: formats

BLAST XML v2 results format
type: Class
subclass of: BLAST results
subclass of: XML
Created in: 1.20
Documentation: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/ProposedBLASTXMLChanges.pdf
Documentation: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
Documentation: http://www.ncbi.nlm.nih.gov/data_specs/schema/NCBI_BlastOutput2.mod.xsd
has definition: XML format as produced by the NCBI Blast package v2.
in subset: bio
in subset: formats

pptx
type: Class
subclass of: XML
subclass of: Image format
Created in: 1.20
Documentation: https://msdn.microsoft.com/en-us/library/dd926741(v=office.12).aspx
Media type: vnd.openxmlformats-officedocument.presentationml.presentation
has definition: Microsoft Powerpoint format.
in subset: bio
in subset: formats

ibd
type: Class
subclass of: Binary format
subclass of: Mass spectrometry data format
Citation: j.jprot.2012.07.026
Created in: 1.20
Documentation: http://www.imzml.org/index.php
File extension: ibd
has db xref: http://www.imzml.org/index.php
has definition: ibd is a data format for mass spectrometry imaging data.
in subset: bio
in subset: formats
comment: 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.

NLP format
type: Class
subclass of: Format (by type of data)
Created in: 1.21
has definition: Data format used in Natural Language Processing.
has exact synonym: Natural Language Processing format
in subset: bio
in subset: formats

BEAST
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: 1.21
Documentation: beast.bio.ed.ac.uk
has definition: XML input file format for BEAST Software (Bayesian Evolutionary Analysis Sampling Trees).
in subset: bio
in subset: formats

Chado-XML
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: 1.21
Documentation: Chado XML
has definition: Chado-XML format is a direct mapping of the Chado relational schema into XML.
in subset: bio
in subset: formats

HSAML
type: Class
subclass of: XML
subclass of: Alignment format (XML)
Created in: 1.21
Documentation: hsaml
has definition: An alignment format generated by PRANK/PRANKSTER consisting of four elements: newick, nodes, selection and model.
in subset: bio
in subset: formats

InterProScan XML
type: Class
subclass of: XML
subclass of: Protein domain classification format
Created in: 1.21
Documentation: OutputFormats
has definition: Output xml file from the InterProScan sequence analysis application.
in subset: bio
in subset: formats

KGML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.21
has db xref: http://www.genome.jp/kegg/xml/
has definition: The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format.
has exact synonym: KEGG Markup Language
in subset: bio
in subset: formats

PubMed XML
type: Class
subclass of: XML
subclass of: Bibliographic reference format
Created in: 1.21
has definition: XML format for collected entries from bibliographic databases MEDLINE and PubMed.
has exact synonym: MEDLINE XML
in subset: bio
in subset: formats

MSAML
type: Class
subclass of: Alignment format
subclass of: Binary format
Created in: 1.21
Documentation: msaml-desc-dec.html
has definition: A set of XML compliant markup components for describing multiple sequence alignments.
in subset: bio
in subset: formats

OrthoXML
type: Class
subclass of: Gene annotation format
subclass of: XML
subclass of: Sequence record format (XML)
Created in: 1.21
Documentation: Documentation.html
has definition: 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.
in subset: bio
in subset: formats

PSDML
type: Class
subclass of: Sequence feature annotation format
subclass of: XML
Created in: 1.21
Documentation: psdml dtdtree.php
has definition: Tree structure of Protein Sequence Database Markup Language generated using Matra software.
in subset: bio
in subset: formats

SeqXML
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
Created in: 1.21
Documentation: Documentation.html
has definition: SeqXML is an XML Schema to describe biological sequences, developed by the Stockholm Bioinformatics Centre.
in subset: bio
in subset: formats

UniParc XML
type: Class
subclass of: Sequence feature annotation format
subclass of: XML
Created in: 1.21
Documentation: uniparc
has definition: XML format for the UniParc database.
in subset: bio
in subset: formats

UniRef XML
type: Class
subclass of: Sequence feature annotation format
subclass of: XML
Created in: 1.21
Documentation: uniref
has definition: XML format for the UniRef reference clusters.
in subset: bio
in subset: formats

CWL
type: Class
subclass of: Workflow format
subclass of: YAML
Citation: m9.figshare.3115156.v2
Created in: 1.21
Documentation: user guide
Documentation: CommandLineTool.html
Documentation: Workflow.html
Example: examples
File extension: cwl
Organisation: sfconservancy.org
Organisation: www.commonwl.org
Repository: common-workflow-language
has definition: Common Workflow Language (CWL) format for description of command-line tools and workflows.
has exact synonym: Common Workflow Language
has exact synonym: CommonWL
in subset: bio
in subset: formats

Waters RAW
type: Class
subclass of: Binary format
subclass of: Mass spectrometry data format
Created in: 1.21
has definition: Proprietary file format for mass spectrometry data from Waters.
in subset: bio
in subset: formats
comment: Proprietary format for which documentation is not available, but used by multiple tools.

JCAMP-DX
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Created in: 1.21
Documentation: JCAMP6 2b Draft.pdf
has definition: A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry.
in subset: bio
in subset: formats
comment: JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression.

NLP annotation format
type: Class
subclass of: NLP format
Created in: 1.21
has definition: An NLP format used for annotated textual documents.
in subset: bio
in subset: formats

NLP corpus format
type: Class
subclass of: NLP annotation format
Created in: 1.21
has definition: NLP format used by a specific type of corpus (collection of texts).
in subset: bio
in subset: formats

mirGFF3
type: Class
subclass of: GFF3
subclass of: RNA annotation format
Citation: f1000research.1115724.1
Created in: 1.21
Documentation: definition.md
Example: example.gff
Repository: mirGFF3
has definition: mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq workflows.
has exact synonym: miRTop format
in subset: bio
in subset: formats
comment: 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.

RNA annotation format
type: Class
subclass of: Format (by type of data)
Created in: 1.21
has definition: A "placeholder" concept for formats of annotated RNA data, including e.g. microRNA and RNA-Seq data.
has exact synonym: RNA data format
has exact synonym: miRNA data format
has exact synonym: microRNA data format
in subset: bio
in subset: formats

Trajectory format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Trajectory data
Created in: 1.22
notRecommendedForAnnotation: true
has definition: File format to store trajectory information for a 3D structure .
has exact synonym: CG trajectory formats
has exact synonym: MD trajectory formats
has exact synonym: NA trajectory formats
has exact synonym: Protein trajectory formats
in subset: bio
in subset: formats
comment: Formats differ on what they are able to store (coordinates, velocities, topologies) and how they are storing it (raw, compressed, textual, binary).

Trajectory format (binary)
type: Class
subclass of: Trajectory format
Created in: 1.22
notRecommendedForAnnotation: true
has definition: Binary file format to store trajectory information for a 3D structure .
in subset: bio
in subset: formats

Trajectory format (text)
type: Class
subclass of: Trajectory format
Created in: 1.22
notRecommendedForAnnotation: true
has definition: Textual file format to store trajectory information for a 3D structure .
in subset: bio
in subset: formats

HDF
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.22
has definition: 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.
in subset: bio
in subset: formats
comment: HDF is currently supported by many commercial and non-commercial software platforms such as Java, MATLAB/Scilab, Octave, Python and R.

PCAzip
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.22
has definition: PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA).
in subset: bio
in subset: formats
comment: 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.

XTC
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.22
has definition: Portable binary format for trajectories produced by GROMACS package.
in subset: bio
in subset: formats
comment: 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.

TNG
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.22
has definition: 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.
has exact synonym: Trajectory Next Generation format
in subset: bio
in subset: formats
comment: 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.

XYZ
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Trajectory format (text)
Created in: 1.22
has definition: 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.
in subset: bio
in subset: formats
comment: 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.

mdcrd
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Trajectory format (text)
Created in: 1.22
Documentation: trajectory
has definition: 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).
has exact synonym: AMBER trajectory format
has exact synonym: inpcrd
in subset: bio
in subset: formats

Topology format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Topology data
Created in: 1.22
notRecommendedForAnnotation: true
has definition: Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation.
has exact synonym: CG topology format
has exact synonym: MD topology format
has exact synonym: NA topology format
has exact synonym: Protein topology format
in subset: bio
in subset: formats
comment: 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).

GROMACS top
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Topology format
Created in: 1.22
Documentation: top
has definition: GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files.
in subset: bio
in subset: formats
comment: 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.

AMBER top
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Topology format
Created in: 1.22
Documentation: topology
has definition: 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.
has exact synonym: AMBER Parm
has exact synonym: AMBER Parm7
has exact synonym: Parm7
has exact synonym: Prmtop
has exact synonym: Prmtop7
in subset: bio
in subset: formats
comment: 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.
comment: 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)

PSF
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Topology format
Created in: 1.22
Documentation: node23.html
has definition: 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.
in subset: bio
in subset: formats
comment: 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.

GROMACS itp
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Topology format
subclass of: FF parameter format
Created in: 1.22
Documentation: itp
has definition: 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.
in subset: bio
in subset: formats
comment: GROMACS itp files are used also to define position restrictions on the molecule, or to define the force field parameters for a particular ligand.

FF parameter format
type: Class
subclass of: Format (by type of data)
subclass of: Restriction
  on property: is format of
  some values from: Topology data
Created in: 1.22
has definition: 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.
comment: 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).

BinPos
type: Class
subclass of: Binary format
subclass of: Trajectory format (binary)
Created in: 1.22
has definition: Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates.
has exact synonym: Scripps Research Institute BinPos
in subset: bio
in subset: formats
comment: 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).

RST
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Trajectory format (text)
Created in: 1.22
Documentation: restart
has definition: 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).
has exact synonym: restrt
has exact synonym: rst7
in subset: bio
in subset: formats

CHARMM rtf
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Topology format
Created in: 1.22
has definition: Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information.
in subset: bio
in subset: formats
comment: 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.

AMBER frcmod
type: Class
subclass of: Textual format
subclass of: FF parameter format
Created in: 1.22
Documentation: frcmod
has definition: 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.
in subset: bio
in subset: formats

AMBER off
type: Class
subclass of: Textual format
subclass of: FF parameter format
Created in: 1.22
Documentation: OFF file format.txt
has definition: AMBER Object File Format library files (OFF library files) store residue libraries (forcefield residue parameters).
has exact synonym: AMBER Object File Format
has exact synonym: AMBER lib

NMReDATA
type: Class
subclass of: Textual format
subclass of: NMR data format
Created in: 1.22
has definition: 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.
in subset: bio
in subset: formats
comment: 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.

BpForms
type: Class
subclass of: Chemical formula format
subclass of: Textual format
subclass of: Raw sequence format
subclass of: Restriction
  on property: is format of
  some values from: Sequence features
Created in: 1.22
Documentation: https://arxiv.org/abs/1903.10042
Documentation: grammar.lark
Ontology used: SMILES string
Organisation: www.karrlab.org
has definition: 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.
in subset: bio
in subset: formats

trr
type: Class
subclass of: Tertiary structure format
subclass of: Textual format
subclass of: Trajectory format (text)
Created in: 1.22
Documentation: trr.html
comment: The first 4 bytes of any trr file containing 1993. See https://github.com/galaxyproject/galaxy/pull/6597/files#diff-409951594551183dbf886e24de6cb129R760
has definition: Format of trr files that contain the trajectory of a simulation experiment used by GROMACS.

msh
type: Class
subclass of: Binary format
subclass of: Raw sequence format
subclass of: Restriction
  on property: is format of
  some values from: Sequence checksum
Created in: 1.22
Documentation: s13059-016-0997-x
Documentation: MinHash
Documentation: sketches.html
Documentation: MinHash.capnp
Example: querying-read-sets-against-an-existing-refseq-sketch
File extension: msh
Information standard: cxx.html
Organisation: bnbi.org
Organisation: phillippy-group
has definition: 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.
has exact synonym: Mash sketch
has exact synonym: min-hash sketch
in subset: bio
in subset: formats

Loom
type: Class
subclass of: Gene expression report format
subclass of: HDF5
subclass of: Restriction
  on property: is format of
  some values from: Sequence tag profile
subclass of: Restriction
  on property: is format of
  some values from: Gene expression matrix
Created in: 1.23
Documentation: index.html
Example: index.html
File extension: loom
has definition: 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.

Zarr
type: Class
subclass of: Gene expression report format
subclass of: Binary format
subclass of: Matrix format
subclass of: Restriction
  on property: is format of
  some values from: Sequence tag profile
subclass of: Restriction
  on property: is format of
  some values from: Gene expression matrix
Created in: 1.23
Documentation: data.html
Documentation: spec.html
Example: examples
File extension: zarray
File extension: zgroup
has definition: The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data.

MTX
type: Class
subclass of: Gene expression report format
subclass of: Textual format
subclass of: Matrix format
subclass of: Restriction
  on property: is format of
  some values from: Sequence tag profile
subclass of: Restriction
  on property: is format of
  some values from: Gene expression matrix
Created in: 1.23
Documentation: MTX.html
Example: MTX.html
File extension: mtx
Organisation: www.nist.gov
has definition: The Matrix Market matrix (MTX) format stores numerical or pattern matrices in a dense (array format) or sparse (coordinate format) representation.

BcForms
type: Class
subclass of: Chemical data format
subclass of: Protein report format
subclass of: Textual format
Created in: 1.24
Documentation: bcforms
Documentation: bcforms.org
Documentation: grammar.lark
Example: bcforms.org
Media type: text/plain
Ontology used: crosslink
Organisation: www.karrlab.org
has definition: 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).
comment: 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).

N-Quads
type: Class
subclass of: Textual format
subclass of: RDF format
Created in: 1.24
Documentation: n-quads
File extension: nq
has definition: N-Quads is a line-based, plain text format for encoding an RDF dataset. It includes information about the graph each triple belongs to.
in subset: bio
in subset: formats
comment: N-Quads should not be confused with N-Triples which does not contain graph information.

Vega
type: Class
subclass of: JSON
subclass of: Image format
Created in: 1.25
Documentation: docs
Documentation: specification
Documentation: https://doi.org/10.1145/2642918.2647360
Example: examples
File extension: json
Media type: application/json
Organisation: idl.cs.washington.edu
has definition: 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.
in subset: bio
in subset: formats

Vega-lite
type: Class
subclass of: JSON
subclass of: Image format
Created in: 1.25
Documentation: TVCG.2016.2599030
Documentation: docs
Documentation: spec
Example: examples
File extension: json
Media type: application/json
Organisation: idl.cs.washington.edu
has definition: 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.
in subset: bio
in subset: formats

NeuroML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
subclass of: Restriction
  on property: is format of
  some values from: Kinetic model
Created in: 1.25
Documentation: journal.pcbi.1000815
Documentation: neuroml.org
Example: neuroml-db.org
Example: neuromlv2
Media type: application/xml
Organisation: editors
has definition: A model description language for computational neuroscience.
in subset: bio
in subset: formats

BNGL
type: Class
subclass of: Biological pathway or network format
subclass of: Textual format
subclass of: Restriction
  on property: is format of
  some values from: Kinetic model
Created in: 1.25
Documentation: bionetgen.org
Documentation: 978-1-59745-525-1 5
Documentation: 978-1-61779-833-7 9
Example: README.md
File extension: bngl
Media type: application/xml
Media type: plain/text
Organisation: Faeder
has definition: BioNetGen is a format for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks.
has exact synonym: BioNetGen Language
in subset: bio
in subset: formats

Docker image
type: Class
subclass of: Binary format
Created in: 1.25
Documentation: v1.2.md
Example: dockerhub.com
Organisation: www.docker.com
has definition: 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.
in subset: bio
in subset: formats

GFA 1
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: 1.25
Documentation: GFA-spec
Example: big1.gfa
File extension: gfa
Organisation: GFA-spec
has definition: 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.
has exact synonym: Graphical Fragment Assembly (GFA) 1.0
in subset: bio
in subset: formats

GFA 2
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: 1.25
Documentation: GFA-spec
Example: big2.gfa
File extension: gfa
Organisation: GFA-spec
has definition: 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.
has exact synonym: Graphical Fragment Assembly (GFA) 2.0
in subset: bio
in subset: formats

ObjTables
type: Class
subclass of: xlsx
Created in: 1.25
Documentation: docs
Example: examples
File extension: xlsx
Media type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
Organisation: www.karrlab.org
has definition: 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.
in subset: bio
in subset: formats

CONTIG
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: 1.25
File extension: contig
has definition: The CONTIG format used for output of the SOAPdenovo alignment program. It contains contig sequences generated without using mate pair information.
in subset: bio
in subset: formats

WEGO
type: Class
subclass of: Gene annotation format
subclass of: TSV
Created in: 1.25
File extension: wego
has definition: 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.
in subset: bio
in subset: formats

RPKM
type: Class
subclass of: Gene expression report format
subclass of: TSV
Created in: 1.25
File extension: rpkm
has definition: Tab-delimited format for gene expression levels table, calculated as Reads Per Kilobase per Million (RPKM) mapped reads.
has exact synonym: Gene expression levels table format
in subset: bio
in subset: formats
comment: 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
type: Class
subclass of: Binary format
Created in: 1.25
File extension: tar
has definition: TAR archive file format generated by the Unix-based utility tar.
has exact synonym: TAR
has exact synonym: Tarball
has exact synonym: tar
in subset: bio
in subset: formats
comment: 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

CHAIN
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: 1.25
File extension: chain
has definition: The CHAIN format describes a pairwise alignment that allow gaps in both sequences simultaneously and is used by the UCSC Genome Browser.
in subset: bio
in subset: formats

NET
type: Class
subclass of: Sequence feature annotation format
subclass of: Textual format
Created in: 1.25
File extension: net
has definition: The NET file format is used to describe the data that underlie the net alignment annotations in the UCSC Genome Browser.
in subset: bio
in subset: formats

QMAP
type: Class
subclass of: Sequence feature annotation format
subclass of: Textual format
Created in: 1.25
File extension: qmap
has definition: Format of QMAP files generated for methylation data from an internal BGI pipeline.
in subset: bio
in subset: formats

gxformat2
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: ga
has definition: An emerging format for high-level Galaxy workflow description.
has exact synonym: Galaxy workflow format
has exact synonym: GalaxyWF
has exact synonym: ga
in subset: bio
in subset: formats

WMV
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: wmv
has definition: The proprietary native video format of various Microsoft programs such as Windows Media Player.
has exact synonym: Windows Media Video format
has exact synonym: Windows movie file format
in subset: bio
in subset: formats

ZIP format
type: Class
subclass of: Binary format
Created in: 1.25
File extension: zip
has definition: ZIP is an archive file format that supports lossless data compression.
has exact synonym: ZIP
in subset: bio
in subset: formats
comment: A ZIP file may contain one or more files or directories that may have been compressed.

LSM
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: lsm
has definition: Zeiss' proprietary image format based on TIFF.
in subset: bio
in subset: formats
comment: 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.

GZIP format
type: Class
subclass of: Binary format
Created in: 1.25
File extension: gz
File extension: gzip
has definition: GNU zip compressed file format common to Unix-based operating systems.
has exact synonym: GNU Zip
has exact synonym: gz
has exact synonym: gzip
in subset: bio
in subset: formats

AVI
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: avi
has definition: Audio Video Interleaved (AVI) format is a multimedia container format for AVI files, that allows synchronous audio-with-video playback.
has exact synonym: Audio Video Interleaved
in subset: bio
in subset: formats

TrackDB
type: Class
subclass of: Binary format
subclass of: Sequence annotation track format
Created in: 1.25
File extension: trackdb
has definition: A declaration file format for UCSC browsers track dataset display charateristics.
in subset: bio
in subset: formats

CIGAR format
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: 1.25
File extension: cigar
has definition: 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.
has exact synonym: CIGAR
in subset: bio
in subset: formats

Stereolithography format
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: stl
has definition: 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.
has exact synonym: stl
in subset: bio
in subset: formats

U3D
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: u3d
has definition: 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.
has exact synonym: Universal 3D
has exact synonym: Universal 3D format
in subset: bio
in subset: formats

Texture file format
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: tex
has definition: Bitmap image format used for storing textures.
in subset: bio
in subset: formats
comment: 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.

Python script
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: py
has definition: Format for scripts writtenin Python - a widely used high-level programming language for general-purpose programming.
has exact synonym: Python
has exact synonym: Python program
has exact synonym: py
in subset: bio
in subset: formats

MPEG-4
type: Class
subclass of: Binary format
subclass of: Image format
Created in: 1.25
File extension: mp4
has definition: A digital multimedia container format most commonly used to store video and audio.
has exact synonym: MP4
in subset: bio
in subset: formats

Perl script
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: pl
has definition: Format for scripts written in Perl - a family of high-level, general-purpose, interpreted, dynamic programming languages.
has exact synonym: Perl
has exact synonym: Perl program
has exact synonym: pl
in subset: bio
in subset: formats

R script
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: r
has definition: 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.
has exact synonym: R
has exact synonym: R program
in subset: bio
in subset: formats

R markdown
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: rmd
has definition: A file format for making dynamic documents (R Markdown scripts) with the R language.
in subset: bio
in subset: formats

NIFTI format
type: Class
subclass of: DeprecatedClass
Created in: 1.25
deprecation_comment: This duplicates an existing concept (http://edamontology.org/format_3549).
Obsolete since: 1.26
Old parent: Image format
has definition: 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.
in subset: obsolete
replaced by: nii
deprecated: true

pickle
type: Class
subclass of: Binary format
Created in: 1.25
File extension: pickle
has definition: Format used by Python pickle module for serializing and de-serializing a Python object structure.
in subset: bio
in subset: formats

NumPy format
type: Class
subclass of: Binary format
Created in: 1.25
File extension: npy
has definition: 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.
has exact synonym: NumPy
has exact synonym: npy
in subset: bio
in subset: formats

SimTools repertoire file format
type: Class
subclass of: Binary format
Created in: 1.25
File extension: repz
has definition: 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.
in subset: bio
in subset: formats

Configuration file format
type: Class
subclass of: Textual format
Created in: 1.25
File extension: cfg
has definition: A configuration file used by various programs to store settings that are specific to their respective software.
in subset: bio
in subset: formats

Zstandard format
type: Class
subclass of: Binary format
Created in: 1.25
File extension: zst
has definition: Format used by the Zstandard real-time compression algorithm.
has exact synonym: Zstandard compression format
has exact synonym: Zstandard-compressed file format
has exact synonym: zst
in subset: bio
in subset: formats

MATLAB script
type: Class
subclass of: Workflow format
subclass of: Textual format
Created in: 1.25
File extension: m
has definition: The file format for MATLAB scripts or functions.
has exact synonym: MATLAB
has exact synonym: m
in subset: bio
in subset: formats

PEtab
type: Class
Created in: 1.26
in subset: bio
in subset: formats
has definition: A data format for specifying parameter estimation problems in systems biology.
subclass of: TSV
subclass of: Restriction
  on property: is format of
  some values from: Simulation
Documentation: documentation data format.html
Example: example.html
Citation: journal.pcbi.1008646
Repository: PEtab

gVCF
type: Class
subclass of: VCF
Created in: 1.26
Documentation: gvcf-conventions
Documentation: 360035531812-GVCF-Genomic-Variant-Call-Format
File extension: g.vcf
File extension: g.vcf.gz
has definition: 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.
has exact synonym: g.vcf
has exact synonym: g.vcf.gz
in subset: bio
in subset: formats

cml
type: Class
subclass of: XML
subclass of: Chemical data format
Created in: 1.26
Example: examples
Citation: CS9972600001
Citation: ci990052b
Citation: https://doi.org/10.1186/1758-2946-3-44
Documentation: cml.sourceforge.net
Organisation: Main Page
File extension: cml
has definition: Chemical Markup Language (CML) is an XML-based format for encoding detailed information about a wide range of chemical concepts.
has exact synonym: ChemML
in subset: bio
in subset: formats

cif
type: Class
subclass of: Chemical data format
subclass of: Restriction
  on property: is format of
  some values from: Structure
Created in: 1.26
Example: examples.html
Citation: S010876739101067X
Documentation: documentation
Organisation: www.iucr.org
File extension: cif
has definition: Crystallographic Information File (CIF) is a data exchange standard file format for Crystallographic Information and related Structural Science data.
in subset: bio
in subset: formats

BioSimulators format for the specifications of biosimulation tools
type: Class
subclass of: JSON
Created in: 1.26
Example: simulator-specs
Documentation: simulator-specs
Organisation: reproduciblebiomodels.org
Ontology used: edamontology.org
Ontology used: sbo
Ontology used: kisao
Ontology used: spdx.dev
Ontology used: funder-registry
Ontology used: languages.yml
Ontology used: semanticscience
File extension: json
Media type: https://www.iana.org/assignments/media-types/application/json
has definition: 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.
in subset: bio
in subset: formats

BioSimulators standard for command-line interfaces for biosimulation tools
type: Class
subclass of: Textual format
Created in: 1.26
Example: simulator-interfaces
Documentation: simulator-interfaces
Organisation: reproduciblebiomodels.org
has definition: Outlines the syntax and semantics of the input and output arguments for command-line interfaces for biosimulation tools.
in subset: bio
in subset: formats

PQR
type: Class
subclass of: PDB database entry format
subclass of: Textual format
Created in: 1.26
has definition: Data format derived from the standard PDB format, which enables user to incorporate parameters for charge and radius to the existing PDB data file.
in subset: bio
in subset: formats

PDBQT
type: Class
subclass of: PDB database entry format
subclass of: Textual format
Created in: 1.26
has definition: Data format used in AutoDock 4 for storing atomic coordinates, partial atomic charges and AutoDock atom types for both receptors and ligands.
in subset: bio
in subset: formats

MSP
type: Class
subclass of: Textual format
subclass of: Mass spectrometry data format
Created in: 1.26
Documentation: Ver20Man 11.pdf
Documentation: MsBackendMsp.html
File extension: msp
has definition: MSP is a data format for mass spectrometry data.
in subset: bio
in subset: formats
comment: 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.

maDMP
type: Class
subclass of: JSON
subclass of: Restriction
  on property: is format of
  some values from: Data management plan
Citation: rda00039
Created in: 1.26
Documentation: RDA-DMP-Common-Standard
Example: JSON
Organisation: www.rd-alliance.org
Repository: RDA-DMP-Common-Standard
has definition: A standard for DMPs developed by the Research Data Alliance
has exact synonym: Machine-actionable data management plan
has exact synonym: RDA Common Standard for Machine-Actionable Data Management Plans (maDMPS)
has exact synonym: RDA DMP
in subset: bio
in subset: formats

Operation
type: Class
disjoint with: Topic
disjoint with: DeprecatedClass
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has broad synonym: Function
has definition: A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).
has narrow synonym: Computational method
has narrow synonym: Computational operation
has narrow synonym: Computational procedure
has narrow synonym: Computational subroutine
has narrow synonym: Function (programming)
has narrow synonym: Lambda abstraction
has narrow synonym: Mathematical function
has narrow synonym: Mathematical operation
has related synonym: Computational tool
has related synonym: Process
has related synonym: sumo:Function
in subset: bio
in subset: operations
comment: 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.
broad match: Method
broad match: Function
broad match: SIO_000017
broad match: BFO_0000002
related match: BFO_0000034
related match: BFO_0000019
related match: BFO_0000015
related match: process
related match: quality
broad match: Perpetuant
related match: Process

Axiom
annotated source: Operation
annotated property: hasBroadSynonym
annotated target: Function
comment: Operation is a function that is computational. It typically has input(s) and output(s), which are always data.

Axiom
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Computational tool
comment: Computational tool provides one or more operations.

Axiom
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Process
comment: Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.

Query and retrieval
type: Class
subclass of: Data handling
Created in: beta12orEarlier
has definition: Search or query a data resource and retrieve entries and / or annotation.
has exact synonym: Database retrieval
has narrow synonym: Query
in subset: bio
in subset: operations

Data retrieval (database cross-reference)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Search database to retrieve all relevant references to a particular entity or entry.
in subset: obsolete
deprecated: true

Annotation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has input
  some values from: Ontology
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.
in subset: bio
in subset: operations
comment: This is a broad concept and is used a placeholder for other, more specific concepts.

Indexing
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has output
  some values from: Data index
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Generate an index of (typically a file of) biological data.
has exact synonym: Data indexing
has exact synonym: Database indexing
in subset: bio
in subset: operations

Data index analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Indexing
has definition: Analyse an index of biological data.
in subset: obsolete
deprecated: true

Annotation retrieval (sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data retrieval
has definition: Retrieve basic information about a molecular sequence.
in subset: obsolete
deprecated: true

Sequence generation
type: Class
subclass of: Sequence analysis
subclass of: Generation
Created in: beta12orEarlier
has definition: Generate a molecular sequence by some means.
has narrow synonym: Sequence generation (nucleic acid)
has narrow synonym: Sequence generation (protein)
in subset: bio
in subset: operations

Sequence editing
type: Class
subclass of: Sequence analysis
subclass of: Data editing
Created in: beta12orEarlier
has definition: Edit or change a molecular sequence, either randomly or specifically.
in subset: bio
in subset: operations

Sequence merging
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Merge two or more (typically overlapping) molecular sequences.
has exact synonym: Sequence splicing
has narrow synonym: Paired-end merging
has narrow synonym: Paired-end stitching
has narrow synonym: Read merging
has narrow synonym: Read stitching
in subset: bio
in subset: operations

Sequence conversion
type: Class
subclass of: Sequence editing
subclass of: Conversion
Created in: beta12orEarlier
has definition: Convert a molecular sequence from one type to another.
in subset: bio
in subset: operations

Sequence complexity calculation
type: Class
subclass of: Sequence composition calculation
subclass of: Restriction
  on property: has output
  some values from: Sequence complexity report
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
Created in: beta12orEarlier
has definition: Calculate sequence complexity, for example to find low-complexity regions in sequences.
in subset: bio
in subset: operations

Sequence ambiguity calculation
type: Class
subclass of: Sequence composition calculation
subclass of: Restriction
  on property: has output
  some values from: Sequence ambiguity report
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
Created in: beta12orEarlier
has definition: Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.
in subset: bio
in subset: operations

Sequence composition calculation
type: Class
subclass of: Sequence analysis
subclass of: Calculation
subclass of: Restriction
  on property: has output
  some values from: Sequence composition report
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
Created in: beta12orEarlier
has definition: Calculate character or word composition or frequency of a molecular sequence.
in subset: bio
in subset: operations

Repeat sequence analysis
type: Class
subclass of: Sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
Created in: beta12orEarlier
has definition: Find and/or analyse repeat sequences in (typically nucleotide) sequences.
in subset: bio
in subset: operations
comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.

Sequence motif discovery
type: Class
subclass of: Sequence feature detection
subclass of: Sequence motif analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence signature matches
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).
has exact synonym: Motif discovery
in subset: bio
in subset: operations
comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency).

Sequence motif recognition
type: Class
subclass of: Sequence feature detection
subclass of: Sequence motif analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence signature matches
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).
has exact synonym: Motif scanning
has exact synonym: Sequence signature detection
has exact synonym: Sequence signature recognition
has narrow synonym: Motif detection
has narrow synonym: Motif recognition
has narrow synonym: Motif search
has narrow synonym: Sequence motif detection
has narrow synonym: Sequence motif search
has narrow synonym: Sequence profile search
in subset: bio
in subset: operations

Sequence motif comparison
type: Class
subclass of: Sequence motif analysis
subclass of: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence signature matches
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Find motifs shared by molecular sequences.
in subset: bio
in subset: operations

Transcription regulatory sequence analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Transcriptional regulatory element prediction
has definition: Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.
in subset: obsolete
comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
deprecated: true

Conserved transcription regulatory sequence identification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Transcriptional regulatory element prediction
has definition: Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).
in subset: obsolete
replaced by: Transcriptional regulatory element prediction
deprecated: true

Protein property calculation (from structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Protein property calculation
Old parent: Protein structure analysis
has definition: Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.
in subset: obsolete
replaced by: Protein property calculation
deprecated: true

Simulation analysis
type: Class
subclass of: Protein property calculation
Created in: beta12orEarlier
has definition: Analyse flexibility and motion in protein structure.
has exact synonym: CG analysis
has exact synonym: MD analysis
has exact synonym: Protein Dynamics Analysis
has exact synonym: Trajectory analysis
has narrow synonym: Nucleic Acid Dynamics Analysis
has narrow synonym: Protein flexibility and motion analysis
has narrow synonym: Protein flexibility prediction
has narrow synonym: Protein motion prediction
in subset: bio
in subset: operations
comment: Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.

Structural motif discovery
type: Class
subclass of: Protein structure analysis
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Protein structural motifs and surfaces
Created in: beta12orEarlier
has definition: Identify or screen for 3D structural motifs in protein structure(s).
has exact synonym: Protein structural feature identification
has exact synonym: Protein structural motif recognition
in subset: bio
in subset: operations
comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.

Protein domain recognition
type: Class
subclass of: Protein structure analysis
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Protein folds and structural domains
Created in: beta12orEarlier
has definition: Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).
in subset: bio
in subset: operations

Protein architecture analysis
type: Class
subclass of: Protein structure analysis
Created in: beta12orEarlier
has definition: Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).
in subset: bio
in subset: operations

Residue interaction calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
Created in: beta12orEarlier
has db xref: WHATIF: SymShellFiveXML
has db xref: WHATIF: SymShellOneXML
has db xref: WHATIF: SymShellTenXML
has db xref: WHATIF: SymShellTwoXML
has db xref: WHATIF:ListContactsNormal
has db xref: WHATIF:ListContactsRelaxed
has db xref: WHATIF:ListSideChainContactsNormal
has db xref: WHATIF:ListSideChainContactsRelaxed
has definition: Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).
in subset: bio
in subset: operations

Protein geometry calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein geometry data
Created in: beta12orEarlier
has db xref: WHATIF:CysteineTorsions
has db xref: WHATIF:ResidueTorsions
has db xref: WHATIF:ResidueTorsionsBB
has db xref: WHATIF:ShowTauAngle
has definition: Calculate, visualise or analyse phi/psi angles of a protein structure.
has narrow synonym: Backbone torsion angle calculation
has narrow synonym: Cysteine torsion angle calculation
has narrow synonym: Tau angle calculation
has narrow synonym: Torsion angle calculation
in subset: bio
in subset: operations

Protein property calculation
type: Class
subclass of: Prediction and recognition
subclass of: Calculation
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Protein property rendering
has narrow synonym: Protein property calculation (from sequence)
has narrow synonym: Protein property calculation (from structure)
has narrow synonym: Protein structural property calculation
has narrow synonym: Structural property calculation
in subset: bio
in subset: operations
comment: 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.

Peptide immunogenicity prediction
type: Class
subclass of: Protein property calculation
subclass of: Protein function prediction
subclass of: Restriction
  on property: has output
  some values from: Peptide immunogenicity data
subclass of: Restriction
  on property: has topic
  some values from: Immunology
Created in: beta12orEarlier
has broad synonym: Immunogen design
has definition: Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.
has exact synonym: Antigenicity prediction
has exact synonym: Immunogenicity prediction
has narrow synonym: B cell peptide immunogenicity prediction
has narrow synonym: Hopp and Woods plotting
has narrow synonym: MHC peptide immunogenicity prediction
in subset: bio
in subset: operations
comment: 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.
comment: This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot.
comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.

Sequence feature detection
type: Class
subclass of: Sequence analysis
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has output
  some values from: Sequence features
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.
has exact synonym: Sequence feature prediction
has exact synonym: Sequence feature recognition
has narrow synonym: Motif database search
has related synonym: SO:0000110
in subset: bio
in subset: operations
comment: 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.

Data retrieval (feature table)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Extract a sequence feature table from a sequence database entry.
in subset: obsolete
deprecated: true

Feature table query
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query the features (in a feature table) of molecular sequence(s).
in subset: obsolete
deprecated: true

Sequence feature comparison
type: Class
subclass of: Sequence analysis
subclass of: Comparison
subclass of: Restriction
  on property: has input
  some values from: Sequence features
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Compare the feature tables of two or more molecular sequences.
has exact synonym: Feature comparison
has exact synonym: Feature table comparison
in subset: bio
in subset: operations

Data retrieval (sequence alignment)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Display basic information about a sequence alignment.
in subset: obsolete
deprecated: true

Sequence alignment analysis
type: Class
subclass of: Sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
Created in: beta12orEarlier
has definition: Analyse a molecular sequence alignment.
in subset: bio
in subset: operations

Sequence alignment comparison
type: Class
subclass of: Sequence alignment analysis
subclass of: Comparison
Created in: beta12orEarlier
has definition: Compare (typically by aligning) two molecular sequence alignments.
in subset: bio
in subset: operations
comment: See also 'Sequence profile alignment'.

Sequence alignment conversion
type: Class
subclass of: Sequence alignment editing
subclass of: Conversion
Created in: beta12orEarlier
has definition: Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).
in subset: bio
in subset: operations

Nucleic acid property processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Nucleic acid property calculation
has definition: Process (read and / or write) physicochemical property data of nucleic acids.
in subset: obsolete
deprecated: true

Nucleic acid property calculation
type: Class
subclass of: Calculation
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid property
Created in: beta12orEarlier
has definition: Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.
in subset: bio
in subset: operations

Alternative splicing prediction
type: Class
subclass of: Splicing analysis
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Predict splicing alternatives or transcript isoforms from analysis of sequence data.
has exact synonym: Alternative splicing analysis
has exact synonym: Alternative splicing detection
has exact synonym: Differential splicing analysis
has exact synonym: Splice transcript prediction
in subset: bio
in subset: operations

Frameshift detection
type: Class
subclass of: Sequencing error detection
subclass of: Variant calling
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
Created in: beta12orEarlier
has definition: Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.
has narrow synonym: Frameshift error detection
in subset: bio
in subset: operations
comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.

Vector sequence detection
type: Class
subclass of: Nucleic acid feature detection
Created in: beta12orEarlier
has definition: Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.
in subset: bio
in subset: operations

Protein secondary structure prediction
type: Class
subclass of: Protein secondary structure analysis
subclass of: Prediction and recognition
subclass of: Protein sequence analysis
subclass of: Protein feature detection
Created in: beta12orEarlier
has definition: Predict secondary structure of protein sequences.
has exact synonym: Secondary structure prediction (protein)
in subset: bio
in subset: operations
comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.

Protein super-secondary structure prediction
type: Class
subclass of: Protein secondary structure prediction
subclass of: Restriction
  on property: has output
  some values from: Protein features
Created in: beta12orEarlier
has definition: Predict super-secondary structure of protein sequence(s).
in subset: bio
in subset: operations
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.

Transmembrane protein prediction
type: Class
subclass of: Protein secondary structure prediction
subclass of: Transmembrane protein analysis
Created in: beta12orEarlier
has definition: Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.
in subset: bio
in subset: operations

Transmembrane protein analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Membrane and lipoproteins
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: operations
comment: Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).

Structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: This is a "organisational class" not very useful for annotation per se.
Obsolete since: 1.19
Old parent: Prediction and recognition
Old parent: Structure analysis
consider: Protein structure prediction
consider: Nucleic acid structure prediction
has definition: Predict tertiary structure of a molecular (biopolymer) sequence.
in subset: obsolete
deprecated: true

Residue contact prediction
type: Class
subclass of: Protein property calculation
subclass of: Protein sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
Created in: beta12orEarlier
has definition: Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.
has exact synonym: Residue interaction prediction
has narrow synonym: Contact map prediction
has narrow synonym: Protein contact map prediction
in subset: bio
in subset: operations
comment: Methods usually involve multiple sequence alignment analysis.

Protein interaction raw data analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Protein-protein interaction analysis
has definition: Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
in subset: obsolete
replaced by: Protein-protein interaction analysis
deprecated: true

Protein-protein interaction prediction (from protein sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.
in subset: obsolete
replaced by: Protein-protein binding site prediction
deprecated: true

Protein-protein interaction prediction (from protein structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.
in subset: obsolete
replaced by: Protein-protein binding site prediction
deprecated: true

Protein interaction network analysis
type: Class
subclass of: Protein-protein interaction analysis
subclass of: Network analysis
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Analyse a network of protein interactions.
has narrow synonym: Protein interaction network comparison
in subset: bio
in subset: operations

Pathway or network comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
Obsolete since: 1.24
Old parent: Pathway or network analysis
consider: Network analysis
consider: Pathway analysis
has definition: Compare two or more biological pathways or networks.
in subset: obsolete
deprecated: true

RNA secondary structure prediction
type: Class
subclass of: Nucleic acid feature detection
subclass of: Nucleic acid structure prediction
subclass of: RNA secondary structure analysis
subclass of: Restriction
  on property: has output
  some values from: RNA secondary structure
Created in: beta12orEarlier
has definition: Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).
has narrow synonym: RNA shape prediction
in subset: bio
in subset: operations
comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).

Nucleic acid folding analysis
type: Class
subclass of: Nucleic acid structure prediction
subclass of: Modelling and simulation
subclass of: Nucleic acid structure analysis
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid folding report
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Nucleic acid folding
has exact synonym: Nucleic acid folding modelling
has exact synonym: Nucleic acid folding prediction
has narrow synonym: Nucleic acid folding energy calculation
in subset: bio
in subset: operations

Data retrieval (restriction enzyme annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on restriction enzymes or restriction enzyme sites.
in subset: obsolete
deprecated: true

Genetic marker identification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Nucleic acid feature detection
has definition: Identify genetic markers in DNA sequences.
in subset: obsolete
comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
deprecated: true

Genetic mapping
type: Class
subclass of: Linkage analysis
subclass of: DNA mapping
subclass of: Restriction
  on property: has output
  some values from: Genetic map
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Functional mapping
has exact synonym: Genetic cartography
has exact synonym: Genetic map construction
has exact synonym: Genetic map generation
has exact synonym: Linkage mapping
has narrow synonym: QTL mapping
in subset: bio
in subset: operations
comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.
comment: 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).

Linkage analysis
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Genetic linkage report
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: Analyse genetic linkage.
in subset: bio
in subset: operations
comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.

Codon usage table generation
type: Class
subclass of: Codon usage analysis
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: Codon usage table
Created in: beta12orEarlier
has definition: Calculate codon usage statistics and create a codon usage table.
has exact synonym: Codon usage table construction
in subset: bio
in subset: operations

Codon usage table comparison
type: Class
subclass of: Codon usage analysis
subclass of: Nucleic acid comparison
Created in: beta12orEarlier
has definition: Compare two or more codon usage tables.
in subset: bio
in subset: operations

Codon usage analysis
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Codon usage table
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
subclass of: Restriction
  on property: has output
  some values from: Codon usage data
subclass of: Restriction
  on property: has output
  some values from: Codon usage table
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Analyse codon usage in molecular sequences or process codon usage data (e.g. a codon usage table).
has exact synonym: Codon usage data analysis
has exact synonym: Codon usage table analysis
in subset: bio
in subset: operations

Base position variability plotting
type: Class
subclass of: Codon usage analysis
subclass of: Sequence visualisation
subclass of: Restriction
  on property: has output
  some values from: Base position variability plot
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Identify and plot third base position variability in a nucleotide sequence.
in subset: bio
in subset: operations

Sequence word comparison
type: Class
subclass of: Sequence comparison
Created in: beta12orEarlier
has definition: Find exact character or word matches between molecular sequences without full sequence alignment.
in subset: bio
in subset: operations

Sequence distance matrix generation
type: Class
subclass of: Sequence comparison
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: Sequence distance matrix
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has definition: Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.
has exact synonym: Phylogenetic distance matrix generation
has exact synonym: Sequence distance calculation
has exact synonym: Sequence distance matrix construction
in subset: bio
in subset: operations

Sequence redundancy removal
type: Class
subclass of: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence
Created in: beta12orEarlier
has definition: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
in subset: bio
in subset: operations

Sequence clustering
type: Class
subclass of: Sequence comparison
subclass of: Generation
subclass of: Clustering
subclass of: Restriction
  on property: has output
  some values from: Sequence cluster
Created in: beta12orEarlier
has definition: Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
has exact synonym: Sequence cluster construction
has exact synonym: Sequence cluster generation
in subset: bio
in subset: operations
comment: The clusters may be output or used internally for some other purpose.

Sequence alignment
type: Class
subclass of: Sequence analysis
subclass of: Sequence comparison
subclass of: Alignment
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment
Created in: beta12orEarlier
comment: 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'.
has definition: Align (identify equivalent sites within) molecular sequences.
has exact synonym: Sequence alignment construction
has exact synonym: Sequence alignment generation
has narrow synonym: Consensus-based sequence alignment
has narrow synonym: Constrained sequence alignment
has narrow synonym: Multiple sequence alignment (constrained)
has narrow synonym: Sequence alignment (constrained)
in subset: bio
in subset: operations
comment: See also "Read mapping"

Hybrid sequence alignment construction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence alignment
has definition: Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).
in subset: obsolete
deprecated: true

Structure-based sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Align molecular sequences using sequence and structural information.
has exact synonym: Sequence alignment (structure-based)
in subset: bio
in subset: operations

Structure alignment
type: Class
subclass of: Structure analysis
subclass of: Structure comparison
subclass of: Alignment
subclass of: Restriction
  on property: has output
  some values from: Structure alignment
Created in: beta12orEarlier
comment: 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.
has definition: Align (superimpose) molecular tertiary structures.
has exact synonym: Structural alignment
has narrow synonym: 3D profile alignment
has narrow synonym: 3D profile-to-3D profile alignment
has narrow synonym: Structural profile alignment
in subset: bio
in subset: operations

Sequence profile generation
type: Class
subclass of: Sequence alignment analysis
subclass of: Generation
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
subclass of: Restriction
  on property: has output
  some values from: Sequence profile
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.
has exact synonym: Sequence profile construction
in subset: bio
in subset: operations

3D profile generation
type: Class
subclass of: Structure analysis
subclass of: Generation
subclass of: Restriction
  on property: has input
  some values from: Structure
subclass of: Restriction
  on property: has input
  some values from: Structure alignment
subclass of: Restriction
  on property: has output
  some values from: Structural profile
Created in: beta12orEarlier
has definition: Generate some type of structural (3D) profile or template from a structure or structure alignment.
has exact synonym: Structural profile construction
has exact synonym: Structural profile generation
in subset: bio
in subset: operations

Profile-profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Sequence alignment
has definition: Align sequence profiles (representing sequence alignments).
in subset: obsolete
replaced by: Sequence profile alignment
deprecated: true

3D profile-to-3D profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Structure alignment
has definition: Align structural (3D) profiles or templates (representing structures or structure alignments).
in subset: obsolete
replaced by: Structure alignment
deprecated: true

Sequence profile alignment
type: Class
subclass of: Sequence alignment
subclass of: Restriction
  on property: has input
  some values from: Sequence profile
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Align molecular sequence(s) to sequence profile(s), or profiles to other profiles. A profile typically represents a sequence alignment.
has narrow synonym: Profile-profile alignment
has narrow synonym: Profile-to-profile alignment
has narrow synonym: Sequence-profile alignment
has narrow synonym: Sequence-to-profile alignment
in subset: bio
in subset: operations
comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.

Sequence-to-3D-profile alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Alignment
has definition: Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).
in subset: obsolete
replaced by: Fold recognition
deprecated: true

Protein threading
type: Class
subclass of: Fold recognition
subclass of: Restriction
  on property: has input
  some values from: Protein structure
subclass of: Restriction
  on property: has output
  some values from: Sequence-structure alignment
Created in: beta12orEarlier
comment: 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.
has definition: Align molecular sequence to structure in 3D space (threading).
has exact synonym: Sequence-structure alignment
has narrow synonym: Sequence-3D profile alignment
has narrow synonym: Sequence-to-3D-profile alignment
in subset: bio
in subset: operations
comment: Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.

Fold recognition
type: Class
subclass of: Protein structure analysis
subclass of: Protein sequence analysis
subclass of: Alignment
subclass of: Protein comparison
subclass of: Protein feature detection
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Domain prediction
has exact synonym: Fold prediction
has exact synonym: Protein domain prediction
has exact synonym: Protein fold prediction
has exact synonym: Protein fold recognition
in subset: bio
in subset: operations
comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.

Metadata retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved.
Obsolete since: 1.17
Old parent: Data retrieval
has definition: Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.
in subset: obsolete
replaced by: Data retrieval
comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
deprecated: true

Literature search
type: Class
subclass of: Database search
subclass of: Restriction
  on property: has topic
  some values from: Literature and language
Created in: beta12orEarlier
has definition: Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics.
in subset: bio
in subset: operations

Text mining
type: Class
subclass of: Prediction and recognition
subclass of: Data analysis
subclass of: Restriction
  on property: has input
  some values from: Text
subclass of: Restriction
  on property: has output
  some values from: Text mining report
subclass of: Restriction
  on property: has topic
  some values from: Natural language processing
Created in: beta12orEarlier
has broad synonym: Text analysis
has definition: Process and analyse text (typically scientific literature) to extract information from it.
has exact synonym: Literature mining
has exact synonym: Text analytics
has exact synonym: Text data mining
has related synonym: Article analysis
has related synonym: Literature analysis
in subset: bio
in subset: operations

Virtual PCR
type: Class
subclass of: Nucleic acid sequence analysis
Created in: beta12orEarlier
has definition: Perform in-silico (virtual) PCR.
in subset: bio
in subset: operations

PCR primer design
type: Class
subclass of: Primer and probe design
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
subclass of: Restriction
  on property: has output
  some values from: PCR primers
subclass of: Restriction
  on property: has topic
  some values from: Probes and primers
Created in: beta12orEarlier
has definition: Design or predict oligonucleotide primers for PCR and DNA amplification etc.
has exact synonym: PCR primer prediction
has exact synonym: Primer design
has narrow synonym: PCR primer design (based on gene structure)
has narrow synonym: PCR primer design (for conserved primers)
has narrow synonym: PCR primer design (for gene transcription profiling)
has narrow synonym: PCR primer design (for genotyping polymorphisms)
has narrow synonym: PCR primer design (for large scale sequencing)
has narrow synonym: PCR primer design (for methylation PCRs)
has narrow synonym: Primer quality estimation
in subset: bio
in subset: operations
comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
comment: 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.

Microarray probe design
type: Class
subclass of: Primer and probe design
subclass of: Design
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
subclass of: Restriction
  on property: has output
  some values from: Oligonucleotide probe annotation
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
subclass of: Restriction
  on property: has topic
  some values from: Probes and primers
Created in: beta12orEarlier
has definition: Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.
has exact synonym: Microarray probe prediction
in subset: bio
in subset: operations

Sequence assembly
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence assembly
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
Created in: beta12orEarlier
has definition: Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
has narrow synonym: Metagenomic assembly
has narrow synonym: Sequence assembly editing
in subset: bio
in subset: operations
comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.

Microarray data standardisation and normalisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Thing
has definition: Standardize or normalize microarray data.
in subset: obsolete
replaced by: Standardisation and normalisation
deprecated: true

Sequencing-based expression profile data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) SAGE, MPSS or SBS experimental data.
in subset: obsolete
deprecated: true

Expression profile clustering
type: Class
subclass of: Expression profile comparison
subclass of: Clustering
subclass of: Restriction
  on property: has output
  some values from: Processed microarray data
Created in: beta12orEarlier
has definition: Perform cluster analysis of expression data to identify groups with similar expression profiles, for example by clustering.
has narrow synonym: Gene expression clustering
has narrow synonym: Gene expression profile clustering
in subset: bio
in subset: operations

Gene expression profiling
type: Class
subclass of: Expression analysis
Created in: beta12orEarlier
has definition: The measurement of the activity (expression) of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function.
has exact synonym: Feature expression analysis
has exact synonym: Functional profiling
has exact synonym: Gene expression profile construction
has exact synonym: Gene expression profile generation
has exact synonym: Gene expression quantification
has exact synonym: Gene transcription profiling
has narrow synonym: Non-coding RNA profiling
has narrow synonym: Protein profiling
has narrow synonym: RNA profiling
has narrow synonym: mRNA profiling
in subset: bio
in subset: operations
comment: Gene expression profiling generates some sort of gene expression profile, for example from microarray data.

Expression profile comparison
type: Class
subclass of: Expression analysis
Created in: beta12orEarlier
has definition: Comparison of expression profiles.
has narrow synonym: Gene expression comparison
has narrow synonym: Gene expression profile comparison
in subset: bio
in subset: operations

Functional profiling
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Interpret (in functional terms) and annotate gene expression data.
in subset: obsolete
replaced by: Expression analysis
deprecated: true

EST and cDNA sequence analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence analysis
has definition: Analyse EST or cDNA sequences.
in subset: obsolete
comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
deprecated: true

Structural genomics target selection
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein structure analysis
has definition: Identify and select targets for protein structural determination.
in subset: obsolete
comment: Methods will typically navigate a graph of protein families of known structure.
deprecated: true

Protein secondary structure assignment
type: Class
subclass of: Protein structure assignment
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
subclass of: Restriction
  on property: has topic
  some values from: Protein structure analysis
Created in: beta12orEarlier
comment: Includes secondary structure assignment from circular dichroism (CD) spectroscopic data, and from protein coordinate data.
has definition: Assign secondary structure from protein coordinate or experimental data.
in subset: bio
in subset: operations

Protein structure assignment
type: Class
subclass of: Protein structure analysis
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has output
  some values from: Protein structure
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: beta12orEarlier
has definition: Assign a protein tertiary structure (3D coordinates), or other aspects of protein structure, from raw experimental data.
has narrow synonym: NOE assignment
has narrow synonym: Structure calculation
in subset: bio
in subset: operations

Protein structure validation
type: Class
subclass of: Protein structure analysis
subclass of: Validation
subclass of: Restriction
  on property: has output
  some values from: Protein structural quality report
subclass of: Restriction
  on property: has topic
  some values from: Molecular modelling
Created in: beta12orEarlier
has db xref: WHATIF: CorrectedPDBasXML
has db xref: WHATIF: UseFileDB
has db xref: WHATIF: UseResidueDB
has definition: Evaluate the quality or correctness a protein three-dimensional model.
has exact synonym: Protein model validation
has narrow synonym: Residue validation
in subset: bio
in subset: operations
comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.
comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
comment: 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).

Molecular model refinement
type: Class
subclass of: Optimisation and refinement
subclass of: Structure analysis
Created in: beta12orEarlier
has db xref: WHATIF: CorrectedPDBasXML
has definition: Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc.
has narrow synonym: Protein model refinement
in subset: bio
in subset: operations

Phylogenetic inference
type: Class
subclass of: Phylogenetic analysis
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree.
has exact synonym: Phlyogenetic tree construction
has exact synonym: Phylogenetic reconstruction
has exact synonym: Phylogenetic tree generation
in subset: bio
in subset: operations
comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.

Phylogenetic analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has definition: Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.
has exact synonym: Phylogenetic tree analysis
has narrow synonym: Phylogenetic modelling
in subset: bio
in subset: operations
comment: Phylgenetic modelling is the modelling of trait evolution and prediction of trait values using phylogeny as a basis.

Phylogenetic tree comparison
type: Class
subclass of: Phylogenetic analysis
subclass of: Comparison
Created in: beta12orEarlier
has definition: Compare two or more phylogenetic trees.
in subset: bio
in subset: operations
comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.

Phylogenetic tree editing
type: Class
subclass of: Phylogenetic analysis
subclass of: Data editing
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic tree
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
Created in: beta12orEarlier
has definition: Edit a phylogenetic tree.
in subset: bio
in subset: operations

Phylogenetic footprinting
type: Class
subclass of: Phylogenetic inference
subclass of: Restriction
  on property: has topic
  some values from: Phylogenomics
Created in: beta12orEarlier
has definition: 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).
has narrow synonym: Phylogenetic shadowing
in subset: bio
in subset: operations
comment: 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.

Protein folding simulation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Protein folding analysis
has definition: Simulate the folding of a protein.
in subset: obsolete
replaced by: Protein folding analysis
deprecated: true

Protein folding pathway prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Protein structure prediction
has definition: Predict the folding pathway(s) or non-native structural intermediates of a protein.
in subset: obsolete
replaced by: Protein structure prediction
deprecated: true

Protein SNP mapping
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).
in subset: obsolete
replaced by: Variant effect prediction
deprecated: true

Variant effect prediction
type: Class
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
subclass of: Restriction
  on property: has topic
  some values from: Genetic variation
Created in: beta12orEarlier
has definition: Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.
has exact synonym: Variant functional prediction
has narrow synonym: Protein SNP mapping
has narrow synonym: Protein mutation modelling
has narrow synonym: Protein stability change prediction
in subset: bio
in subset: operations
comment: Protein SNP mapping maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations.

Immunogen design
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Design molecules that elicit an immune response (immunogens).
in subset: obsolete
replaced by: Peptide immunogenicity prediction
deprecated: true

Zinc finger prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Nucleic acids-binding site prediction
has definition: Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
in subset: obsolete
replaced by: Nucleic acids-binding site prediction
deprecated: true

Enzyme kinetics calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Enzyme kinetics data
subclass of: Restriction
  on property: has topic
  some values from: Enzymes
Created in: beta12orEarlier
has definition: Calculate Km, Vmax and derived data for an enzyme reaction.
in subset: bio
in subset: operations

Data formatting
type: Class
subclass of: Data handling
Created in: beta12orEarlier
has definition: Reformat a file of data (or equivalent entity in memory).
has exact synonym: File format conversion
has exact synonym: File formatting
has exact synonym: File reformatting
has exact synonym: Format conversion
has exact synonym: Data reformatting
in subset: bio
in subset: operations

Format validation
type: Class
subclass of: Validation
Created in: beta12orEarlier
has definition: Test and validate the format and content of a data file.
has exact synonym: File format validation
in subset: bio
in subset: operations

Visualisation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has input
  some values from: Image
subclass of: Restriction
  on property: has output
  some values from: Image
subclass of: Restriction
  on property: has topic
  some values from: Data visualisation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.
has exact synonym: Data visualisation
has exact synonym: Rendering
has narrow synonym: Molecular visualisation
has narrow synonym: Plotting
in subset: bio
in subset: operations
comment: This includes methods to render and visualise molecules.

Sequence database search
type: Class
subclass of: Sequence analysis
subclass of: Database search
subclass of: Restriction
  on property: has output
  some values from: Sequence search results
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: operations
comment: This excludes direct retrieval methods (e.g. the dbfetch program).

Structure database search
type: Class
subclass of: Database search
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data.
in subset: bio
in subset: operations

Protein secondary database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.
in subset: obsolete
replaced by: Protein feature detection
deprecated: true

Motif database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Sequence feature detection
has definition: Screen a sequence against a motif or pattern database.
in subset: obsolete
deprecated: true

Sequence profile database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Sequence motif recognition
has definition: Search a database of sequence profiles with a query sequence.
in subset: obsolete
deprecated: true

Transmembrane protein database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Database search
has definition: Search a database of transmembrane proteins, for example for sequence or structural similarities.
in subset: obsolete
deprecated: true

Sequence retrieval (by code)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query a database and retrieve sequences with a given entry code or accession number.
in subset: obsolete
deprecated: true

Sequence retrieval (by keyword)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query a database and retrieve sequences containing a given keyword.
in subset: obsolete
deprecated: true

Sequence similarity search
type: Class
subclass of: Sequence database search
subclass of: Structure database search
subclass of: Sequence comparison
Created in: beta12orEarlier
has definition: Search a sequence database and retrieve sequences that are similar to a query sequence.
has narrow synonym: Sequence database search (by sequence)
has narrow synonym: Structure database search (by sequence)
in subset: bio
in subset: operations

Sequence database search (by motif or pattern)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.
in subset: obsolete
replaced by: Sequence motif recognition
deprecated: true

Sequence database search (by amino acid composition)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence database search
has definition: Search a sequence database and retrieve sequences of a given amino acid composition.
in subset: obsolete
deprecated: true

Sequence database search (by property)
type: Class
subclass of: Sequence database search
Created in: beta12orEarlier
has definition: Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property.
in subset: bio
in subset: operations

Sequence database search (by sequence using word-based methods)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence similarity search
has definition: Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.
in subset: obsolete
comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.
deprecated: true

Sequence database search (by sequence using profile-based methods)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence similarity search
has definition: 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.
in subset: obsolete
comment: This includes tools based on PSI-BLAST.
deprecated: true

Sequence database search (by sequence using local alignment-based methods)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence similarity search
has definition: Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.
in subset: obsolete
comment: This includes tools based on the Smith-Waterman algorithm or FASTA.
deprecated: true

Sequence database search (by sequence using global alignment-based methods)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence similarity search
has definition: Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.
in subset: obsolete
comment: This includes tools based on the Needleman and Wunsch algorithm.
deprecated: true

Sequence database search (by sequence for primer sequences)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence similarity search
has definition: Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.
in subset: obsolete
comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
deprecated: true

Sequence database search (by molecular weight)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Protein fragment weight comparison
deprecated: true

Sequence database search (by isoelectric point)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence database search
has definition: Search sequence(s) or a sequence database for sequences of a given isoelectric point.
in subset: obsolete
deprecated: true

Structure retrieval (by code)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query a tertiary structure database and retrieve entries with a given entry code or accession number.
in subset: obsolete
deprecated: true

Structure retrieval (by keyword)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query a tertiary structure database and retrieve entries containing a given keyword.
in subset: obsolete
deprecated: true

Structure database search (by sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.
in subset: obsolete
replaced by: Sequence similarity search
deprecated: true

Structural similarity search
type: Class
subclass of: Structure database search
subclass of: Structure comparison
Created in: beta12orEarlier
has definition: Search a database of molecular structure and retrieve structures that are similar to a query structure.
has exact synonym: Structure database search (by structure)
has exact synonym: Structure retrieval by structure
in subset: bio
in subset: operations

Sequence annotation
type: Class
subclass of: Annotation
subclass of: Restriction
  on property: has input
  some values from: Sequence record
subclass of: Restriction
  on property: has output
  some values from: Sequence record
Created in: beta12orEarlier
has definition: Annotate a molecular sequence record with terms from a controlled vocabulary.
in subset: bio
in subset: operations

Genome annotation
type: Class
subclass of: Sequence annotation
subclass of: Genome analysis
Created in: beta12orEarlier
has definition: Annotate a genome sequence with terms from a controlled vocabulary.
has narrow synonym: Functional genome annotation
has narrow synonym: Metagenome annotation
has narrow synonym: Structural genome annotation
in subset: bio
in subset: operations

Reverse complement
type: Class
subclass of: Sequence generation
Created in: beta12orEarlier
has definition: Generate the reverse and / or complement of a nucleotide sequence.
has exact synonym: Nucleic acid sequence reverse and complement
has exact synonym: Reverse / complement
has exact synonym: Reverse and complement
in subset: bio
in subset: operations

Random sequence generation
type: Class
subclass of: Sequence generation
Created in: beta12orEarlier
has definition: Generate a random sequence, for example, with a specific character composition.
in subset: bio
in subset: operations

Restriction digest
type: Class
subclass of: Sequence generation
subclass of: Nucleic acid property calculation
subclass of: Restriction
  on property: has output
  some values from: Restriction digest
Created in: beta12orEarlier
has definition: Generate digest fragments for a nucleotide sequence containing restriction sites.
has exact synonym: Nucleic acid restriction digest
in subset: bio
in subset: operations

Protein sequence cleavage
type: Class
subclass of: Sequence generation
subclass of: Restriction
  on property: has output
  some values from: Proteolytic digest
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
comment: This is often followed by calculation of protein fragment masses (http://edamontology.org/operation_0398).
has definition: Cleave a protein sequence into peptide fragments (corresponding to enzymatic or chemical cleavage).
in subset: bio
in subset: operations

Sequence mutation and randomisation
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition.
in subset: bio
in subset: operations

Sequence masking
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Mask characters in a molecular sequence (replacing those characters with a mask character).
in subset: bio
in subset: operations
comment: For example, SNPs or repeats in a DNA sequence might be masked.

Sequence cutting
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Cut (remove) characters or a region from a molecular sequence.
in subset: bio
in subset: operations

Restriction site creation
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Create (or remove) restriction sites in sequences, for example using silent mutations.
in subset: bio
in subset: operations

DNA translation
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
Created in: beta12orEarlier
has definition: Translate a DNA sequence into protein.
in subset: bio
in subset: operations

DNA transcription
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Transcribe a nucleotide sequence into mRNA sequence(s).
in subset: bio
in subset: operations

Sequence composition calculation (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Calculate base frequency or word composition of a nucleotide sequence.
in subset: obsolete
replaced by: Sequence composition calculation
deprecated: true

Sequence composition calculation (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Calculate amino acid frequency or word composition of a protein sequence.
in subset: obsolete
replaced by: Sequence composition calculation
deprecated: true

Repeat sequence detection
type: Class
subclass of: Repeat sequence analysis
subclass of: Nucleic acid feature detection
Created in: beta12orEarlier
has definition: Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
in subset: bio
in subset: operations

Repeat sequence organisation analysis
type: Class
subclass of: Sequence composition calculation
subclass of: Repeat sequence analysis
Created in: beta12orEarlier
has definition: Analyse repeat sequence organisation such as periodicity.
in subset: bio
in subset: operations

Protein hydropathy calculation (from structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.
in subset: obsolete
replaced by: Protein hydropathy calculation
deprecated: true

Accessible surface calculation
type: Class
subclass of: Molecular surface analysis
subclass of: Restriction
  on property: has output
  some values from: Protein solvent accessibility
Created in: beta12orEarlier
has db xref: WHATIF:AtomAccessibilitySolvent
has db xref: WHATIF:AtomAccessibilitySolventPlus
has definition: Calculate solvent accessible or buried surface areas in protein or other molecular structures.
has narrow synonym: Protein solvent accessibility calculation
in subset: bio
in subset: operations
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).

Protein hydropathy cluster calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify clusters of hydrophobic or charged residues in a protein structure.
in subset: obsolete
replaced by: Residue cluster calculation
deprecated: true

Protein dipole moment calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein dipole moment
Created in: beta12orEarlier
has definition: Calculate whether a protein structure has an unusually large net charge (dipole moment).
in subset: bio
in subset: operations

Molecular surface calculation
type: Class
subclass of: Molecular surface analysis
Created in: beta12orEarlier
has db xref: WHATIF:AtomAccessibilityMolecular
has db xref: WHATIF:AtomAccessibilityMolecularPlus
has db xref: WHATIF:ResidueAccessibilityMolecular
has db xref: WHATIF:ResidueAccessibilitySolvent
has db xref: WHATIF:ResidueAccessibilityVacuum
has db xref: WHATIF:ResidueAccessibilityVacuumMolecular
has db xref: WHATIF:TotAccessibilityMolecular
has db xref: WHATIF:TotAccessibilitySolvent
has definition: Calculate the molecular surface area in proteins and other macromolecules.
has narrow synonym: Protein atom surface calculation
has narrow synonym: Protein residue surface calculation
has narrow synonym: Protein surface and interior calculation
has narrow synonym: Protein surface calculation
in subset: bio
in subset: operations

Protein binding site prediction (from structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.
in subset: obsolete
replaced by: Binding site prediction
deprecated: true

Protein-nucleic acid interaction analysis
type: Class
subclass of: Protein function prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Analyse the interaction of protein with nucleic acids, e.g. RNA or DNA-binding sites, interfaces etc.
has exact synonym: Protein-nucleic acid binding site analysis
has narrow synonym: Protein-DNA interaction analysis
has narrow synonym: Protein-RNA interaction analysis
in subset: bio
in subset: operations

Protein peeling
type: Class
subclass of: Protein domain recognition
Created in: beta12orEarlier
has definition: Decompose a structure into compact or globular fragments (protein peeling).
in subset: bio
in subset: operations

Protein distance matrix calculation
type: Class
subclass of: Residue distance calculation
subclass of: Restriction
  on property: has output
  some values from: Protein distance matrix
Created in: beta12orEarlier
has definition: Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.
in subset: bio
in subset: operations

Contact map calculation
type: Class
subclass of: Protein distance matrix calculation
subclass of: Restriction
  on property: has output
  some values from: Protein contact map
Created in: beta12orEarlier
has definition: Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.
has exact synonym: Protein contact map calculation
in subset: bio
in subset: operations

Residue cluster calculation
type: Class
subclass of: Residue distance calculation
subclass of: Restriction
  on property: has output
  some values from: Protein residue 3D cluster
Created in: beta12orEarlier
has definition: Calculate clusters of contacting residues in protein structures.
in subset: bio
in subset: operations
comment: This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role.

Hydrogen bond calculation
type: Class
subclass of: Residue interaction calculation
subclass of: Restriction
  on property: has output
  some values from: Protein hydrogen bonds
Created in: beta12orEarlier
has db xref: WHATIF:HasHydrogenBonds
has db xref: WHATIF:ShowHydrogenBonds
has db xref: WHATIF:ShowHydrogenBondsM
has definition: Identify potential hydrogen bonds between amino acids and other groups.
in subset: bio
in subset: operations
comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.

Residue non-canonical interaction detection
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Protein geometry calculation
has definition: Calculate non-canonical atomic interactions in protein structures.
in subset: obsolete
deprecated: true

Ramachandran plot calculation
type: Class
subclass of: Protein geometry calculation
subclass of: Restriction
  on property: has output
  some values from: Ramachandran plot
Created in: beta12orEarlier
has definition: Calculate a Ramachandran plot of a protein structure.
in subset: bio
in subset: operations

Ramachandran plot validation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.22
Old parent: Protein geometry validation
has definition: Validate a Ramachandran plot of a protein structure.
in subset: obsolete
replaced by: Protein geometry validation
deprecated: true

Protein molecular weight calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Peptide molecular weights
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: Calculate the molecular weight of a protein sequence or fragments.
has exact synonym: Peptide mass calculation
in subset: bio
in subset: operations

Protein extinction coefficient calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein extinction coefficient
Created in: beta12orEarlier
has definition: Predict extinction coefficients or optical density of a protein sequence.
in subset: bio
in subset: operations

Protein pKa calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein property
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
Created in: beta12orEarlier
has definition: Calculate pH-dependent properties from pKa calculations of a protein sequence.
has exact synonym: Protein pH-dependent property calculation
in subset: bio
in subset: operations

Protein hydropathy calculation (from sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Hydropathy calculation on a protein sequence.
in subset: obsolete
replaced by: Protein hydropathy calculation
deprecated: true

Protein titration curve plotting
type: Class
subclass of: Visualisation
subclass of: Protein pKa calculation
subclass of: Restriction
  on property: has output
  some values from: Protein titration curve
Created in: beta12orEarlier
has definition: Plot a protein titration curve.
in subset: bio
in subset: operations

Protein isoelectric point calculation
type: Class
subclass of: Protein pKa calculation
subclass of: Restriction
  on property: has output
  some values from: Protein isoelectric point
Created in: beta12orEarlier
has definition: Calculate isoelectric point of a protein sequence.
in subset: bio
in subset: operations

Protein hydrogen exchange rate calculation
type: Class
subclass of: Protein pKa calculation
subclass of: Restriction
  on property: has output
  some values from: Protein hydrogen exchange rate
Created in: beta12orEarlier
has definition: Estimate hydrogen exchange rate of a protein sequence.
in subset: bio
in subset: operations

Protein hydrophobic region calculation
type: Class
subclass of: Protein hydropathy calculation
Created in: beta12orEarlier
has definition: Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.
in subset: bio
in subset: operations

Protein aliphatic index calculation
type: Class
subclass of: Protein hydropathy calculation
subclass of: Restriction
  on property: has output
  some values from: Protein aliphatic index
Created in: beta12orEarlier
has definition: Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.
in subset: bio
in subset: operations

Protein hydrophobic moment plotting
type: Class
subclass of: Sequence visualisation
subclass of: Protein hydropathy calculation
subclass of: Restriction
  on property: has output
  some values from: Peptide hydrophobic moment
Created in: beta12orEarlier
has definition: Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.
in subset: bio
in subset: operations
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.

Protein globularity prediction
type: Class
subclass of: Protein hydropathy calculation
subclass of: Restriction
  on property: has output
  some values from: Protein globularity
Created in: beta12orEarlier
has definition: Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.
in subset: bio
in subset: operations

Protein solubility prediction
type: Class
subclass of: Protein hydropathy calculation
subclass of: Restriction
  on property: has output
  some values from: Protein solubility
Created in: beta12orEarlier
has definition: Predict the solubility or atomic solvation energy of a protein sequence.
in subset: bio
in subset: operations

Protein crystallizability prediction
type: Class
subclass of: Protein hydropathy calculation
subclass of: Restriction
  on property: has output
  some values from: Protein crystallizability
Created in: beta12orEarlier
has definition: Predict crystallizability of a protein sequence.
in subset: bio
in subset: operations

Protein signal peptide detection (eukaryotes)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (jison)Too fine-grained.
Obsolete since: 1.17
Old parent: Protein signal peptide detection
has definition: Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins.
in subset: obsolete
replaced by: Protein signal peptide detection
deprecated: true

Protein signal peptide detection (bacteria)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (jison)Too fine-grained.
Obsolete since: 1.17
Old parent: Protein signal peptide detection
has definition: Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins.
in subset: obsolete
replaced by: Protein signal peptide detection
deprecated: true

MHC peptide immunogenicity prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.
in subset: obsolete
replaced by: Peptide immunogenicity prediction
deprecated: true

Protein feature prediction (from sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Protein feature detection
has definition: Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.
in subset: obsolete
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
deprecated: true

Nucleic acid feature detection
type: Class
subclass of: Prediction and recognition
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.
has exact synonym: Sequence feature detection (nucleic acid)
has narrow synonym: Nucleic acid feature prediction
has narrow synonym: Nucleic acid feature recognition
has narrow synonym: Nucleic acid site detection
has narrow synonym: Nucleic acid site prediction
has narrow synonym: Nucleic acid site recognition
in subset: bio
in subset: operations
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
comment: 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.

Epitope mapping
type: Class
subclass of: Mapping
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Immunology
Created in: beta12orEarlier
has definition: Predict antigenic determinant sites (epitopes) in protein sequences.
has exact synonym: Antibody epitope prediction
has exact synonym: Epitope prediction
has narrow synonym: B cell epitope mapping
has narrow synonym: B cell epitope prediction
has narrow synonym: Epitope mapping (MHC Class I)
has narrow synonym: Epitope mapping (MHC Class II)
has narrow synonym: T cell epitope mapping
has narrow synonym: T cell epitope prediction
in subset: bio
in subset: operations
comment: Epitope mapping is commonly done during vaccine design.

Post-translational modification site prediction
type: Class
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Protein modifications
Created in: beta12orEarlier
has definition: Predict post-translation modification sites in protein sequences.
has exact synonym: PTM analysis
has exact synonym: PTM prediction
has exact synonym: PTM site analysis
has exact synonym: Post-translation modification site prediction
has exact synonym: Post-translational modification analysis
has exact synonym: PTM site prediction
has exact synonym: Protein post-translation modification site prediction
has narrow synonym: Acetylation prediction
has narrow synonym: Acetylation site prediction
has narrow synonym: Dephosphorylation prediction
has narrow synonym: Dephosphorylation site prediction
has narrow synonym: GPI anchor prediction
has narrow synonym: GPI anchor site prediction
has narrow synonym: GPI modification prediction
has narrow synonym: GPI modification site prediction
has narrow synonym: Glycosylation prediction
has narrow synonym: Glycosylation site prediction
has narrow synonym: Hydroxylation prediction
has narrow synonym: Hydroxylation site prediction
has narrow synonym: Methylation prediction
has narrow synonym: Methylation site prediction
has narrow synonym: N-myristoylation prediction
has narrow synonym: N-myristoylation site prediction
has narrow synonym: N-terminal acetylation prediction
has narrow synonym: N-terminal acetylation site prediction
has narrow synonym: N-terminal myristoylation prediction
has narrow synonym: N-terminal myristoylation site prediction
has narrow synonym: Palmitoylation prediction
has narrow synonym: Palmitoylation site prediction
has narrow synonym: Phosphoglycerylation prediction
has narrow synonym: Phosphoglycerylation site prediction
has narrow synonym: Phosphorylation prediction
has narrow synonym: Phosphorylation site prediction
has narrow synonym: Phosphosite localization
has narrow synonym: Prenylation prediction
has narrow synonym: Prenylation site prediction
has narrow synonym: Pupylation prediction
has narrow synonym: Pupylation site prediction
has narrow synonym: S-nitrosylation prediction
has narrow synonym: S-nitrosylation site prediction
has narrow synonym: S-sulfenylation prediction
has narrow synonym: S-sulfenylation site prediction
has narrow synonym: Succinylation prediction
has narrow synonym: Succinylation site prediction
has narrow synonym: Sulfation prediction
has narrow synonym: Sulfation site prediction
has narrow synonym: Sumoylation prediction
has narrow synonym: Sumoylation site prediction
has narrow synonym: Tyrosine nitration prediction
has narrow synonym: Tyrosine nitration site prediction
has narrow synonym: Ubiquitination prediction
has narrow synonym: Ubiquitination site prediction
in subset: bio
in subset: operations
comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.

Protein signal peptide detection
type: Class
subclass of: Protein function prediction
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Protein targeting and localisation
Created in: beta12orEarlier
has definition: Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.
in subset: bio
in subset: operations
comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.

Protein binding site prediction (from sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.
in subset: obsolete
replaced by: Binding site prediction
deprecated: true

Nucleic acids-binding site prediction
type: Class
subclass of: Binding site prediction
Created in: beta12orEarlier
has definition: Predict or detect RNA and DNA-binding binding sites in protein sequences.
has exact synonym: Protein-nucleic acid binding detection
has exact synonym: Protein-nucleic acid binding prediction
has exact synonym: Protein-nucleic acid binding site detection
has exact synonym: Protein-nucleic acid binding site prediction
has narrow synonym: Zinc finger prediction
in subset: bio
in subset: operations
comment: This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).

Protein folding site prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Protein folding analysis
has definition: Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation.
in subset: obsolete
replaced by: Protein folding analysis
deprecated: true

Protein cleavage site prediction
type: Class
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.
in subset: bio
in subset: operations

Epitope mapping (MHC Class I)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Predict epitopes that bind to MHC class I molecules.
in subset: obsolete
replaced by: Epitope mapping
deprecated: true

Epitope mapping (MHC Class II)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Predict epitopes that bind to MHC class II molecules.
in subset: obsolete
replaced by: Epitope mapping
deprecated: true

Whole gene prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.
in subset: obsolete
replaced by: Gene prediction
deprecated: true

Gene component prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.
in subset: obsolete
replaced by: Gene prediction
comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
deprecated: true

Transposon prediction
type: Class
subclass of: Nucleic acid feature detection
Created in: beta12orEarlier
has definition: Detect or predict transposons, retrotransposons / retrotransposition signatures etc.
in subset: bio
in subset: operations

PolyA signal detection
type: Class
subclass of: Nucleic acid feature detection
Created in: beta12orEarlier
has definition: Detect polyA signals in nucleotide sequences.
has exact synonym: PolyA detection
has exact synonym: PolyA prediction
has exact synonym: PolyA signal prediction
has exact synonym: Polyadenylation signal detection
has exact synonym: Polyadenylation signal prediction
in subset: bio
in subset: operations

Quadruplex formation site detection
type: Class
subclass of: Nucleic acid feature detection
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid structure report
Created in: beta12orEarlier
has definition: Detect quadruplex-forming motifs in nucleotide sequences.
has exact synonym: Quadruplex structure prediction
in subset: bio
in subset: operations
comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.

CpG island and isochore detection
type: Class
subclass of: Nucleic acid feature detection
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
Created in: beta12orEarlier
has definition: Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.
has exact synonym: CpG island and isochores detection
has exact synonym: CpG island and isochores rendering
in subset: bio
in subset: operations
comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.

Restriction site recognition
type: Class
subclass of: Nucleic acid feature detection
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.
in subset: bio
in subset: operations

Nucleosome position prediction
type: Class
subclass of: Nucleic acid feature detection
Created in: beta12orEarlier
has definition: Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.
has narrow synonym: Nucleosome exclusion sequence prediction
has narrow synonym: Nucleosome formation sequence prediction
in subset: bio
in subset: operations

Splice site prediction
type: Class
subclass of: Splicing analysis
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Identify, predict or analyse splice sites in nucleotide sequences.
has exact synonym: Splice prediction
in subset: bio
in subset: operations
comment: Methods might require a pre-mRNA or genomic DNA sequence.

Integrated gene prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Gene prediction
has definition: Predict whole gene structure using a combination of multiple methods to achieve better predictions.
in subset: obsolete
replaced by: Gene prediction
deprecated: true

Operon prediction
type: Class
subclass of: Gene prediction
Created in: beta12orEarlier
has definition: Find operons (operators, promoters and genes) in bacteria genes.
in subset: bio
in subset: operations

Coding region prediction
type: Class
subclass of: Gene prediction
Created in: beta12orEarlier
has definition: Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.
has exact synonym: ORF finding
has exact synonym: ORF prediction
in subset: bio
in subset: operations

SECIS element prediction
type: Class
subclass of: Gene prediction
subclass of: Restriction
  on property: has output
  some values from: Gene report
Created in: beta12orEarlier
has definition: Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.
has exact synonym: Selenocysteine insertion sequence (SECIS) prediction
in subset: bio
in subset: operations
comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.

Transcriptional regulatory element prediction
type: Class
subclass of: Gene prediction
subclass of: Restriction
  on property: has topic
  some values from: Transcription factors and regulatory sites
Created in: beta12orEarlier
comment: 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.
has definition: Identify or predict transcriptional regulatory motifs, patterns, elements or regions in DNA sequences.
has exact synonym: Regulatory element prediction
has exact synonym: Transcription regulatory element prediction
has narrow synonym: Conserved transcription regulatory sequence identification
has narrow synonym: Translational regulatory element prediction
in subset: bio
in subset: operations
comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.

Translation initiation site prediction
type: Class
subclass of: Coding region prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
Created in: beta12orEarlier
has definition: Predict translation initiation sites, possibly by searching a database of sites.
in subset: bio
in subset: operations

Promoter prediction
type: Class
subclass of: Transcriptional regulatory element prediction
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: operations
comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.

cis-regulatory element prediction
type: Class
subclass of: Transcriptional regulatory element prediction
Created in: beta12orEarlier
has definition: 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).
has narrow synonym: Transcriptional regulatory element prediction (DNA-cis)
has narrow synonym: Transcriptional regulatory element prediction (RNA-cis)
in subset: bio
in subset: operations
comment: 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.

Transcriptional regulatory element prediction (RNA-cis)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Transcriptional regulatory element prediction
has definition: Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.
in subset: obsolete
replaced by: cis-regulatory element prediction
deprecated: true

trans-regulatory element prediction
type: Class
subclass of: Transcriptional regulatory element prediction
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
Created in: beta12orEarlier
has definition: Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.
has exact synonym: Functional RNA identification
has exact synonym: Transcriptional regulatory element prediction (trans)
in subset: bio
in subset: operations
comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.

S/MAR prediction
type: Class
subclass of: Transcriptional regulatory element prediction
Created in: beta12orEarlier
has definition: Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.
has exact synonym: MAR/SAR prediction
has exact synonym: Matrix/scaffold attachment site prediction
in subset: bio
in subset: operations
comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.

Transcription factor binding site prediction
type: Class
subclass of: Promoter prediction
Created in: beta12orEarlier
has definition: Identify or predict transcription factor binding sites in DNA sequences.
in subset: bio
in subset: operations

Exonic splicing enhancer prediction
type: Class
subclass of: Promoter prediction
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Identify or predict exonic splicing enhancers (ESE) in exons.
in subset: bio
in subset: operations
comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.

Sequence alignment validation
type: Class
subclass of: Sequence alignment analysis
subclass of: Validation
Created in: beta12orEarlier
has definition: Evaluate molecular sequence alignment accuracy.
has exact synonym: Sequence alignment quality evaluation
in subset: bio
in subset: operations
comment: Evaluation might be purely sequence-based or use structural information.

Sequence alignment analysis (conservation)
type: Class
subclass of: Sequence alignment analysis
Created in: beta12orEarlier
has definition: Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.
has exact synonym: Residue conservation analysis
in subset: bio
in subset: operations
comment: Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.

Sequence alignment analysis (site correlation)
type: Class
subclass of: Sequence alignment analysis
subclass of: Correlation
Created in: beta12orEarlier
has definition: Analyse correlations between sites in a molecular sequence alignment.
in subset: bio
in subset: operations
comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.

Chimera detection
type: Class
subclass of: Nucleic acid sequence analysis
Created in: beta12orEarlier
has definition: Detects chimeric sequences (chimeras) from a sequence alignment.
has exact synonym: Chimeric sequence detection
in subset: bio
in subset: operations
comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.

Recombination detection
type: Class
subclass of: Nucleic acid sequence analysis
Created in: beta12orEarlier
has definition: Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.
has exact synonym: Sequence alignment analysis (recombination detection)
in subset: bio
in subset: operations
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.

Indel detection
type: Class
subclass of: Variant calling
Created in: beta12orEarlier
has definition: Identify insertion, deletion and duplication events from a sequence alignment.
has exact synonym: Indel discovery
has exact synonym: Sequence alignment analysis (indel detection)
in subset: bio
in subset: operations
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.

Nucleosome formation potential prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleosome position prediction
has definition: Predict nucleosome formation potential of DNA sequences.
in subset: obsolete
deprecated: true

Nucleic acid thermodynamic property calculation
type: Class
subclass of: Nucleic acid property calculation
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid thermodynamic data
Created in: beta12orEarlier
has definition: Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.
in subset: bio
in subset: operations

Nucleic acid melting profile plotting
type: Class
subclass of: Nucleic acid property calculation
subclass of: Visualisation
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid melting profile
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA melting profile.
in subset: bio
in subset: operations
comment: A melting profile is used to visualise and analyse partly melted DNA conformations.

Nucleic acid stitch profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA stitch profile.
in subset: bio
in subset: operations
comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.

Nucleic acid melting curve plotting
type: Class
subclass of: Nucleic acid melting profile plotting
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA melting curve.
in subset: bio
in subset: operations

Nucleic acid probability profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA probability profile.
in subset: bio
in subset: operations

Nucleic acid temperature profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA temperature profile.
in subset: bio
in subset: operations

Nucleic acid curvature calculation
type: Class
subclass of: Nucleic acid property calculation
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid property
Created in: beta12orEarlier
has definition: Calculate curvature and flexibility / stiffness of a nucleotide sequence.
in subset: bio
in subset: operations
comment: This includes properties such as.

miRNA target prediction
type: Class
subclass of: trans-regulatory element prediction
Created in: beta12orEarlier
has definition: Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence.
has exact synonym: miRNA prediction
has exact synonym: microRNA detection
has exact synonym: microRNA target detection
in subset: bio
in subset: operations

tRNA gene prediction
type: Class
subclass of: Gene prediction
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
Created in: beta12orEarlier
has definition: Identify or predict tRNA genes in genomic sequences (tRNA).
in subset: bio
in subset: operations

siRNA binding specificity prediction
type: Class
subclass of: trans-regulatory element prediction
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
Created in: beta12orEarlier
has definition: Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.
in subset: bio
in subset: operations

Protein secondary structure prediction (integrated)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Protein secondary structure prediction
has definition: Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.
in subset: obsolete
replaced by: Protein secondary structure prediction
deprecated: true

Protein secondary structure prediction (helices)
type: Class
subclass of: Protein secondary structure prediction
Created in: beta12orEarlier
has definition: Predict helical secondary structure of protein sequences.
in subset: bio
in subset: operations

Protein secondary structure prediction (turns)
type: Class
subclass of: Protein secondary structure prediction
Created in: beta12orEarlier
has definition: Predict turn structure (for example beta hairpin turns) of protein sequences.
in subset: bio
in subset: operations

Protein secondary structure prediction (coils)
type: Class
subclass of: Protein secondary structure prediction
Created in: beta12orEarlier
has definition: Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.
in subset: bio
in subset: operations

Disulfide bond prediction
type: Class
subclass of: Protein feature detection
Created in: beta12orEarlier
has definition: Predict cysteine bonding state and disulfide bond partners in protein sequences.
in subset: bio
in subset: operations

GPCR prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Not sustainable to have protein type-specific concepts.
Obsolete since: 1.19
Old parent: Transmembrane protein prediction
has definition: Predict G protein-coupled receptors (GPCR).
in subset: obsolete
replaced by: Transmembrane protein prediction
deprecated: true

GPCR analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Not sustainable to have protein type-specific concepts.
Obsolete since: 1.19
Old parent: Transmembrane protein analysis
has definition: Analyse G-protein coupled receptor proteins (GPCRs).
in subset: obsolete
replaced by: Transmembrane protein analysis
deprecated: true

Protein structure prediction
type: Class
subclass of: Protein structure analysis
subclass of: Prediction and recognition
subclass of: Protein sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Protein structure
Created in: beta12orEarlier
comment: This includes methods that predict the folding pathway(s) or non-native structural intermediates of a protein.
has definition: Predict tertiary structure (backbone and side-chain conformation) of protein sequences.
has narrow synonym: Protein folding pathway prediction
in subset: bio
in subset: operations

Nucleic acid structure prediction
type: Class
subclass of: Prediction and recognition
subclass of: Nucleic acid structure analysis
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid structure
Created in: beta12orEarlier
has definition: Predict structure of DNA or RNA.
in subset: bio
in subset: operations
comment: Methods might identify thermodynamically stable or evolutionarily conserved structures.

Ab initio structure prediction
type: Class
subclass of: Protein structure prediction
Created in: beta12orEarlier
has definition: Predict tertiary structure of protein sequence(s) without homologs of known structure.
has exact synonym: de novo structure prediction
in subset: bio
in subset: operations

Protein modelling
type: Class
subclass of: Protein structure prediction
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has topic
  some values from: Molecular modelling
Created in: beta12orEarlier
has definition: Build a three-dimensional protein model based on known (for example homologs) structures.
has exact synonym: Comparative modelling
has exact synonym: Homology modelling
has exact synonym: Homology structure modelling
has exact synonym: Protein structure comparative modelling
in subset: bio
in subset: operations
comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc.

Molecular docking
type: Class
subclass of: Protein function prediction
subclass of: Structure analysis
subclass of: Restriction
  on property: has output
  some values from: Protein-ligand complex
subclass of: Restriction
  on property: has output
  some values from: Protein complex
Created in: beta12orEarlier
has definition: Model the structure of a protein in complex with a small molecule or another macromolecule.
has exact synonym: Docking simulation
has exact synonym: Macromolecular docking
in subset: bio
in subset: operations
comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.

Backbone modelling
type: Class
subclass of: Protein modelling
Created in: beta12orEarlier
has definition: Model protein backbone conformation.
has exact synonym: Protein modelling (backbone)
has narrow synonym: Design optimization
has narrow synonym: Epitope grafting
has narrow synonym: Scaffold search
has narrow synonym: Scaffold selection
in subset: bio
in subset: operations
comment: Methods might require a preliminary C(alpha) trace.
comment: Scaffold selection, scaffold search, epitope grafting and design optimization are stages of backbone modelling done during rational vaccine design.

Side chain modelling
type: Class
subclass of: Protein modelling
Created in: beta12orEarlier
has definition: Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.
has exact synonym: Protein modelling (side chains)
has narrow synonym: Antibody optimisation
has narrow synonym: Antigen optimisation
has narrow synonym: Antigen resurfacing
has narrow synonym: Rotamer likelihood prediction
in subset: bio
in subset: operations
comment: 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.
comment: Methods might use a residue rotamer library.
comment: 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.

Loop modelling
type: Class
subclass of: Protein modelling
Created in: beta12orEarlier
has definition: Model loop conformation in protein structures.
has exact synonym: Protein loop modelling
has exact synonym: Protein modelling (loops)
in subset: bio
in subset: operations

Protein-ligand docking
type: Class
subclass of: Molecular docking
subclass of: Restriction
  on property: has output
  some values from: Protein-ligand complex
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.
has exact synonym: Ligand-binding simulation
has narrow synonym: Protein-peptide docking
in subset: bio
in subset: operations
comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.
comment: 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).

RNA inverse folding
type: Class
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has output
  some values from: Sequence set (nucleic acid)
Created in: beta12orEarlier
has definition: Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.
has exact synonym: Nucleic acid folding family identification
has exact synonym: Structured RNA prediction and optimisation
in subset: bio
in subset: operations

SNP detection
type: Class
subclass of: Variant calling
Created in: beta12orEarlier
has definition: 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.
has exact synonym: SNP calling
has exact synonym: SNP discovery
has exact synonym: Single nucleotide polymorphism detection
in subset: bio
in subset: operations
comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.

Radiation Hybrid Mapping
type: Class
subclass of: Physical mapping
subclass of: Restriction
  on property: has output
  some values from: Radiation hybrid map
Created in: beta12orEarlier
has definition: Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.
in subset: bio
in subset: operations

Functional mapping
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Genetic mapping
has definition: Map the genetic architecture of dynamic complex traits.
in subset: obsolete
comment: This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
deprecated: true

Haplotype mapping
type: Class
subclass of: Genetic mapping
subclass of: Restriction
  on property: has output
  some values from: Haplotype map
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Haplotype inference
has exact synonym: Haplotype map generation
has exact synonym: Haplotype reconstruction
in subset: bio
in subset: operations
comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).

Linkage disequilibrium calculation
type: Class
subclass of: Linkage analysis
subclass of: Restriction
  on property: has output
  some values from: Genetic linkage report
Created in: beta12orEarlier
has definition: Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
in subset: bio
in subset: operations
comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.

Genetic code prediction
type: Class
subclass of: Codon usage analysis
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has output
  some values from: Genetic code
Created in: beta12orEarlier
has definition: Predict genetic code from analysis of codon usage data.
in subset: bio
in subset: operations

Dot plot plotting
type: Class
subclass of: Sequence word comparison
subclass of: Sequence visualisation
subclass of: Restriction
  on property: has output
  some values from: Dotplot
Created in: beta12orEarlier
has definition: Render a representation of a distribution that consists of group of data points plotted on a simple scale.
has exact synonym: Categorical plot plotting
has exact synonym: Dotplot plotting
in subset: bio
in subset: operations
comment: 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.

Pairwise sequence alignment
type: Class
subclass of: Sequence alignment
subclass of: Restriction
  on property: has output
  some values from: Pair sequence alignment
Created in: beta12orEarlier
has definition: Align exactly two molecular sequences.
has exact synonym: Pairwise alignment
in subset: bio
in subset: operations
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.

Multiple sequence alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Align more than two molecular sequences.
has exact synonym: Multiple alignment
in subset: bio
in subset: operations
comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.

Pairwise sequence alignment generation (local)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Pairwise sequence alignment
consider: Local alignment
has definition: Locally align exactly two molecular sequences.
in subset: obsolete
comment: Local alignment methods identify regions of local similarity.
deprecated: true

Pairwise sequence alignment generation (global)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Pairwise sequence alignment
consider: Global alignment
has definition: Globally align exactly two molecular sequences.
in subset: obsolete
comment: Global alignment methods identify similarity across the entire length of the sequences.
deprecated: true

Local alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Locally align two or more molecular sequences.
has exact synonym: Local sequence alignment
has exact synonym: Sequence alignment (local)
has narrow synonym: Smith-Waterman
in subset: bio
in subset: operations
comment: Local alignment methods identify regions of local similarity.

Global alignment
type: Class
subclass of: Sequence alignment
Created in: beta12orEarlier
has definition: Globally align two or more molecular sequences.
has exact synonym: Global sequence alignment
has exact synonym: Sequence alignment (global)
in subset: bio
in subset: operations
comment: Global alignment methods identify similarity across the entire length of the sequences.

Constrained sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Sequence alignment
has definition: Align two or more molecular sequences with user-defined constraints.
in subset: obsolete
replaced by: Sequence alignment
deprecated: true

Consensus-based sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Thing
has definition: Align two or more molecular sequences using multiple methods to achieve higher quality.
in subset: obsolete
replaced by: Sequence alignment
deprecated: true

Tree-based sequence alignment
type: Class
subclass of: Sequence alignment
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has definition: Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.
has exact synonym: Multiple sequence alignment (phylogenetic tree-based)
has exact synonym: Multiple sequence alignment construction (phylogenetic tree-based)
has exact synonym: Phylogenetic tree-based multiple sequence alignment construction
has exact synonym: Sequence alignment (phylogenetic tree-based)
has exact synonym: Sequence alignment generation (phylogenetic tree-based)
in subset: bio
in subset: operations
comment: This is supposed to give a more biologically meaningful alignment than standard alignments.

Secondary structure alignment generation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Alignment
has definition: Align molecular secondary structure (represented as a 1D string).
in subset: obsolete
deprecated: true

Protein secondary structure alignment generation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Protein secondary structure comparison
has definition: Align protein secondary structures.
in subset: obsolete
replaced by: Protein secondary structure comparison
deprecated: true

RNA secondary structure alignment
type: Class
subclass of: RNA secondary structure analysis
subclass of: Generation
subclass of: Restriction
  on property: has input
  some values from: RNA secondary structure
subclass of: Restriction
  on property: has output
  some values from: RNA secondary structure alignment
Created in: beta12orEarlier
has definition: Align RNA secondary structures.
has exact synonym: RNA secondary structure alignment construction
has exact synonym: RNA secondary structure alignment generation
has exact synonym: Secondary structure alignment construction (RNA)
in subset: bio
in subset: operations

Pairwise structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Align (superimpose) exactly two molecular tertiary structures.
has exact synonym: Structure alignment (pairwise)
has narrow synonym: Pairwise protein structure alignment
in subset: bio
in subset: operations

Multiple structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Align (superimpose) more than two molecular tertiary structures.
has exact synonym: Structure alignment (multiple)
has narrow synonym: Multiple protein structure alignment
in subset: bio
in subset: operations
comment: This includes methods that use an existing alignment.

Structure alignment (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure alignment
has definition: Align protein tertiary structures.
in subset: obsolete
deprecated: true

Structure alignment (RNA)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure alignment
has definition: Align RNA tertiary structures.
in subset: obsolete
deprecated: true

Pairwise structure alignment generation (local)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Structure alignment
consider: Local structure alignment
has definition: Locally align (superimpose) exactly two molecular tertiary structures.
in subset: obsolete
comment: Local alignment methods identify regions of local similarity, common substructures etc.
deprecated: true

Pairwise structure alignment generation (global)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Structure alignment
consider: Global structure alignment
has definition: Globally align (superimpose) exactly two molecular tertiary structures.
in subset: obsolete
comment: Global alignment methods identify similarity across the entire structures.
deprecated: true

Local structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Locally align (superimpose) two or more molecular tertiary structures.
has exact synonym: Structure alignment (local)
has narrow synonym: Local protein structure alignment
in subset: bio
in subset: operations
comment: Local alignment methods identify regions of local similarity, common substructures etc.

Global structure alignment
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Globally align (superimpose) two or more molecular tertiary structures.
has exact synonym: Structure alignment (global)
has narrow synonym: Global protein structure alignment
in subset: bio
in subset: operations
comment: Global alignment methods identify similarity across the entire structures.

Profile-profile alignment (pairwise)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Profile-profile alignment
consider: Sequence alignment
consider: Sequence profile alignment
has definition: Align exactly two molecular profiles.
in subset: obsolete
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
deprecated: true

Sequence alignment generation (multiple profile)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Profile-profile alignment
consider: Sequence alignment
consider: Sequence profile alignment
has definition: Align two or more molecular profiles.
in subset: obsolete
deprecated: true

3D profile-to-3D profile alignment (pairwise)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: 3D profile-to-3D profile alignment
consider: Structure-based sequence alignment
consider: Structure alignment
consider: Pairwise structure alignment
has definition: Align exactly two molecular Structural (3D) profiles.
in subset: obsolete
deprecated: true

Structural profile alignment generation (multiple)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: 3D profile-to-3D profile alignment
consider: Structure-based sequence alignment
consider: Structure alignment
consider: Multiple structure alignment
has definition: Align two or more molecular 3D profiles.
in subset: obsolete
deprecated: true

Data retrieval (tool metadata)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.
in subset: obsolete
deprecated: true

Data retrieval (database metadata)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.
in subset: obsolete
deprecated: true

PCR primer design (for large scale sequencing)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers for large scale sequencing.
in subset: obsolete
replaced by: PCR primer design
deprecated: true

PCR primer design (for genotyping polymorphisms)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).
in subset: obsolete
replaced by: PCR primer design
deprecated: true

PCR primer design (for gene transcription profiling)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers for gene transcription profiling.
in subset: obsolete
replaced by: PCR primer design
deprecated: true

PCR primer design (for conserved primers)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers that are conserved across multiple genomes or species.
in subset: obsolete
replaced by: PCR primer design
deprecated: true

PCR primer design (based on gene structure)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers based on gene structure.
in subset: obsolete
replaced by: PCR primer design
deprecated: true

PCR primer design (for methylation PCRs)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Predict primers for methylation PCRs.
in subset: obsolete
replaced by: PCR primer design
deprecated: true

Mapping assembly
type: Class
subclass of: Sequence assembly
Created in: beta12orEarlier
has definition: Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.
has exact synonym: Sequence assembly (mapping assembly)
in subset: bio
in subset: operations
comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.

De-novo assembly
type: Class
subclass of: Sequence assembly
Created in: beta12orEarlier
has definition: Sequence assembly by combining fragments without the aid of a reference sequence or genome.
has exact synonym: De Bruijn graph
has exact synonym: Sequence assembly (de-novo assembly)
in subset: bio
in subset: operations
comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers.

Genome assembly
type: Class
subclass of: Sequence assembly
subclass of: Genome analysis
Created in: beta12orEarlier
has definition: The process of assembling many short DNA sequences together such that they represent the original chromosomes from which the DNA originated.
has exact synonym: Genomic assembly
has exact synonym: Sequence assembly (genome assembly)
has narrow synonym: Breakend assembly
in subset: bio
in subset: operations

EST assembly
type: Class
subclass of: Sequence assembly
Created in: beta12orEarlier
has definition: Sequence assembly for EST sequences (transcribed mRNA).
has exact synonym: Sequence assembly (EST assembly)
in subset: bio
in subset: operations
comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.

Sequence tag mapping
type: Class
subclass of: Annotation
subclass of: DNA mapping
Created in: beta12orEarlier
has definition: Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data.
has exact synonym: Tag to gene assignment
in subset: bio
in subset: operations
comment: Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome.

SAGE data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) serial analysis of gene expression (SAGE) data.
in subset: obsolete
deprecated: true

MPSS data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) massively parallel signature sequencing (MPSS) data.
in subset: obsolete
deprecated: true

SBS data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) sequencing by synthesis (SBS) data.
in subset: obsolete
deprecated: true

Heat map generation
type: Class
subclass of: Expression data visualisation
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: Heat map
Created in: beta12orEarlier
has definition: Generate a heat map of expression data from e.g. microarray data.
has exact synonym: Heat map construction
has exact synonym: Heatmap generation
in subset: bio
in subset: operations
comment: The heat map usually uses a coloring scheme to represent expression values. They can show how quantitative measurements were influenced by experimental conditions.

Gene expression profile analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Expression analysis
has definition: Analyse one or more gene expression profiles, typically to interpret them in functional terms.
in subset: obsolete
deprecated: true

Expression profile pathway mapping
type: Class
subclass of: Mapping
subclass of: Expression analysis
subclass of: Pathway analysis
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
Created in: beta12orEarlier
has definition: Map an expression profile to known biological pathways, for example, to identify or reconstruct a pathway.
has exact synonym: Pathway mapping
has narrow synonym: Gene expression profile pathway mapping
has narrow synonym: Gene to pathway mapping
has narrow synonym: Gene-to-pathway mapping
in subset: bio
in subset: operations

Protein secondary structure assignment (from coordinate data)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Protein secondary structure assignment
has definition: Assign secondary structure from protein coordinate data.
in subset: obsolete
replaced by: Protein secondary structure assignment
deprecated: true

Protein secondary structure assignment (from CD data)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Protein secondary structure assignment
has definition: Assign secondary structure from circular dichroism (CD) spectroscopic data.
in subset: obsolete
replaced by: Protein secondary structure assignment
deprecated: true

Protein structure assignment (from X-ray crystallographic data)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.
in subset: obsolete
replaced by: Protein structure assignment
deprecated: true

Protein structure assignment (from NMR data)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.
in subset: obsolete
replaced by: Protein structure assignment
deprecated: true

Phylogenetic inference (data centric)
type: Class
subclass of: Phylogenetic inference
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Construct a phylogenetic tree from a specific type of data.
has exact synonym: Phylogenetic tree construction (data centric)
has exact synonym: Phylogenetic tree generation (data centric)
in subset: bio
in subset: operations
comment: Subconcepts of this concept reflect different types of data used to generate a tree, and provide an alternate axis for curation.

Phylogenetic inference (method centric)
type: Class
subclass of: Phylogenetic inference
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Construct a phylogenetic tree using a specific method.
has exact synonym: Phylogenetic tree construction (method centric)
has exact synonym: Phylogenetic tree generation (method centric)
in subset: bio
in subset: operations
comment: Subconcepts of this concept reflect different computational methods used to generate a tree, and provide an alternate axis for curation.

Phylogenetic inference (from molecular sequences)
type: Class
subclass of: Phylogenetic inference (data centric)
subclass of: Sequence analysis
Created in: beta12orEarlier
has definition: Phylogenetic tree construction from molecular sequences.
has exact synonym: Phylogenetic tree construction (from molecular sequences)
has exact synonym: Phylogenetic tree generation (from molecular sequences)
in subset: bio
in subset: operations
comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.

Phylogenetic inference (from continuous quantitative characters)
type: Class
subclass of: Phylogenetic inference (data centric)
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic continuous quantitative data
Created in: beta12orEarlier
has definition: Phylogenetic tree construction from continuous quantitative character data.
has exact synonym: Phylogenetic tree construction (from continuous quantitative characters)
has exact synonym: Phylogenetic tree generation (from continuous quantitative characters)
in subset: bio
in subset: operations

Phylogenetic inference (from gene frequencies)
type: Class
subclass of: Phylogenetic inference (data centric)
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic gene frequencies data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Phylogenetic tree construction from gene frequency data.
has exact synonym: Phylogenetic tree construction (from gene frequencies)
has exact synonym: Phylogenetic tree generation (from gene frequencies)
in subset: bio
in subset: operations

Phylogenetic inference (from polymorphism data)
type: Class
subclass of: Phylogenetic inference (data centric)
subclass of: Restriction
  on property: has topic
  some values from: Genetic variation
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Phylogenetic tree construction (from polymorphism data)
has exact synonym: Phylogenetic tree generation (from polymorphism data)
in subset: bio
in subset: operations

Species tree construction
type: Class
subclass of: Phylogenetic inference
Created in: beta12orEarlier
has definition: Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.
has exact synonym: Phylogenetic species tree construction
has exact synonym: Phylogenetic species tree generation
in subset: bio
in subset: operations

Phylogenetic inference (parsimony methods)
type: Class
subclass of: Phylogenetic inference (method centric)
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Phylogenetic tree construction (parsimony methods)
has exact synonym: Phylogenetic tree generation (parsimony methods)
in subset: bio
in subset: operations
comment: This includes evolutionary parsimony (invariants) methods.

Phylogenetic inference (minimum distance methods)
type: Class
subclass of: Phylogenetic inference (method centric)
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.
has exact synonym: Phylogenetic tree construction (minimum distance methods)
has exact synonym: Phylogenetic tree generation (minimum distance methods)
in subset: bio
in subset: operations
comment: This includes neighbor joining (NJ) clustering method.

Phylogenetic inference (maximum likelihood and Bayesian methods)
type: Class
subclass of: Phylogenetic inference (method centric)
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.
has exact synonym: Phylogenetic tree construction (maximum likelihood and Bayesian methods)
has exact synonym: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
in subset: bio
in subset: operations
comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.

Phylogenetic inference (quartet methods)
type: Class
subclass of: Phylogenetic inference (method centric)
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.
has exact synonym: Phylogenetic tree construction (quartet methods)
has exact synonym: Phylogenetic tree generation (quartet methods)
in subset: bio
in subset: operations

Phylogenetic inference (AI methods)
type: Class
subclass of: Phylogenetic inference (method centric)
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.
has exact synonym: Phylogenetic tree construction (AI methods)
has exact synonym: Phylogenetic tree generation (AI methods)
in subset: bio
in subset: operations

DNA substitution modelling
type: Class
subclass of: Codon usage analysis
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has output
  some values from: DNA substitution model
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: beta12orEarlier
has definition: Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment.
has exact synonym: Nucleotide substitution modelling
in subset: bio
in subset: operations

Phylogenetic tree topology analysis
type: Class
subclass of: Phylogenetic analysis
Created in: beta12orEarlier
has definition: Analyse the shape (topology) of a phylogenetic tree.
has exact synonym: Phylogenetic tree analysis (shape)
in subset: bio
in subset: operations

Phylogenetic tree bootstrapping
type: Class
subclass of: Phylogenetic analysis
subclass of: Validation
Created in: beta12orEarlier
has definition: Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.
in subset: bio
in subset: operations

Gene tree construction
type: Class
subclass of: Phylogenetic inference
subclass of: Restriction
  on property: has output
  some values from: Gene report
subclass of: Restriction
  on property: has topic
  some values from: Phylogenomics
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Phylogenetic tree analysis (gene family prediction)
in subset: bio
in subset: operations
comment: 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.

Allele frequency distribution analysis
type: Class
subclass of: Phylogenetic analysis
Created in: beta12orEarlier
has definition: 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).
has exact synonym: Phylogenetic tree analysis (natural selection)
in subset: bio
in subset: operations
comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.

Consensus tree construction
type: Class
subclass of: Phylogenetic inference
subclass of: Phylogenetic tree comparison
Created in: beta12orEarlier
has definition: Compare two or more phylogenetic trees to produce a consensus tree.
has exact synonym: Phylogenetic tree construction (consensus)
has exact synonym: Phylogenetic tree generation (consensus)
in subset: bio
in subset: operations
comment: Methods typically test for topological similarity between trees using for example a congruence index.

Phylogenetic sub/super tree construction
type: Class
subclass of: Phylogenetic tree comparison
Created in: beta12orEarlier
has definition: Compare two or more phylogenetic trees to detect subtrees or supertrees.
has exact synonym: Phylogenetic sub/super tree detection
has narrow synonym: Subtree construction
has narrow synonym: Supertree construction
in subset: bio
in subset: operations

Phylogenetic tree distances calculation
type: Class
subclass of: Phylogenetic tree comparison
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree distances
Created in: beta12orEarlier
has definition: Compare two or more phylogenetic trees to calculate distances between trees.
in subset: bio
in subset: operations

Phylogenetic tree annotation
type: Class
subclass of: Annotation
Created in: beta12orEarlier
has definition: Annotate a phylogenetic tree with terms from a controlled vocabulary.
in subset: bio
in subset: operations

Immunogenicity prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Predict and optimise peptide ligands that elicit an immunological response.
in subset: obsolete
replaced by: Peptide immunogenicity prediction
deprecated: true

DNA vaccine design
type: Class
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has topic
  some values from: Immunology
Created in: beta12orEarlier
has definition: Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.
in subset: bio
in subset: operations

Sequence formatting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Reformat (a file or other report of) molecular sequence(s).
in subset: obsolete
replaced by: Data formatting
deprecated: true

Sequence alignment formatting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Reformat (a file or other report of) molecular sequence alignment(s).
in subset: obsolete
replaced by: Data formatting
deprecated: true

Codon usage table formatting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Reformat a codon usage table.
in subset: obsolete
replaced by: Data formatting
deprecated: true

Sequence visualisation
type: Class
subclass of: Visualisation
subclass of: Sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has output
  some values from: Sequence image
Created in: beta12orEarlier
has definition: Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown.
has exact synonym: Sequence rendering
has narrow synonym: Sequence alignment visualisation
in subset: bio
in subset: operations

Sequence alignment visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.15
Old parent: Thing
has definition: Visualise, format or print a molecular sequence alignment.
in subset: obsolete
replaced by: Sequence visualisation
deprecated: true

Sequence cluster visualisation
type: Class
subclass of: Visualisation
subclass of: Restriction
  on property: has input
  some values from: Sequence cluster
Created in: beta12orEarlier
has definition: Visualise, format or render sequence clusters.
has exact synonym: Sequence cluster rendering
in subset: bio
in subset: operations

Phylogenetic tree visualisation
type: Class
subclass of: Phylogenetic analysis
subclass of: Visualisation
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
Created in: beta12orEarlier
has definition: Render or visualise a phylogenetic tree.
has exact synonym: Phylogenetic tree rendering
in subset: bio
in subset: operations

RNA secondary structure visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.15
Old parent: Thing
has definition: Visualise RNA secondary structure, knots, pseudoknots etc.
in subset: obsolete
replaced by: Structure visualisation
deprecated: true

Protein secondary structure visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.15
Old parent: Thing
has definition: Render and visualise protein secondary structure.
in subset: obsolete
replaced by: Structure visualisation
deprecated: true

Structure visualisation
type: Class
subclass of: Visualisation
subclass of: Structure analysis
subclass of: Restriction
  on property: has input
  some values from: Structure
subclass of: Restriction
  on property: has output
  some values from: Structure image
Created in: beta12orEarlier
has definition: Visualise or render molecular 3D structure, for example a high-quality static picture or animation.
has exact synonym: Structure rendering
has narrow synonym: Protein secondary structure visualisation
has narrow synonym: RNA secondary structure visualisation
in subset: bio
in subset: operations
comment: This includes visualisation of protein secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure.

Expression data visualisation
type: Class
subclass of: Visualisation
subclass of: Expression analysis
subclass of: Restriction
  on property: has input
  some values from: Microarray hybridisation data
Created in: beta12orEarlier
has definition: Visualise microarray or other expression data.
has exact synonym: Expression data rendering
has narrow synonym: Gene expression data visualisation
has narrow synonym: Microarray data rendering
in subset: bio
in subset: operations

Protein interaction network visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Pathway or network visualisation
has definition: Identify and analyse networks of protein interactions.
in subset: obsolete
replaced by: Network visualisation
deprecated: true

Map drawing
type: Class
subclass of: Visualisation
subclass of: Restriction
  on property: has input
  some values from: Map
Created in: beta12orEarlier
has definition: Draw or visualise a DNA map.
has exact synonym: DNA map drawing
has exact synonym: Map rendering
in subset: bio
in subset: operations

Sequence motif rendering
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence visualisation
has definition: Render a sequence with motifs.
in subset: obsolete
deprecated: true

Restriction map drawing
type: Class
subclass of: Map drawing
subclass of: Restriction
  on property: has output
  some values from: Restriction map
Created in: beta12orEarlier
has definition: Draw or visualise restriction maps in DNA sequences.
in subset: bio
in subset: operations

DNA linear map rendering
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Map drawing
has definition: Draw a linear maps of DNA.
in subset: obsolete
deprecated: true

Plasmid map drawing
type: Class
subclass of: Map drawing
Created in: beta12orEarlier
has broad synonym: DNA circular map rendering
has definition: Draw a circular maps of DNA, for example a plasmid map.
in subset: bio
in subset: operations

Operon drawing
type: Class
subclass of: Map drawing
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Visualise operon structure etc.
has exact synonym: Operon rendering
in subset: bio
in subset: operations

Nucleic acid folding family identification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: RNA inverse folding
has definition: Identify folding families of related RNAs.
in subset: obsolete
deprecated: true

Nucleic acid folding energy calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.20
Old parent: Nucleic acid folding analysis
has definition: Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.
in subset: obsolete
replaced by: Nucleic acid folding analysis
deprecated: true

Annotation retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data retrieval
has definition: Retrieve existing annotation (or documentation), typically annotation on a database entity.
in subset: obsolete
comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
deprecated: true

Protein function prediction
type: Class
subclass of: Prediction and recognition
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: beta12orEarlier
has definition: Predict the biological or biochemical role of a protein, or other aspects of a protein function.
has exact synonym: Protein function analysis
has exact synonym: Protein functional analysis
in subset: bio
in subset: operations
comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.

Protein function comparison
type: Class
subclass of: Protein function prediction
subclass of: Protein comparison
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: beta12orEarlier
has definition: Compare the functional properties of two or more proteins.
in subset: bio
in subset: operations

Sequence submission
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data deposition
has definition: Submit a molecular sequence to a database.
in subset: obsolete
deprecated: true

Gene regulatory network analysis
type: Class
subclass of: Expression analysis
subclass of: Network analysis
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: Analyse a known network of gene regulation.
has narrow synonym: Gene regulatory network comparison
has narrow synonym: Gene regulatory network modelling
has narrow synonym: Regulatory network comparison
has narrow synonym: Regulatory network modelling
in subset: bio
in subset: operations

Data parsing
type: Class
subclass of: Data handling
Created in: beta12orEarlier
has db xref: WHATIF:UploadPDB
has definition: Parse, prepare or load a user-specified data file so that it is available for use.
has exact synonym: Data loading
has exact synonym: Loading
in subset: bio
in subset: operations

Sequence retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has definition: Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
in subset: obsolete
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
deprecated: true

Structure retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has db xref: WHATIF:DownloadPDB
has db xref: WHATIF:EchoPDB
has definition: Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.
in subset: obsolete
comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
deprecated: true

Surface rendering
type: Class
subclass of: Structure visualisation
subclass of: Molecular surface analysis
Created in: beta12orEarlier
has db xref: WHATIF:GetSurfaceDots
has definition: Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.
in subset: bio
in subset: operations
comment: A dot has three coordinates (x,y,z) and (typically) a color.

Protein atom surface calculation (accessible)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible surface') for each atom in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Waters are not considered.
deprecated: true

Protein atom surface calculation (accessible molecular)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Waters are not considered.
deprecated: true

Protein residue surface calculation (accessible)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible surface') for each residue in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
deprecated: true

Protein residue surface calculation (vacuum accessible)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
deprecated: true

Protein residue surface calculation (accessible molecular)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
deprecated: true

Protein residue surface calculation (vacuum molecular)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
deprecated: true

Protein surface calculation (accessible molecular)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole.
in subset: obsolete
replaced by: Molecular surface calculation
deprecated: true

Protein surface calculation (accessible)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility ('accessible surface') for a structure as a whole.
in subset: obsolete
replaced by: Molecular surface calculation
deprecated: true

Backbone torsion angle calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate for each residue in a protein structure all its backbone torsion angles.
in subset: obsolete
replaced by: Protein geometry calculation
deprecated: true

Full torsion angle calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate for each residue in a protein structure all its torsion angles.
in subset: obsolete
replaced by: Protein geometry calculation
deprecated: true

Cysteine torsion angle calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate for each cysteine (bridge) all its torsion angles.
in subset: obsolete
replaced by: Protein geometry calculation
deprecated: true

Tau angle calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: For each amino acid in a protein structure calculate the backbone angle tau.
in subset: obsolete
replaced by: Protein geometry calculation
comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
deprecated: true

Cysteine bridge detection
type: Class
subclass of: Protein cysteine and disulfide bond assignment
Created in: beta12orEarlier
has db xref: WHATIF:ShowCysteineBridge
has definition: Detect cysteine bridges (from coordinate data) in a protein structure.
in subset: bio
in subset: operations

Free cysteine detection
type: Class
subclass of: Protein cysteine and disulfide bond assignment
Created in: beta12orEarlier
has db xref: WHATIF:ShowCysteineFree
has definition: Detect free cysteines in a protein structure.
in subset: bio
in subset: operations
comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.

Metal-bound cysteine detection
type: Class
subclass of: Residue interaction calculation
subclass of: Protein cysteine and disulfide bond assignment
Created in: beta12orEarlier
has db xref: WHATIF:ShowCysteineMetal
has definition: Detect cysteines that are bound to metal in a protein structure.
in subset: bio
in subset: operations

Residue contact calculation (residue-nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate protein residue contacts with nucleic acids in a structure.
in subset: obsolete
replaced by: Residue distance calculation
deprecated: true

Protein-metal contact calculation
type: Class
subclass of: Residue interaction calculation
Created in: beta12orEarlier
has definition: Calculate protein residue contacts with metal in a structure.
has exact synonym: Residue-metal contact calculation
in subset: bio
in subset: operations

Residue contact calculation (residue-negative ion)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate ion contacts in a structure (all ions for all side chain atoms).
in subset: obsolete
replaced by: Residue distance calculation
deprecated: true

Residue bump detection
type: Class
subclass of: Protein structure validation
Created in: beta12orEarlier
has db xref: WHATIF:ShowBumps
has definition: 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.
in subset: bio
in subset: operations

Residue symmetry contact calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has db xref: WHATIF:SymmetryContact
has definition: Calculate the number of symmetry contacts made by residues in a protein structure.
in subset: obsolete
replaced by: Residue distance calculation
comment: A symmetry contact is a contact between two atoms in different asymmetric unit.
deprecated: true

Residue contact calculation (residue-ligand)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate contacts between residues and ligands in a protein structure.
in subset: obsolete
replaced by: Residue distance calculation
deprecated: true

Salt bridge calculation
type: Class
subclass of: Residue interaction calculation
Created in: beta12orEarlier
has db xref: WHATIF:HasSaltBridge
has db xref: WHATIF:HasSaltBridgePlus
has db xref: WHATIF:ShowSaltBridges
has db xref: WHATIF:ShowSaltBridgesH
has definition: Calculate (and possibly score) salt bridges in a protein structure.
in subset: bio
in subset: operations
comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.

Rotamer likelihood prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has db xref: WHATIF:ShowLikelyRotamers
has db xref: WHATIF:ShowLikelyRotamers100
has db xref: WHATIF:ShowLikelyRotamers200
has db xref: WHATIF:ShowLikelyRotamers300
has db xref: WHATIF:ShowLikelyRotamers400
has db xref: WHATIF:ShowLikelyRotamers500
has db xref: WHATIF:ShowLikelyRotamers600
has db xref: WHATIF:ShowLikelyRotamers700
has db xref: WHATIF:ShowLikelyRotamers800
has db xref: WHATIF:ShowLikelyRotamers900
has definition: Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.
in subset: obsolete
replaced by: Side chain modelling
comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
deprecated: true

Proline mutation value calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has db xref: WHATIF:ProlineMutationValue
has definition: 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.
in subset: obsolete
replaced by: Variant effect prediction
deprecated: true

Residue packing validation
type: Class
subclass of: Protein structure validation
Created in: beta12orEarlier
has db xref: WHATIF: PackingQuality
has definition: Identify poorly packed residues in protein structures.
in subset: bio
in subset: operations

Protein geometry validation
type: Class
subclass of: Protein structure validation
Created in: beta12orEarlier
has db xref: WHATIF: ImproperQualityMax
has db xref: WHATIF: ImproperQualitySum
has definition: 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.
has narrow synonym: Ramachandran plot validation
in subset: bio
in subset: operations

PDB file sequence retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has db xref: WHATIF: PDB_sequence
has definition: Extract a molecular sequence from a PDB file.
in subset: obsolete
replaced by: Data retrieval
deprecated: true

HET group detection
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify HET groups in PDB files.
in subset: obsolete
replaced by: Residue distance calculation
comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
deprecated: true

DSSP secondary structure assignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Protein secondary structure assignment
has definition: Determine for residue the DSSP determined secondary structure in three-state (HSC).
in subset: obsolete
deprecated: true

Structure formatting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has db xref: WHATIF: PDBasXML
has definition: Reformat (a file or other report of) tertiary structure data.
in subset: obsolete
replaced by: Data formatting
deprecated: true

Protein cysteine and disulfide bond assignment
type: Class
subclass of: Protein structure assignment
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
Created in: beta12orEarlier
has definition: Assign cysteine bonding state and disulfide bond partners in protein structures.
in subset: bio
in subset: operations

Residue validation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify poor quality amino acid positions in protein structures.
in subset: obsolete
replaced by: Protein structure validation
deprecated: true

Structure retrieval (water)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data retrieval
has db xref: WHATIF:MovedWaterPDB
has definition: Query a tertiary structure database and retrieve water molecules.
in subset: obsolete
deprecated: true

siRNA duplex prediction
type: Class
subclass of: trans-regulatory element prediction
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
Created in: beta12orEarlier
has definition: Identify or predict siRNA duplexes in RNA.
in subset: bio
in subset: operations

Sequence alignment refinement
type: Class
subclass of: Sequence alignment analysis
subclass of: Optimisation and refinement
Created in: beta12orEarlier
has definition: Refine an existing sequence alignment.
in subset: bio
in subset: operations

Listfile processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data handling
has definition: Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).
in subset: obsolete
deprecated: true

Sequence file editing
type: Class
subclass of: Sequence editing
subclass of: Sequence analysis
Created in: beta12orEarlier
has definition: 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.
in subset: bio
in subset: operations

Sequence alignment file processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data handling
has definition: Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.
in subset: obsolete
deprecated: true

Small molecule data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure analysis
has definition: Process (read and / or write) physicochemical property data for small molecules.
in subset: obsolete
deprecated: true

Data retrieval (ontology annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Search and retrieve documentation on a bioinformatics ontology.
in subset: obsolete
deprecated: true

Data retrieval (ontology concept)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Query an ontology and retrieve concepts or relations.
in subset: obsolete
deprecated: true

Representative sequence identification
type: Class
subclass of: Sequence comparison
Created in: beta12orEarlier
has definition: Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
in subset: bio
in subset: operations

Structure file processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Data handling
has definition: Perform basic (non-analytical) operations on a file of molecular tertiary structural data.
in subset: obsolete
deprecated: true

Data retrieval (sequence profile)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.
in subset: obsolete
comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
deprecated: true

Statistical calculation
type: Class
subclass of: Calculation
Created in: beta12orEarlier
has definition: Perform a statistical data operation of some type, e.g. calibration or validation.
has exact synonym: Significance testing
has exact synonym: Statistical analysis
has exact synonym: Statistical test
has exact synonym: Statistical testing
has narrow synonym: Expectation maximisation
has narrow synonym: Gibbs sampling
has narrow synonym: Hypothesis testing
has narrow synonym: Omnibus test
in subset: bio
in subset: operations

3D-1D scoring matrix generation
type: Class
subclass of: Protein property calculation
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: 3D-1D scoring matrix
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.
has exact synonym: 3D-1D scoring matrix construction
in subset: bio
in subset: operations
comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.

Transmembrane protein visualisation
type: Class
subclass of: Transmembrane protein analysis
subclass of: Structure visualisation
subclass of: Restriction
  on property: has output
  some values from: Protein structure image
Created in: beta12orEarlier
has definition: Visualise transmembrane proteins, typically the transmembrane regions within a sequence.
has exact synonym: Transmembrane protein rendering
in subset: bio
in subset: operations

Demonstration
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Operation
has definition: An operation performing purely illustrative (pedagogical) purposes.
in subset: obsolete
deprecated: true

Data retrieval (pathway or network)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Query a biological pathways database and retrieve annotation on one or more pathways.
in subset: obsolete
deprecated: true

Data retrieval (identifier)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Query a database and retrieve one or more data identifiers.
in subset: obsolete
deprecated: true

Nucleic acid density plotting
type: Class
subclass of: Sequence composition calculation
subclass of: Sequence visualisation
Created in: beta12orEarlier
has definition: Calculate a density plot (of base composition) for a nucleotide sequence.
in subset: bio
in subset: operations

Sequence analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
Created in: beta12orEarlier
has definition: Analyse one or more known molecular sequences.
has exact synonym: Sequence analysis (general)
in subset: bio
in subset: operations

Sequence motif analysis
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
has definition: Analyse molecular sequence motifs.
has exact synonym: Sequence motif processing
in subset: bio
in subset: operations

Protein interaction data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Protein-protein interaction analysis
has definition: Process (read and / or write) protein interaction data.
in subset: obsolete
deprecated: true

Protein structure analysis
type: Class
subclass of: Structure analysis
subclass of: Restriction
  on property: has input
  some values from: Protein structure
subclass of: Restriction
  on property: has topic
  some values from: Protein structure analysis
Created in: beta12orEarlier
has definition: Analyse protein structural data.
has exact synonym: Structure analysis (protein)
in subset: bio
in subset: operations

Annotation processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data retrieval
has definition: Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.
in subset: obsolete
deprecated: true

Sequence feature analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence feature detection
has definition: Analyse features in molecular sequences.
in subset: obsolete
deprecated: true

Data handling
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Database management
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: 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.
has exact synonym: File handling
has exact synonym: File processing
has exact synonym: Report handling
has exact synonym: Utility operation
has narrow synonym: Processing
in subset: bio
in subset: operations

Gene expression analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Analyse gene expression and regulation data.
in subset: obsolete
deprecated: true

Structural profile processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: 3D profile generation
has definition: Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.
in subset: obsolete
deprecated: true

Data index processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Indexing
has definition: Process (read and / or write) an index of (typically a file of) biological data.
in subset: obsolete
deprecated: true

Sequence profile processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence profile generation
has definition: Process (read and / or write) some type of sequence profile.
in subset: obsolete
deprecated: true

Protein function analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.22
Old parent: Data analysis
has definition: Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.
in subset: obsolete
replaced by: Protein function prediction
deprecated: true

Protein folding analysis
type: Class
subclass of: Protein structure analysis
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has output
  some values from: Protein structure report
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Protein folding modelling
has narrow synonym: Protein folding simulation
has narrow synonym: Protein folding site prediction
in subset: bio
in subset: operations

Protein secondary structure analysis
type: Class
subclass of: Protein structure analysis
subclass of: Restriction
  on property: has output
  some values from: Protein secondary structure
subclass of: Restriction
  on property: has topic
  some values from: Protein structure analysis
Created in: beta12orEarlier
has definition: Analyse protein secondary structure data.
has exact synonym: Secondary structure analysis (protein)
in subset: bio
in subset: operations

Physicochemical property data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data analysis
has definition: Process (read and / or write) data on the physicochemical property of a molecule.
in subset: obsolete
deprecated: true

Primer and probe design
type: Class
subclass of: Prediction and recognition
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has topic
  some values from: Probes and primers
Created in: beta12orEarlier
has definition: Predict oligonucleotide primers or probes.
has exact synonym: Primer and probe prediction
in subset: bio
in subset: operations

Operation (typed)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Process (read and / or write) data of a specific type, for example applying analytical methods.
in subset: obsolete
replaced by: Data analysis
deprecated: true

Database search
type: Class
subclass of: Query and retrieval
subclass of: Restriction
  on property: has output
  some values from: Database search results
Created in: beta12orEarlier
has definition: Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.
has exact synonym: Search
in subset: bio
in subset: operations
comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.

Data retrieval
type: Class
subclass of: Query and retrieval
subclass of: Information retrieval
subclass of: Restriction
  on property: has input
  some values from: Identifier
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Data extraction
has exact synonym: Retrieval
has narrow synonym: Data retrieval (metadata)
has narrow synonym: Metadata retrieval
in subset: bio
in subset: operations

Prediction and recognition
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Predict, recognise, detect or identify some properties of a biomolecule.
has narrow synonym: Detection
has narrow synonym: Prediction
has narrow synonym: Recognition
in subset: bio
in subset: operations

Comparison
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Compare two or more things to identify similarities.
in subset: bio
in subset: operations

Optimisation and refinement
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Refine or optimise some data model.
in subset: bio
in subset: operations

Modelling and simulation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Molecular modelling
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
has narrow synonym: Mathematical modelling
in subset: bio
in subset: operations

Data handling
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: Perform basic operations on some data or a database.
in subset: obsolete
replaced by: Data handling
deprecated: true

Validation
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Validate some data.
has narrow synonym: Quality control
in subset: bio
in subset: operations

Mapping
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.
has exact synonym: Cartography
in subset: bio
in subset: operations

Design
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Design a biological entity (typically a molecular sequence or structure) with specific properties.
in subset: bio
in subset: operations

Microarray data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) microarray data.
in subset: obsolete
deprecated: true

Codon usage table processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Codon usage analysis
consider: Codon usage table generation
consider: Codon usage table comparison
has definition: Process (read and / or write) a codon usage table.
in subset: obsolete
deprecated: true

Data retrieval (codon usage table)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve a codon usage table and / or associated annotation.
in subset: obsolete
deprecated: true

Gene expression profile processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Expression analysis
has definition: Process (read and / or write) a gene expression profile.
in subset: obsolete
deprecated: true

Gene-set enrichment analysis
type: Class
subclass of: Expression analysis
subclass of: Enrichment analysis
subclass of: Restriction
  on property: has output
  some values from: GO-term enrichment data
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: beta12orEarlier
comment: Analyse gene expression patterns to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.
comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on.
has broad synonym: Gene set testing
has definition: 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.
has exact synonym: Functional enrichment analysis
has exact synonym: GSEA
has exact synonym: Gene-set over-represenation analysis
has narrow synonym: Gene set analysis
has related synonym: GO-term enrichment
has related synonym: Gene Ontology concept enrichment
has related synonym: Gene Ontology term enrichment
in subset: bio
in subset: operations
comment: "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.
comment: 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 regulatory network prediction
type: Class
subclass of: Prediction and recognition
subclass of: Expression analysis
subclass of: Network analysis
Created in: beta12orEarlier
has definition: Predict a network of gene regulation.
in subset: bio
in subset: operations

Pathway or network processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
consider: Network analysis
consider: Pathway analysis
has definition: Generate, analyse or handle a biological pathway or network.
in subset: obsolete
deprecated: true

RNA secondary structure analysis
type: Class
subclass of: Nucleic acid structure analysis
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: beta12orEarlier
has definition: Process (read and / or write) RNA secondary structure data.
in subset: bio
in subset: operations

Structure processing (RNA)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: Process (read and / or write) RNA tertiary structure data.
in subset: obsolete
replaced by: Structure analysis
deprecated: true

RNA structure prediction
type: Class
subclass of: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: RNA structure
Created in: beta12orEarlier
has definition: Predict RNA tertiary structure.
in subset: bio
in subset: operations

DNA structure prediction
type: Class
subclass of: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: DNA structure
Created in: beta12orEarlier
has definition: Predict DNA tertiary structure.
in subset: bio
in subset: operations

Phylogenetic tree processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Generate, process or analyse phylogenetic tree or trees.
in subset: obsolete
replaced by: Phylogenetic analysis
deprecated: true

Protein secondary structure processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Protein secondary structure analysis
has definition: Process (read and / or write) protein secondary structure data.
in subset: obsolete
deprecated: true

Protein interaction network processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Protein interaction network analysis
has definition: Process (read and / or write) a network of protein interactions.
in subset: obsolete
deprecated: true

Sequence processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence analysis
has definition: Process (read and / or write) one or more molecular sequences and associated annotation.
in subset: obsolete
deprecated: true

Sequence processing (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
has definition: Process (read and / or write) a protein sequence and associated annotation.
in subset: obsolete
replaced by: Protein sequence analysis
deprecated: true

Sequence processing (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Nucleic acid sequence analysis
has definition: Process (read and / or write) a nucleotide sequence and associated annotation.
in subset: obsolete
deprecated: true

Sequence comparison
type: Class
subclass of: Sequence analysis
subclass of: Comparison
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has output
  some values from: Sequence report
Created in: beta12orEarlier
has definition: Compare two or more molecular sequences.
in subset: bio
in subset: operations

Sequence cluster processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence clustering
has definition: Process (read and / or write) a sequence cluster.
in subset: obsolete
deprecated: true

Feature table processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence analysis
has definition: Process (read and / or write) a sequence feature table.
in subset: obsolete
deprecated: true

Gene prediction
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Gene report
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
comment: Includes methods that predict whole gene structure using a combination of multiple methods to achieve better predictions.
has definition: Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc.
has exact synonym: Gene calling
has exact synonym: Gene finding
has narrow synonym: Whole gene prediction
in subset: bio
in subset: operations
comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.

GPCR classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Thing
has definition: Classify G-protein coupled receptors (GPCRs) into families and subfamilies.
in subset: obsolete
replaced by: Sequence classification
deprecated: true

GPCR coupling selectivity prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Not sustainable to have protein type-specific concepts.
Obsolete since: 1.19
Old parent: GPCR analysis
consider: Transmembrane protein prediction
has definition: Predict G-protein coupled receptor (GPCR) coupling selectivity.
in subset: obsolete
deprecated: true

Structure processing (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
has definition: Process (read and / or write) a protein tertiary structure.
in subset: obsolete
replaced by: Protein structure analysis
deprecated: true

Protein atom surface calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility for each atom in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
comment: Waters are not considered.
deprecated: true

Protein residue surface calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility for each residue in a structure.
in subset: obsolete
replaced by: Molecular surface calculation
deprecated: true

Protein surface calculation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate the solvent accessibility of a structure as a whole.
in subset: obsolete
replaced by: Molecular surface calculation
deprecated: true

Sequence alignment processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence alignment
has definition: Process (read and / or write) a molecular sequence alignment.
in subset: obsolete
deprecated: true

Protein-protein binding site prediction
type: Class
subclass of: Binding site prediction
subclass of: Restriction
  on property: has output
  some values from: Protein interaction data
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Identify or predict protein-protein binding sites.
has exact synonym: Protein-protein binding site detection
in subset: bio
in subset: operations

Structure processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Structure analysis
has definition: Process (read and / or write) a molecular tertiary structure.
in subset: obsolete
deprecated: true

Map annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Genome annotation
has definition: Annotate a DNA map of some type with terms from a controlled vocabulary.
in subset: obsolete
deprecated: true

Data retrieval (protein annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on a protein.
in subset: obsolete
deprecated: true

Data retrieval (phylogenetic tree)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve a phylogenetic tree from a data resource.
in subset: obsolete
deprecated: true

Data retrieval (protein interaction annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on a protein interaction.
in subset: obsolete
deprecated: true

Data retrieval (protein family annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on a protein family.
in subset: obsolete
deprecated: true

Data retrieval (RNA family annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on an RNA family.
in subset: obsolete
deprecated: true

Data retrieval (gene annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on a specific gene.
in subset: obsolete
deprecated: true

Data retrieval (genotype and phenotype annotation)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Data retrieval
has definition: Retrieve information on a specific genotype or phenotype.
in subset: obsolete
deprecated: true

Protein architecture comparison
type: Class
subclass of: Protein architecture analysis
subclass of: Protein comparison
Created in: beta12orEarlier
has definition: Compare the architecture of two or more protein structures.
in subset: bio
in subset: operations

Protein architecture recognition
type: Class
subclass of: Protein architecture analysis
subclass of: Prediction and recognition
subclass of: Structure classification
Created in: beta12orEarlier
has definition: Identify the architecture of a protein structure.
in subset: bio
in subset: operations
comment: 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.

Molecular dynamics
type: Class
subclass of: Prediction and recognition
subclass of: Modelling and simulation
subclass of: Structure analysis
subclass of: Restriction
  on property: has output
  some values from: Structure
subclass of: Restriction
  on property: has topic
  some values from: Structure prediction
subclass of: Restriction
  on property: has topic
  some values from: Molecular dynamics
Created in: beta12orEarlier
has definition: The simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
has exact synonym: Molecular dynamics simulation
has narrow synonym: Protein dynamics
in subset: bio
in subset: operations

Nucleic acid sequence analysis
type: Class
subclass of: Sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
Created in: beta12orEarlier
has definition: Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).
has exact synonym: Sequence analysis (nucleic acid)
has narrow synonym: Nucleic acid sequence alignment analysis
has narrow synonym: Sequence alignment analysis (nucleic acid)
in subset: bio
in subset: operations

Protein sequence analysis
type: Class
subclass of: Sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Protein sequence
subclass of: Restriction
  on property: has topic
  some values from: Proteins
Created in: beta12orEarlier
has definition: Analyse a protein sequence (using methods that are only applicable to protein sequences).
has exact synonym: Sequence analysis (protein)
has narrow synonym: Protein sequence alignment analysis
has narrow synonym: Sequence alignment analysis (protein)
in subset: bio
in subset: operations

Structure analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Analyse known molecular tertiary structures.
in subset: bio
in subset: operations

Nucleic acid structure analysis
type: Class
subclass of: Structure analysis
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid structure
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: beta12orEarlier
has definition: Analyse nucleic acid tertiary structural data.
in subset: bio
in subset: operations

Secondary structure processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Structure analysis
has definition: Process (read and / or write) a molecular secondary structure.
in subset: obsolete
deprecated: true

Structure comparison
type: Class
subclass of: Comparison
subclass of: Structure analysis
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Compare two or more molecular tertiary structures.
in subset: bio
in subset: operations

Helical wheel drawing
type: Class
subclass of: Structure visualisation
subclass of: Restriction
  on property: has output
  some values from: Helical wheel
Created in: beta12orEarlier
has definition: Render a helical wheel representation of protein secondary structure.
has exact synonym: Helical wheel rendering
in subset: bio
in subset: operations

Topology diagram drawing
type: Class
subclass of: Structure visualisation
subclass of: Restriction
  on property: has output
  some values from: Protein structure image
Created in: beta12orEarlier
has definition: Render a topology diagram of protein secondary structure.
has exact synonym: Topology diagram rendering
in subset: bio
in subset: operations

Protein structure comparison
type: Class
subclass of: Protein structure analysis
subclass of: Structure comparison
subclass of: Protein comparison
subclass of: Restriction
  on property: has input
  some values from: Protein structure
Created in: beta12orEarlier
has definition: Compare protein tertiary structures.
has exact synonym: Structure comparison (protein)
in subset: bio
in subset: operations
comment: Methods might identify structural neighbors, find structural similarities or define a structural core.

Protein secondary structure comparison
type: Class
subclass of: Protein secondary structure analysis
subclass of: Protein comparison
Created in: beta12orEarlier
has definition: Compare protein secondary structures.
has exact synonym: Protein secondary structure
has exact synonym: Secondary structure comparison (protein)
has narrow synonym: Protein secondary structure alignment
in subset: bio
in subset: operations

Subcellular localisation prediction
type: Class
subclass of: Protein function prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein targeting and localisation
Created in: beta12orEarlier
has definition: Predict the subcellular localisation of a protein sequence.
has exact synonym: Protein cellular localization prediction
has exact synonym: Protein subcellular localisation prediction
has exact synonym: Protein targeting prediction
in subset: bio
in subset: operations
comment: The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.

Residue contact calculation (residue-residue)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Calculate contacts between residues in a protein structure.
in subset: obsolete
replaced by: Residue distance calculation
deprecated: true

Hydrogen bond calculation (inter-residue)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Identify potential hydrogen bonds between amino acid residues.
in subset: obsolete
replaced by: Hydrogen bond calculation
deprecated: true

Protein interaction prediction
type: Class
subclass of: Protein-protein interaction analysis
subclass of: Restriction
  on property: has output
  some values from: Protein interaction data
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Predict the interactions of proteins with other proteins.
has exact synonym: Protein-protein interaction detection
has narrow synonym: Protein-protein binding prediction
has narrow synonym: Protein-protein interaction prediction
in subset: bio
in subset: operations

Codon usage data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Codon usage analysis
has definition: Process (read and / or write) codon usage data.
in subset: obsolete
deprecated: true

Expression analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
comment: Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function.
has definition: 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.
has exact synonym: Expression data analysis
has narrow synonym: Gene expression analysis
has narrow synonym: Gene expression data analysis
has narrow synonym: Gene expression regulation analysis
has narrow synonym: Metagenomic inference
has narrow synonym: Microarray data analysis
has narrow synonym: Protein expression analysis
in subset: bio
in subset: operations

Gene regulatory network processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
has definition: Process (read and / or write) a network of gene regulation.
in subset: obsolete
replaced by: Gene regulatory network analysis
deprecated: true

Pathway or network analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
Obsolete since: 1.24
Old parent: Thing
consider: Network analysis
consider: Pathway analysis
has definition: Generate, process or analyse a biological pathway or network.
in subset: obsolete
deprecated: true

Sequencing-based expression profile data analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.
in subset: obsolete
deprecated: true

Splicing analysis
type: Class
subclass of: Prediction and recognition
subclass of: Modelling and simulation
subclass of: Gene prediction
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Predict, analyse, characterize or model splice sites, splicing events and so on, typically by comparing multiple nucleic acid sequences.
has exact synonym: Splicing model analysis
in subset: bio
in subset: operations

Microarray raw data analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Expression analysis
has definition: Analyse raw microarray data.
in subset: obsolete
deprecated: true

Nucleic acid analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Data analysis
consider: Nucleic acid sequence analysis
consider: Nucleic acid structure analysis
has definition: Process (read and / or write) nucleic acid sequence or structural data.
in subset: obsolete
deprecated: true

Protein analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Data analysis
consider: Protein structure analysis
consider: Protein sequence analysis
has definition: Process (read and / or write) protein sequence or structural data.
in subset: obsolete
deprecated: true

Sequence data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
has definition: Process (read and / or write) molecular sequence data.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Structural data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Structure analysis
has definition: Process (read and / or write) molecular structural data.
in subset: obsolete
deprecated: true

Text processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Text mining
consider: Text annotation
has definition: Process (read and / or write) text.
in subset: obsolete
deprecated: true

Protein sequence alignment analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Sequence alignment analysis
Old parent: Protein analysis
Old parent: Prediction and recognition (protein)
has definition: Analyse a protein sequence alignment, typically to detect features or make predictions.
in subset: obsolete
replaced by: Protein sequence analysis
deprecated: true

Nucleic acid sequence alignment analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Sequence alignment analysis
Old parent: Nucleic acid analysis
Old parent: Prediction and recognition (nucleic acid)
has definition: Analyse a protein sequence alignment, typically to detect features or make predictions.
in subset: obsolete
replaced by: Nucleic acid sequence analysis
deprecated: true

Nucleic acid sequence comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Sequence comparison
Old parent: Nucleic acid sequence analysis
Old parent: Nucleic acid comparison
has definition: Compare two or more nucleic acid sequences.
in subset: obsolete
replaced by: Sequence comparison
deprecated: true

Protein sequence comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Sequence comparison
has definition: Compare two or more protein sequences.
in subset: obsolete
replaced by: Sequence comparison
deprecated: true

DNA back-translation
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
Created in: beta12orEarlier
has definition: Back-translate a protein sequence into DNA.
in subset: bio
in subset: operations

Sequence editing (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Edit or change a nucleic acid sequence, either randomly or specifically.
in subset: obsolete
replaced by: Sequence editing
deprecated: true

Sequence editing (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Edit or change a protein sequence, either randomly or specifically.
in subset: obsolete
replaced by: Sequence editing
deprecated: true

Sequence generation (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.22
Old parent: Sequence generation
has definition: Generate a nucleic acid sequence by some means.
in subset: obsolete
replaced by: Sequence generation
deprecated: true

Sequence generation (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.22
Old parent: Sequence generation
has definition: Generate a protein sequence by some means.
in subset: obsolete
replaced by: Sequence generation
deprecated: true

Nucleic acid sequence visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Visualise, format or render a nucleic acid sequence.
in subset: obsolete
replaced by: Sequence visualisation
comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
deprecated: true

Protein sequence visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Visualise, format or render a protein sequence.
in subset: obsolete
replaced by: Sequence visualisation
comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
deprecated: true

Nucleic acid structure comparison
type: Class
subclass of: Nucleic acid structure analysis
subclass of: Structure comparison
subclass of: Nucleic acid comparison
Created in: beta12orEarlier
has definition: Compare nucleic acid tertiary structures.
has exact synonym: Structure comparison (nucleic acid)
in subset: bio
in subset: operations

Structure processing (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
has definition: Process (read and / or write) nucleic acid tertiary structure data.
in subset: obsolete
consider: Nucleic acid structure analysis
deprecated: true

DNA mapping
type: Class
subclass of: Mapping
subclass of: Restriction
  on property: has output
  some values from: Map
subclass of: Restriction
  on property: has topic
  some values from: Mapping
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
Created in: beta12orEarlier
has definition: Generate a map of a DNA sequence annotated with positional or non-positional features of some type.
in subset: bio
in subset: operations

Map data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: DNA mapping
has definition: Process (read and / or write) a DNA map of some type.
in subset: obsolete
deprecated: true

Protein hydropathy calculation
type: Class
subclass of: Protein property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein hydropathy data
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
Created in: beta12orEarlier
has definition: Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).
in subset: bio
in subset: operations

Binding site prediction
type: Class
subclass of: Protein function prediction
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.
has exact synonym: Protein binding site detection
has exact synonym: Protein binding site prediction
in subset: bio
in subset: operations

Structure clustering
type: Class
subclass of: Clustering
Created in: beta12orEarlier
has definition: Build clusters of similar structures, typically using scores from structural alignment methods.
has exact synonym: Structural clustering
in subset: bio
in subset: operations

Sequence tagged site (STS) mapping
type: Class
subclass of: Physical mapping
subclass of: Restriction
  on property: has output
  some values from: Sequence map
Created in: beta12orEarlier
has definition: Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
has exact synonym: Sequence mapping
in subset: bio
in subset: operations
comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.

Alignment
type: Class
subclass of: Operation
subclass of: Generation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.
has exact synonym: Alignment construction
has exact synonym: Alignment generation
in subset: bio
in subset: operations

Protein fragment weight comparison
type: Class
subclass of: Protein molecular weight calculation
subclass of: Protein property comparison
Created in: beta12orEarlier
has definition: Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification.
has exact synonym: PMF
has exact synonym: Peptide mass fingerprinting
has exact synonym: Protein fingerprinting
in subset: bio
in subset: operations

Protein property comparison
type: Class
subclass of: Protein comparison
subclass of: Restriction
  on property: has output
  some values from: Protein property
Created in: beta12orEarlier
has definition: Compare the physicochemical properties of two or more proteins (or reference data).
in subset: bio
in subset: operations

Secondary structure comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Comparison
consider: Protein structure comparison
consider: Nucleic acid structure comparison
has definition: Compare two or more molecular secondary structures.
in subset: obsolete
deprecated: true

Hopp and Woods plotting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: Generate a Hopp and Woods plot of antigenicity of a protein.
in subset: obsolete
replaced by: Peptide immunogenicity prediction
deprecated: true

Cluster textual view generation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Visualisation
has definition: Generate a view of clustered quantitative data, annotated with textual information.
in subset: obsolete
replaced by: Dendrogram visualisation
deprecated: true

Clustering profile plotting
type: Class
subclass of: Expression data visualisation
Created in: beta12orEarlier
comment: 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.
has definition: Visualise clustered quantitative data as set of different profiles, where each profile is plotted versus different entities or samples on the X-axis.
has exact synonym: Clustered quantitative data plotting
has exact synonym: Clustered quantitative data rendering
has exact synonym: Wave graph plotting
has narrow synonym: Microarray cluster temporal graph rendering
has narrow synonym: Microarray wave graph plotting
has narrow synonym: Microarray wave graph rendering
in subset: bio
in subset: operations

Dendrograph plotting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Expression data visualisation
has definition: Generate a dendrograph of raw, preprocessed or clustered expression (e.g. microarray) data.
in subset: obsolete
replaced by: Dendrogram visualisation
deprecated: true

Proximity map plotting
type: Class
subclass of: Expression data visualisation
Created in: beta12orEarlier
has definition: Generate a plot of distances (distance or correlation matrix) between expression values.
has exact synonym: Distance map rendering
has exact synonym: Distance matrix plotting
has exact synonym: Distance matrix rendering
has exact synonym: Proximity map rendering
has narrow synonym: Correlation matrix plotting
has narrow synonym: Correlation matrix rendering
has narrow synonym: Microarray distance map rendering
has narrow synonym: Microarray proximity map plotting
has narrow synonym: Microarray proximity map rendering
in subset: bio
in subset: operations

Dendrogram visualisation
type: Class
subclass of: Expression data visualisation
Created in: beta12orEarlier
has definition: Visualise clustered expression data using a tree diagram.
has exact synonym: Dendrogram plotting
has exact synonym: Dendrograph plotting
has exact synonym: Dendrograph visualisation
has exact synonym: Expression data tree or dendrogram rendering
has exact synonym: Expression data tree visualisation
has narrow synonym: Microarray 2-way dendrogram rendering
has narrow synonym: Microarray checks view rendering
has narrow synonym: Microarray matrix tree plot rendering
has narrow synonym: Microarray tree or dendrogram rendering
in subset: bio
in subset: operations

Principal component visualisation
type: Class
subclass of: Visualisation
Created in: beta12orEarlier
comment: Examples for visualization are the distribution of variance over the components, loading and score plots.
has definition: 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.
has exact synonym: PCA plotting
has exact synonym: Principal component plotting
has narrow synonym: ED visualization
has narrow synonym: Essential Dynamics visualization
has narrow synonym: Microarray principal component plotting
has narrow synonym: Microarray principal component rendering
has narrow synonym: PCA visualization
has narrow synonym: Principal modes visualization
in subset: bio
in subset: operations
comment: 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.

Scatter plot plotting
type: Class
subclass of: Visualisation
Created in: beta12orEarlier
comment: Comparison of two sets of quantitative data such as two samples of gene expression values.
has definition: Render a graph in which the values of two variables are plotted along two axes; the pattern of the points reveals any correlation.
has exact synonym: Scatter chart plotting
has narrow synonym: Microarray scatter plot plotting
has narrow synonym: Microarray scatter plot rendering
in subset: bio
in subset: operations

Whole microarray graph plotting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.18
Old parent: Expression data visualisation
has definition: Visualise gene expression data where each band (or line graph) corresponds to a sample.
in subset: obsolete
replaced by: Expression data visualisation
deprecated: true

Treemap visualisation
type: Class
subclass of: Expression data visualisation
Created in: beta12orEarlier
has definition: Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.
has exact synonym: Expression data tree-map rendering
has exact synonym: Treemapping
has narrow synonym: Microarray tree-map rendering
in subset: bio
in subset: operations

Box-Whisker plot plotting
type: Class
subclass of: Visualisation
Created in: beta12orEarlier
comment: 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.
has definition: Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles.
has exact synonym: Box plot plotting
has narrow synonym: Microarray Box-Whisker plot plotting
in subset: bio
in subset: operations

Physical mapping
type: Class
subclass of: DNA mapping
subclass of: Restriction
  on property: has output
  some values from: Physical map
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Physical cartography
in subset: bio
in subset: operations

Data analysis
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Apply analytical methods to existing data of a specific type.
in subset: bio
in subset: operations
comment: This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling').

Alignment analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
consider: Alignment
has definition: Process or analyse an alignment of molecular sequences or structures.
in subset: obsolete
deprecated: true

Article analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.16
Old parent: Thing
consider: Text mining
consider: Text annotation
has definition: Analyse a body of scientific text (typically a full text article from a scientific journal).
in subset: obsolete
deprecated: true

Molecular interaction analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein-protein interaction analysis
has definition: Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.
in subset: obsolete
deprecated: true

Protein-protein interaction analysis
type: Class
subclass of: Protein function prediction
subclass of: Restriction
  on property: has output
  some values from: Protein interaction data
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
comment: 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.
has definition: Analyse the interactions of proteins with other proteins.
has exact synonym: Protein interaction analysis
has narrow synonym: Protein interaction raw data analysis
has narrow synonym: Protein interaction simulation
in subset: bio
in subset: operations

Residue distance calculation
type: Class
subclass of: Residue interaction calculation
Created in: beta12orEarlier
has db xref: WHATIF: HETGroupNames
has db xref: WHATIF:HasMetalContacts
has db xref: WHATIF:HasMetalContactsPlus
has db xref: WHATIF:HasNegativeIonContacts
has db xref: WHATIF:HasNegativeIonContactsPlus
has db xref: WHATIF:HasNucleicContacts
has db xref: WHATIF:ShowDrugContacts
has db xref: WHATIF:ShowDrugContactsShort
has db xref: WHATIF:ShowLigandContacts
has db xref: WHATIF:ShowProteiNucleicContacts
has definition: Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations.
has narrow synonym: HET group detection
has narrow synonym: Residue contact calculation (residue-ligand)
has narrow synonym: Residue contact calculation (residue-metal)
has narrow synonym: Residue contact calculation (residue-negative ion)
has narrow synonym: Residue contact calculation (residue-nucleic acid)
has narrow synonym: WHATIF:SymmetryContact
in subset: bio
in subset: operations
comment: 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.

Alignment processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Sequence alignment
consider: Structure alignment
has definition: Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.
in subset: obsolete
deprecated: true

Structure alignment processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.6
Old parent: Thing
consider: Structure alignment
has definition: Process (read and / or write) a molecular tertiary (3D) structure alignment.
in subset: obsolete
deprecated: true

Codon usage bias calculation
type: Class
subclass of: Codon usage analysis
subclass of: Restriction
  on property: has output
  some values from: Codon usage bias
Created in: beta12orEarlier
has definition: Calculate codon usage bias, e.g. generate a codon usage bias plot.
has narrow synonym: Codon usage bias plotting
in subset: bio
in subset: operations

Codon usage bias plotting
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.22
Old parent: Codon usage bias calculation
has definition: Generate a codon usage bias plot.
in subset: obsolete
replaced by: Codon usage bias calculation
deprecated: true

Codon usage fraction calculation
type: Class
subclass of: Codon usage analysis
subclass of: Restriction
  on property: has output
  some values from: Codon usage fraction difference
Created in: beta12orEarlier
has definition: Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.
in subset: bio
in subset: operations

Classification
type: Class
subclass of: Operation
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.
in subset: bio
in subset: operations

Molecular interaction data processing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Protein-protein interaction analysis
has definition: Process (read and / or write) molecular interaction data.
in subset: obsolete
deprecated: true

Sequence classification
type: Class
subclass of: Sequence analysis
subclass of: Classification
Created in: beta12orEarlier
has definition: Assign molecular sequence(s) to a group or category.
in subset: bio
in subset: operations

Structure classification
type: Class
subclass of: Structure analysis
subclass of: Classification
Created in: beta12orEarlier
has definition: Assign molecular structure(s) to a group or category.
in subset: bio
in subset: operations

Protein comparison
type: Class
subclass of: Comparison
Created in: beta12orEarlier
has definition: Compare two or more proteins (or some aspect) to identify similarities.
in subset: bio
in subset: operations

Nucleic acid comparison
type: Class
subclass of: Comparison
Created in: beta12orEarlier
has definition: Compare two or more nucleic acids to identify similarities.
in subset: bio
in subset: operations

Prediction and recognition (protein)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Prediction and recognition
has definition: Predict, recognise, detect or identify some properties of proteins.
in subset: obsolete
replaced by: Prediction and recognition
deprecated: true

Prediction and recognition (nucleic acid)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.19
Old parent: Prediction and recognition
has definition: Predict, recognise, detect or identify some properties of nucleic acids.
in subset: obsolete
replaced by: Prediction and recognition
deprecated: true

Structure editing
type: Class
subclass of: Data editing
subclass of: Restriction
  on property: has input
  some values from: Structure
Created in: beta13
has definition: Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically.
in subset: bio
in subset: operations

Sequence alignment editing
type: Class
subclass of: Data editing
Created in: beta13
has definition: Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.
in subset: bio
in subset: operations

Pathway or network visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta13
deprecation_comment: Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
Obsolete since: 1.24
Old parent: Pathway or network analysis
consider: Network visualisation
consider: Pathway visualisation
has definition: Render (visualise) a biological pathway or network.
in subset: obsolete
deprecated: true

Protein function prediction (from sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.6
Old parent: Thing
consider: Protein function prediction
has definition: Predict general (non-positional) functional properties of a protein from analysing its sequence.
in subset: obsolete
comment: For functional properties that are positional, use 'Protein site detection' instead.
deprecated: true

Protein sequence feature detection
type: Class
subclass of: DeprecatedClass
Created in: beta13
deprecation_comment: (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").
Obsolete since: 1.17
Old parent: Sequence feature detection
Old parent: Protein sequence analysis
Old parent: Protein feature detection
has definition: Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.
in subset: obsolete
replaced by: Protein feature detection
deprecated: true

Protein property calculation (from sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.18
Old parent: Protein property calculation
Old parent: Protein sequence analysis
has definition: Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.
in subset: obsolete
replaced by: Protein property calculation
deprecated: true

Protein feature prediction (from structure)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.6
Old parent: Thing
consider: Protein feature detection
has definition: Predict, recognise and identify positional features in proteins from analysing protein structure.
in subset: obsolete
deprecated: true

Protein feature detection
type: Class
subclass of: Prediction and recognition
subclass of: Protein sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Protein features
subclass of: Restriction
  on property: has topic
  some values from: Proteins
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta13
has definition: Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.
has exact synonym: Protein feature prediction
has exact synonym: Protein feature recognition
has narrow synonym: Protein secondary database search
has narrow synonym: Protein site detection
has narrow synonym: Protein site prediction
has narrow synonym: Protein site recognition
has narrow synonym: Sequence feature detection (protein)
has narrow synonym: Sequence profile database search
in subset: bio
in subset: operations
comment: 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.

Database search (by sequence)
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.6
Old parent: Thing
consider: Database search
has definition: Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.
in subset: obsolete
deprecated: true

Protein interaction network prediction
type: Class
subclass of: Protein-protein interaction analysis
subclass of: Network analysis
Created in: beta13
has definition: Predict a network of protein interactions.
in subset: bio
in subset: operations

Nucleic acid design
type: Class
subclass of: Design
subclass of: Nucleic acid sequence analysis
Created in: beta13
has definition: Design (or predict) nucleic acid sequences with specific chemical or physical properties.
has narrow synonym: Gene design
in subset: bio
in subset: operations

Data editing
type: Class
subclass of: Data handling
Created in: beta13
has definition: Edit a data entity, either randomly or specifically.
in subset: bio
in subset: operations

Sequence assembly validation
type: Class
subclass of: Validation
subclass of: Sequencing quality control
subclass of: Restriction
  on property: has input
  some values from: Sequence assembly
subclass of: Restriction
  on property: has output
  some values from: Sequence assembly report
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
Created in: 1.1
has definition: Evaluate a DNA sequence assembly, typically for purposes of quality control.
has exact synonym: Assembly QC
has exact synonym: Assembly quality evaluation
has exact synonym: Sequence assembly QC
has exact synonym: Sequence assembly quality evaluation
in subset: bio
in subset: operations

Genome alignment
type: Class
subclass of: Sequence alignment
subclass of: Genome analysis
Created in: 1.1
has definition: Align two or more (tpyically huge) molecular sequences that represent genomes.
has exact synonym: Genome alignment construction
has exact synonym: Whole genome alignment
in subset: bio
in subset: operations

Localised reassembly
type: Class
subclass of: Sequence assembly
Created in: 1.1
has definition: Reconstruction of a sequence assembly in a localised area.
in subset: bio
in subset: operations

Sequence assembly visualisation
type: Class
subclass of: Sequence visualisation
Created in: 1.1
has definition: Render and visualise a DNA sequence assembly.
has exact synonym: Assembly rendering
has exact synonym: Assembly visualisation
has exact synonym: Sequence assembly rendering
in subset: bio
in subset: operations

Base-calling
type: Class
subclass of: Sequence generation
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
Created in: 1.1
has definition: Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer.
has exact synonym: Base calling
has exact synonym: Phred base calling
has exact synonym: Phred base-calling
in subset: bio
in subset: operations

Bisulfite mapping
type: Class
subclass of: Physical mapping
subclass of: Methylation analysis
Created in: 1.1
has definition: The mapping of methylation sites in a DNA (genome) sequence. Typically, the mapping of high-throughput bisulfite reads to the reference genome.
has exact synonym: Bisulfite read mapping
has exact synonym: Bisulfite sequence alignment
has exact synonym: Bisulfite sequence mapping
in subset: bio
in subset: operations
comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.

Sequence contamination filtering
type: Class
subclass of: Sequencing quality control
Created in: 1.1
has definition: Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.
in subset: bio
in subset: operations

Trim ends
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.12
Old parent: Thing
has definition: Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
in subset: obsolete
replaced by: Sequence trimming
comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
deprecated: true

Trim vector
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.12
Old parent: Thing
has definition: Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
in subset: obsolete
replaced by: Sequence trimming
deprecated: true

Trim to reference
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.12
Old parent: Thing
has definition: Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
in subset: obsolete
replaced by: Sequence trimming
deprecated: true

Sequence trimming
type: Class
subclass of: Sequence cutting
Created in: 1.1
has definition: Cut (remove) the end from a molecular sequence.
has exact synonym: Trimming
has narrow synonym: Barcode sequence removal
has narrow synonym: Trim ends
has narrow synonym: Trim to reference
has narrow synonym: Trim vector
in subset: bio
in subset: operations
comment: 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.

Genome feature comparison
type: Class
subclass of: Sequence feature comparison
subclass of: Genome analysis
Created in: 1.1
has definition: Compare the features of two genome sequences.
in subset: bio
in subset: operations
comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.

Sequencing error detection
type: Class
subclass of: Sequence comparison
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
Created in: 1.1
has definition: Detect errors in DNA sequences generated from sequencing projects).
has exact synonym: Short read error correction
has exact synonym: Short-read error correction
in subset: bio
in subset: operations

Genotyping
type: Class
subclass of: Genetic variation analysis
Created in: 1.1
has definition: Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.
in subset: bio
in subset: operations
comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.

Genetic variation analysis
type: Class
subclass of: Data analysis
Created in: 1.1
has definition: Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
has exact synonym: Genetic variation annotation
has exact synonym: Sequence variation analysis
has exact synonym: Variant analysis
has narrow synonym: Transcript variant analysis
in subset: bio
in subset: operations
comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.

Read mapping
type: Class
subclass of: Physical mapping
subclass of: Sequence read processing
Created in: 1.1
has definition: Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
has exact synonym: Oligonucleotide alignment
has exact synonym: Oligonucleotide alignment construction
has exact synonym: Oligonucleotide alignment generation
has exact synonym: Oligonucleotide mapping
has exact synonym: Read alignment
has exact synonym: Short oligonucleotide alignment
has exact synonym: Short read alignment
has exact synonym: Short read mapping
has exact synonym: Short sequence read mapping
in subset: bio
in subset: operations
comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.

Split read mapping
type: Class
subclass of: Read mapping
Created in: 1.1
has definition: A variant of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.
has exact synonym: Split-read mapping
in subset: bio
in subset: operations

DNA barcoding
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.1
has definition: 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.
has exact synonym: Community profiling
has exact synonym: Sample barcoding
in subset: bio
in subset: operations

SNP calling
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.19
Old parent: SNP detection
has definition: 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.
in subset: obsolete
replaced by: SNP detection
deprecated: true

Polymorphism detection
type: Class
subclass of: DeprecatedClass
Created in: 1.1
deprecation_comment: "Polymorphism detection" and "Variant calling" are essentially the same thing - keeping the later as a more prevalent term nowadays.
Obsolete since: 1.24
Old parent: Nucleic acid sequence analysis
Old parent: Genetic variation analysis
has definition: Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.
in subset: obsolete
replaced by: Variant calling
deprecated: true

Chromatogram visualisation
type: Class
subclass of: Visualisation
Created in: 1.1
has definition: Visualise, format or render an image of a Chromatogram.
has exact synonym: Chromatogram viewing
in subset: bio
in subset: operations

Methylation analysis
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.1
has definition: Analyse cytosine methylation states in nucleic acid sequences.
has exact synonym: Methylation profile analysis
in subset: bio
in subset: operations

Methylation calling
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.19
Old parent: Methylation analysis
has definition: Determine cytosine methylation status of specific positions in a nucleic acid sequences.
in subset: obsolete
replaced by: Methylation analysis
deprecated: true

Whole genome methylation analysis
type: Class
subclass of: Methylation analysis
subclass of: Genome analysis
Created in: 1.1
has definition: Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.
has exact synonym: Genome methylation analysis
has exact synonym: Global methylation analysis
has exact synonym: Methylation level analysis (global)
in subset: bio
in subset: operations

Gene methylation analysis
type: Class
subclass of: Methylation analysis
Created in: 1.1
has definition: Analysing the DNA methylation of specific genes or regions of interest.
has exact synonym: Gene-specific methylation analysis
has exact synonym: Methylation level analysis (gene-specific)
in subset: bio
in subset: operations

Genome visualisation
type: Class
subclass of: Sequence visualisation
subclass of: Genome analysis
Created in: 1.1
has definition: Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.
has exact synonym: Genome browser
has exact synonym: Genome browsing
has exact synonym: Genome rendering
has exact synonym: Genome viewing
in subset: bio
in subset: operations

Genome comparison
type: Class
subclass of: Sequence comparison
subclass of: Genome analysis
Created in: 1.1
has definition: Compare the sequence or features of two or more genomes, for example, to find matching regions.
has exact synonym: Genomic region matching
in subset: bio
in subset: operations

Genome indexing
type: Class
subclass of: Indexing
subclass of: Genome analysis
subclass of: Restriction
  on property: has output
  some values from: Genome index
Created in: 1.1
has definition: Generate an index of a genome sequence.
has narrow synonym: Burrows-Wheeler
has narrow synonym: Genome indexing (Burrows-Wheeler)
has narrow synonym: Genome indexing (suffix arrays)
has narrow synonym: Suffix arrays
in subset: bio
in subset: operations
comment: 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 (Burrows-Wheeler)
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.12
Old parent: Thing
has definition: Generate an index of a genome sequence using the Burrows-Wheeler algorithm.
in subset: obsolete
replaced by: Genome indexing
comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
deprecated: true

Genome indexing (suffix arrays)
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.12
Old parent: Thing
has definition: Generate an index of a genome sequence using a suffix arrays algorithm.
in subset: obsolete
replaced by: Genome indexing
comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome.
deprecated: true

Spectral analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.1
has definition: Analyse one or more spectra from mass spectrometry (or other) experiments.
has exact synonym: Mass spectrum analysis
has exact synonym: Spectrum analysis
in subset: bio
in subset: operations

Peak detection
type: Class
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.1
has definition: Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment.
has exact synonym: Peak assignment
has exact synonym: Peak finding
in subset: bio
in subset: operations

Scaffolding
type: Class
subclass of: Sequence assembly
subclass of: Generation
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
Created in: 1.1
has definition: 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.
has exact synonym: Scaffold construction
has exact synonym: Scaffold generation
in subset: bio
in subset: operations
comment: Scaffold may be positioned along a chromosome physical map to create a "golden path".

Scaffold gap completion
type: Class
subclass of: Scaffolding
Created in: 1.1
has definition: Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.
in subset: bio
in subset: operations
comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.

Sequencing quality control
type: Class
subclass of: Validation
subclass of: Nucleic acid sequence analysis
Created in: 1.1
has definition: Raw sequence data quality control.
has exact synonym: Sequencing QC
has exact synonym: Sequencing quality assessment
in subset: bio
in subset: operations
comment: Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems.

Read pre-processing
type: Class
subclass of: Sequencing quality control
subclass of: Sequence read processing
Created in: 1.1
has definition: Pre-process sequence reads to ensure (or improve) quality and reliability.
has exact synonym: Sequence read pre-processing
in subset: bio
in subset: operations
comment: 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.

Species frequency estimation
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Metagenomics
Created in: 1.1
has definition: Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.
in subset: bio
in subset: operations

Peak calling
type: Class
subclass of: Nucleic acid feature detection
Created in: 1.1
has definition: Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.
has exact synonym: Protein binding peak detection
has narrow synonym: Peak-pair calling
in subset: bio
in subset: operations
comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo.

Differential gene expression profiling
type: Class
subclass of: Gene expression profiling
Created in: 1.1
has definition: 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.
has exact synonym: Differential expression analysis
has exact synonym: Differential gene analysis
has exact synonym: Differential gene expression analysis
has exact synonym: Differentially expressed gene identification
in subset: bio
in subset: operations
comment: 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.

Gene set testing
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.21
Old parent: Expression analysis
has definition: 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.
in subset: obsolete
replaced by: Gene-set enrichment analysis
deprecated: true

Variant classification
type: Class
subclass of: Sequence classification
subclass of: Genetic variation analysis
Created in: 1.1
has definition: Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.
in subset: bio
in subset: operations
comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)

Variant prioritisation
type: Class
subclass of: Genetic variation analysis
Created in: 1.1
has definition: Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
in subset: bio
in subset: operations
comment: 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 calling
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Genetic variation analysis
Created in: 1.1
has definition: 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.
has exact synonym: Variant mapping
has narrow synonym: Allele calling
has narrow synonym: Exome variant detection
has narrow synonym: Genome variant detection
has narrow synonym: Germ line variant calling
has narrow synonym: Mutation detection
has narrow synonym: Somatic variant calling
has narrow synonym: de novo mutation detection
in subset: bio
in subset: operations
comment: Methods often utilise a database of aligned reads.
comment: Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant.
comment: Variant detection

Structural variation detection
type: Class
subclass of: Genetic variation analysis
Created in: 1.1
has definition: Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).
has exact synonym: Structural variation discovery
in subset: bio
in subset: operations
comment: 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.

Exome assembly
type: Class
subclass of: Sequence assembly
Created in: 1.1
has definition: Analyse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.
has exact synonym: Exome sequence analysis
in subset: bio
in subset: operations

Read depth analysis
type: Class
subclass of: Sequence read processing
Created in: 1.1
has definition: Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.
in subset: bio
in subset: operations

Gene expression QTL analysis
type: Class
subclass of: Expression analysis
Created in: 1.1
has definition: 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.
has exact synonym: Gene expression QTL profiling
has exact synonym: Gene expression quantitative trait loci profiling
has exact synonym: eQTL profiling
in subset: bio
in subset: operations

Copy number estimation
type: Class
subclass of: Copy number variation detection
Created in: 1.1
has definition: 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.
has exact synonym: Transcript copy number estimation
in subset: bio
in subset: operations
comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).

Primer removal
type: Class
subclass of: Sequence cutting
Created in: 1.2
has broad synonym: Adapter removal
has definition: Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).
in subset: bio
in subset: operations

Transcriptome assembly
type: Class
subclass of: Sequence assembly
subclass of: Restriction
  on property: has output
  some values from: Sequence assembly
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
Created in: 1.2
has definition: Infer a transcriptome sequence by analysis of short sequence reads.
in subset: bio
in subset: operations

Transcriptome assembly (de novo)
type: Class
subclass of: DeprecatedClass
Created in: 1.2
Obsolete since: 1.6
Old parent: Thing
consider: De-novo assembly
has definition: Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.
in subset: obsolete
deprecated: true

Transcriptome assembly (mapping)
type: Class
subclass of: DeprecatedClass
Created in: 1.2
Obsolete since: 1.6
Old parent: Thing
consider: Mapping assembly
has definition: Infer a transcriptome sequence by mapping short reads to a reference genome.
in subset: obsolete
deprecated: true

Sequence coordinate conversion
type: Class
subclass of: Conversion
subclass of: Restriction
  on property: has input
  some values from: Sequence coordinates
subclass of: Restriction
  on property: has output
  some values from: Sequence coordinates
Created in: 1.3
has definition: 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.
in subset: bio
in subset: operations

Document similarity calculation
type: Class
subclass of: Article comparison
Created in: 1.3
has definition: Calculate similarity between 2 or more documents.
in subset: bio
in subset: operations

Document clustering
type: Class
subclass of: Clustering
subclass of: Article comparison
Created in: 1.3
has definition: Cluster (group) documents on the basis of their calculated similarity.
in subset: bio
in subset: operations

Named-entity and concept recognition
type: Class
subclass of: Information extraction
Created in: 1.3
has definition: Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents.
has narrow synonym: Concept mining
has narrow synonym: Entity chunking
has narrow synonym: Entity extraction
has narrow synonym: Entity identification
has narrow synonym: Event extraction
has narrow synonym: NER
has narrow synonym: Named-entity recognition
in subset: bio
in subset: operations

ID mapping
type: Class
subclass of: Comparison
subclass of: Mapping
Created in: 1.3
has definition: Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.
has exact synonym: Accession mapping
has exact synonym: Identifier mapping
in subset: bio
in subset: operations
comment: The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.

Anonymisation
type: Class
subclass of: Data handling
Created in: 1.3
has definition: Process data in such a way that makes it hard to trace to the person which the data concerns.
has exact synonym: Data anonymisation
in subset: bio
in subset: operations

ID retrieval
type: Class
subclass of: DeprecatedClass
Created in: 1.3
deprecation_comment: (jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved.
Obsolete since: 1.17
Old parent: Metadata retrieval
has definition: Search for and retrieve a data identifier of some kind, e.g. a database entry accession.
in subset: obsolete
replaced by: Data retrieval
deprecated: true

Sequence checksum generation
type: Class
subclass of: Generation
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has topic
  some values from: Data acquisition
Created in: 1.4
has definition: Generate a checksum of a molecular sequence.
in subset: bio
in subset: operations

Bibliography generation
type: Class
subclass of: Generation
subclass of: Restriction
  on property: has output
  some values from: Bibliography
Created in: 1.4
has definition: Construct a bibliography from the scientific literature.
has exact synonym: Bibliography construction
in subset: bio
in subset: operations

Protein quaternary structure prediction
type: Class
subclass of: Prediction and recognition
Created in: 1.4
has definition: Predict the structure of a multi-subunit protein and particularly how the subunits fit together.
in subset: bio
in subset: operations

Molecular surface analysis
type: Class
subclass of: Structure analysis
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
subclass of: Restriction
  on property: has topic
  some values from: Protein structural motifs and surfaces
Created in: 1.4
has definition: Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc.
in subset: bio
in subset: operations

Ontology comparison
type: Class
subclass of: Comparison
Created in: 1.4
has definition: Compare two or more ontologies, e.g. identify differences.
in subset: bio
in subset: operations

Ontology comparison
type: Class
subclass of: DeprecatedClass
Created in: 1.4
Obsolete since: 1.9
Old parent: Thing
has definition: Compare two or more ontologies, e.g. identify differences.
in subset: obsolete
replaced by: Ontology comparison
deprecated: true

Format detection
type: Class
subclass of: Data handling
subclass of: Restriction
  on property: has output
  some values from: Format identifier
comment handle: comment handle
Created in: 1.4
has definition: Recognition of which format the given data is in.
has exact synonym: Format identification
has exact synonym: Format inference
has exact synonym: Format recognition
in subset: bio
in subset: operations
comment: '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.

Axiom
annotated source: Format detection
annotated property: comment handle
annotated target: comment handle
comment: 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.

Splitting
type: Class
subclass of: Data handling
Created in: 1.4
has definition: Split a file containing multiple data items into many files, each containing one item.
has exact synonym: File splitting
in subset: bio
in subset: operations

Generation
type: Class
subclass of: Operation
Created in: 1.6
notRecommendedForAnnotation: true
has definition: Construct some data entity.
has exact synonym: Construction
in subset: bio
in subset: operations
comment: For non-analytical operations, see the 'Processing' branch.

Nucleic acid sequence feature detection
type: Class
subclass of: DeprecatedClass
Created in: 1.6
deprecation_comment: (jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed.
Obsolete since: 1.17
Old parent: Sequence feature detection
Old parent: Nucleic acid feature detection
has definition: Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions.
in subset: obsolete
replaced by: Nucleic acid feature detection
deprecated: true

Data deposition
type: Class
subclass of: Data handling
subclass of: Restriction
  on property: has topic
  some values from: Data curation and archival
Created in: 1.6
Related term: Data publication
has definition: Data deposition is the submission and upload of data to a dedicated repository, archive, or deposition database, usually with accompanying metadata.
has exact synonym: Data submission
has exact synonym: Database deposition
has exact synonym: Database submission
has narrow synonym: Data brokering
has narrow synonym: Data deposition brokering
has related synonym: Data publishing
in subset: bio
in subset: operations

Clustering
type: Class
subclass of: Operation
Created in: 1.6
notRecommendedForAnnotation: true
has definition: 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).
in subset: bio
in subset: operations

Assembly
type: Class
subclass of: DeprecatedClass
Created in: 1.6
Obsolete since: 1.19
Old parent: Operation
has definition: Construct some entity (typically a molecule sequence) from component pieces.
in subset: obsolete
replaced by: Sequence assembly
deprecated: true

Conversion
type: Class
subclass of: Operation
Created in: 1.6
notRecommendedForAnnotation: true
has definition: Convert a data set from one form to another.
in subset: bio
in subset: operations

Standardisation and normalisation
type: Class
subclass of: Statistical calculation
Created in: 1.6
has definition: Standardize or normalize data by some statistical method.
has narrow synonym: Normalisation
has narrow synonym: Standardisation
in subset: bio
in subset: operations
comment: 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.

Aggregation
type: Class
subclass of: Data handling
Created in: 1.6
has definition: Combine multiple files or data items into a single file or object.
in subset: bio
in subset: operations

Article comparison
type: Class
subclass of: Comparison
subclass of: Restriction
  on property: has topic
  some values from: Literature and language
Created in: 1.6
has definition: Compare two or more scientific articles.
in subset: bio
in subset: operations

Calculation
type: Class
subclass of: Operation
Created in: 1.6
notRecommendedForAnnotation: true
has definition: Mathematical determination of the value of something, typically a properly of a molecule.
in subset: bio
in subset: operations

Pathway or network prediction
type: Class
subclass of: DeprecatedClass
Created in: 1.6
deprecation_comment: Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
Obsolete since: 1.24
Old parent: Pathway or network analysis
consider: Gene regulatory network prediction
consider: Protein interaction network prediction
consider: Metabolic pathway prediction
has definition: Predict a molecular pathway or network.
in subset: obsolete
deprecated: true

Genome assembly
type: Class
subclass of: DeprecatedClass
Created in: 1.6
Obsolete since: 1.12
Old parent: Thing
has definition: The process of assembling many short DNA sequences together such that they represent the original chromosomes from which the DNA originated.
in subset: obsolete
replaced by: Genome assembly
deprecated: true

Plotting
type: Class
subclass of: DeprecatedClass
Created in: 1.6
Obsolete since: 1.19
Old parent: Visualisation
has definition: Generate a graph, or other visual representation, of data, showing the relationship between two or more variables.
in subset: obsolete
replaced by: Visualisation
deprecated: true

Image analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Imaging
Created in: 1.7
has broad synonym: Image processing
has definition: The analysis of a image (typically a digital image) of some type in order to extract information from it.
in subset: bio
in subset: operations

Diffraction data analysis
type: Class
subclass of: Structure analysis
Created in: 1.7
has definition: Analysis of data from a diffraction experiment.
in subset: bio
in subset: operations

Cell migration analysis
type: Class
subclass of: Image analysis
subclass of: Restriction
  on property: has topic
  some values from: Cell biology
Created in: 1.7
has definition: 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.
in subset: bio
in subset: operations

Diffraction data reduction
type: Class
subclass of: Diffraction data analysis
Created in: 1.7
has definition: Processing of diffraction data into a corrected, ordered, and simplified form.
in subset: bio
in subset: operations

Neurite measurement
type: Class
subclass of: Image analysis
subclass of: Restriction
  on property: has topic
  some values from: Cell biology
Created in: 1.7
has definition: Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images.
in subset: bio
in subset: operations

Diffraction data integration
type: Class
subclass of: Diffraction data analysis
Created in: 1.7
has definition: The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment.
has narrow synonym: Diffraction profile fitting
has narrow synonym: Diffraction summation integration
in subset: bio
in subset: operations

Phasing
type: Class
subclass of: Diffraction data analysis
Created in: 1.7
has definition: Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods.
in subset: bio
in subset: operations

Molecular replacement
type: Class
subclass of: Molecular model refinement
Created in: 1.7
has definition: 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.
in subset: bio
in subset: operations
comment: The technique solves the phase problem, i.e. retrieve information concern phases of the structure.

Rigid body refinement
type: Class
subclass of: Molecular model refinement
Created in: 1.7
has definition: 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.
in subset: bio
in subset: operations
comment: Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.

Single particle analysis
type: Class
subclass of: Structure analysis
subclass of: Image analysis
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
Created in: 1.7
has definition: 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.
in subset: bio
in subset: operations
comment: 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 alignment and classification
type: Class
subclass of: Classification
subclass of: Single particle analysis
Created in: 1.7
refactor_candidate: true
refactor_comment: This is two related concepts.
has definition: Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle.
in subset: bio
in subset: operations
comment: 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.

Functional clustering
type: Class
subclass of: Sequence clustering
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: 1.7
has definition: 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.
has exact synonym: Functional sequence clustering
in subset: bio
in subset: operations

Taxonomic classification
type: Class
subclass of: Sequence classification
Created in: 1.7
has definition: Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy.
has exact synonym: Taxonomy assignment
has narrow synonym: Taxonomic profiling
in subset: bio
in subset: operations

Virulence prediction
type: Class
subclass of: Sequence analysis
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has topic
  some values from: Microbiology
Created in: 1.7
has definition: The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences.
has exact synonym: Pathogenicity prediction
in subset: bio
in subset: operations

Expression correlation analysis
type: Class
subclass of: Expression profile comparison
subclass of: Correlation
Created in: 1.7
has definition: Analyse the correlation patterns among features/molecules across across a variety of experiments, samples etc.
has exact synonym: Co-expression analysis
has narrow synonym: Gene co-expression network analysis
has narrow synonym: Gene expression correlation
has narrow synonym: Gene expression correlation analysis
in subset: bio
in subset: operations

Correlation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.7
notRecommendedForAnnotation: true
has definition: Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.
in subset: bio
in subset: operations

RNA structure covariance model generation
type: Class
subclass of: RNA secondary structure analysis
subclass of: Generation
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
Created in: 1.7
has definition: Compute the covariance model for (a family of) RNA secondary structures.
in subset: bio
in subset: operations

RNA secondary structure prediction (shape-based)
type: Class
subclass of: DeprecatedClass
Created in: 1.7
Obsolete since: 1.18
Old parent: RNA secondary structure prediction
has definition: Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds.
in subset: obsolete
replaced by: RNA secondary structure prediction
deprecated: true

Nucleic acid folding prediction (alignment-based)
type: Class
subclass of: DeprecatedClass
Created in: 1.7
Obsolete since: 1.18
Old parent: Nucleic acid folding analysis
has definition: Prediction of nucleic-acid folding using sequence alignments as a source of data.
in subset: obsolete
replaced by: Nucleic acid folding analysis
deprecated: true

k-mer counting
type: Class
subclass of: Sequence composition calculation
Created in: 1.7
has definition: Count k-mers (substrings of length k) in DNA sequence data.
in subset: bio
in subset: operations
comment: k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads.

Phylogenetic reconstruction
type: Class
subclass of: Phylogenetic inference
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: 1.7
has definition: Reconstructing the inner node labels of a phylogenetic tree from its leafes.
has exact synonym: Phylogenetic tree reconstruction
has narrow synonym: Gene tree reconstruction
has narrow synonym: Species tree reconstruction
in subset: bio
in subset: operations
comment: Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.

Probabilistic data generation
type: Class
subclass of: Generation
Created in: 1.7
has definition: Generate some data from a chosen probibalistic model, possibly to evaluate algorithms.
in subset: bio
in subset: operations

Probabilistic sequence generation
type: Class
subclass of: Sequence generation
subclass of: Probabilistic data generation
Created in: 1.7
has definition: Generate sequences from some probabilistic model, e.g. a model that simulates evolution.
in subset: bio
in subset: operations

Antimicrobial resistance prediction
type: Class
subclass of: Sequence analysis
subclass of: Prediction and recognition
subclass of: Restriction
  on property: has topic
  some values from: Microbiology
Created in: 1.7
has definition: Identify or predict causes for antibiotic resistance from molecular sequence analysis.
in subset: bio
in subset: operations

Enrichment analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has output
  some values from: Over-representation data
Created in: 1.8
has definition: 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.
has exact synonym: Enrichment
has exact synonym: Over-representation analysis
has narrow synonym: Functional enrichment
in subset: bio
in subset: operations
comment: 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.

Chemical similarity enrichment
type: Class
subclass of: Enrichment analysis
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
Created in: 1.8
has definition: Analyse a dataset with respect to concepts from an ontology of chemical structure, leveraging chemical similarity information.
has exact synonym: Chemical class enrichment
in subset: bio
in subset: operations

Incident curve plotting
type: Class
subclass of: Visualisation
Created in: 1.8
has definition: Plot an incident curve such as a survival curve, death curve, mortality curve.
in subset: bio
in subset: operations

Variant pattern analysis
type: Class
subclass of: Genetic variation analysis
Created in: 1.8
has definition: Identify and map patterns of genomic variations.
in subset: bio
in subset: operations
comment: Methods often utilise a database of aligned reads.

Mathematical modelling
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.12
Old parent: Thing
has definition: Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
in subset: obsolete
replaced by: Modelling and simulation
deprecated: true

Microscope image visualisation
type: Class
subclass of: Visualisation
subclass of: Restriction
  on property: has topic
  some values from: Imaging
Created in: 1.9
has definition: Visualise images resulting from various types of microscopy.
in subset: bio
in subset: operations

Image annotation
type: Class
subclass of: Annotation
Created in: 1.9
has definition: Annotate an image of some sort, typically with terms from a controlled vocabulary.
in subset: bio
in subset: operations

Imputation
type: Class
subclass of: Statistical calculation
Created in: 1.9
has definition: Replace missing data with substituted values, usually by using some statistical or other mathematical approach.
has exact synonym: Data imputation
in subset: bio
in subset: operations

Ontology visualisation
type: Class
subclass of: Visualisation
Created in: 1.9
has definition: Visualise, format or render data from an ontology, typically a tree of terms.
has exact synonym: Ontology browsing
in subset: bio
in subset: operations

Maximum occurrence analysis
type: Class
subclass of: Protein structure validation
Created in: 1.9
has definition: 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.
in subset: bio
in subset: operations

Database comparison
type: Class
subclass of: Comparison
subclass of: Mapping
Created in: 1.9
has definition: 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.
has narrow synonym: Data model comparison
has narrow synonym: Schema comparison
in subset: bio
in subset: operations

Network simulation
type: Class
subclass of: DeprecatedClass
Created in: 1.9
Obsolete since: 1.24
Old parent: Modelling and simulation
consider: Network analysis
consider: Pathway analysis
has definition: Simulate the bevaviour of a biological pathway or network.
in subset: obsolete
comment: Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
deprecated: true

RNA-seq read count analysis
type: Class
subclass of: RNA-Seq analysis
Created in: 1.9
has definition: Analyze read counts from RNA-seq experiments.
in subset: bio
in subset: operations

Chemical redundancy removal
type: Class
subclass of: Structure comparison
Created in: 1.9
has definition: Identify and remove redundancy from a set of small molecule structures.
in subset: bio
in subset: operations

RNA-seq time series data analysis
type: Class
subclass of: RNA-Seq analysis
Created in: 1.9
has definition: Analyze time series data from an RNA-seq experiment.
in subset: bio
in subset: operations

Simulated gene expression data generation
type: Class
subclass of: Modelling and simulation
Created in: 1.9
has definition: Simulate gene expression data, e.g. for purposes of benchmarking.
in subset: bio
in subset: operations

Relation extraction
type: Class
subclass of: Text mining
Created in: 1.12
has definition: Identify semantic relations among entities and concepts within a text, using text mining techniques.
has exact synonym: Relation discovery
has exact synonym: Relation inference
has exact synonym: Relationship discovery
has exact synonym: Relationship extraction
has exact synonym: Relationship inference
in subset: bio
in subset: operations

Mass spectra calibration
type: Class
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.12
has definition: Re-adjust the output of mass spectrometry experiments with shifted ppm values.
in subset: bio
in subset: operations

Chromatographic alignment
type: Class
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.12
has definition: Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments.
in subset: bio
in subset: operations

Deisotoping
type: Class
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.12
has definition: The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point.
has exact synonym: Deconvolution
in subset: bio
in subset: operations
comment: Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution.

Protein quantification
type: Class
subclass of: Spectral analysis
subclass of: Quantification
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.12
has definition: Technique for determining the amount of proteins in a sample.
has exact synonym: Protein quantitation
in subset: bio
in subset: operations

Peptide identification
type: Class
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.12
has definition: Determination of peptide sequence from mass spectrum.
has exact synonym: Peptide-spectrum-matching
in subset: bio
in subset: operations

Isotopic distributions calculation
type: Class
subclass of: Calculation
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.12
has definition: Calculate the isotope distribution of a given chemical species.
in subset: bio
in subset: operations

Retention time prediction
type: Class
subclass of: Calculation
Created in: 1.12
has definition: Prediction of retention time in a mass spectrometry experiment based on compositional and structural properties of the separated species.
has exact synonym: Retention time calculation
in subset: bio
in subset: operations

Label-free quantification
type: Class
subclass of: Protein quantification
Created in: 1.12
has definition: Quantification without the use of chemical tags.
in subset: bio
in subset: operations

Labeled quantification
type: Class
subclass of: Protein quantification
Created in: 1.12
has definition: Quantification based on the use of chemical tags.
in subset: bio
in subset: operations

MRM/SRM
type: Class
subclass of: Protein quantification
Created in: 1.12
has definition: Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair).
in subset: bio
in subset: operations

Spectral counting
type: Class
subclass of: Label-free quantification
Created in: 1.12
has definition: Calculate number of identified MS2 spectra as approximation of peptide / protein quantity.
in subset: bio
in subset: operations

SILAC
type: Class
subclass of: Labeled quantification
Created in: 1.12
has definition: Quantification analysis using stable isotope labeling by amino acids in cell culture.
in subset: bio
in subset: operations

iTRAQ
type: Class
subclass of: Labeled quantification
Created in: 1.12
has definition: Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z.
in subset: bio
in subset: operations

18O labeling
type: Class
subclass of: Labeled quantification
Created in: 1.12
has definition: Quantification analysis using labeling based on 18O-enriched H2O.
in subset: bio
in subset: operations

TMT-tag
type: Class
subclass of: Labeled quantification
Created in: 1.12
has definition: Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow.
in subset: bio
in subset: operations

Stable isotope dimethyl labelling
type: Class
subclass of: Labeled quantification
Created in: 1.12
has definition: Quantification analysis using chemical labeling by stable isotope dimethylation.
in subset: bio
in subset: operations

Tag-based peptide identification
type: Class
subclass of: Peptide identification
Created in: 1.12
has definition: Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry.
in subset: bio
in subset: operations

de Novo sequencing
type: Class
subclass of: Sequence generation
subclass of: Peptide identification
Created in: 1.12
has definition: Analytical process that derives a peptide's amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database.
in subset: bio
in subset: operations

PTM identification
type: Class
subclass of: Peptide identification
Created in: 1.12
has definition: Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum.
in subset: bio
in subset: operations

Peptide database search
type: Class
subclass of: Database search
subclass of: Peptide identification
Created in: 1.12
has definition: Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences.
in subset: bio
in subset: operations

Blind peptide database search
type: Class
subclass of: Peptide database search
Created in: 1.12
has definition: Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches.
has exact synonym: Modification-tolerant peptide database search
has exact synonym: Unrestricted peptide database search
in subset: bio
in subset: operations

Validation of peptide-spectrum matches
type: Class
subclass of: DeprecatedClass
Created in: 1.12
Obsolete since: 1.19
Old parent: Validation
Old parent: Peptide database search
has definition: Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search.
in subset: obsolete
replaced by: Target-Decoy
deprecated: true

Target-Decoy
type: Class
subclass of: Validation
subclass of: Peptide database search
Created in: 1.12
has broad synonym: Validation of peptide-spectrum matches
has definition: 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.
in subset: bio
in subset: operations

Statistical inference
type: Class
subclass of: Statistical calculation
Created in: 1.12
has definition: Analyse data in order to deduce properties of an underlying distribution or population.
has narrow synonym: Empirical Bayes
in subset: bio
in subset: operations

Regression analysis
type: Class
subclass of: Statistical calculation
Created in: 1.12
has definition: A statistical calculation to estimate the relationships among variables.
has narrow synonym: Regression
in subset: bio
in subset: operations

Metabolic network modelling
type: Class
subclass of: Network analysis
subclass of: Pathway analysis
subclass of: Restriction
  on property: has topic
  some values from: Systems biology
Created in: 1.12
has definition: 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.
has exact synonym: Metabolic pathway modelling
has narrow synonym: Metabolic network reconstruction
has narrow synonym: Metabolic network simulation
has narrow synonym: Metabolic pathway reconstruction
has narrow synonym: Metabolic pathway simulation
has narrow synonym: Metabolic reconstruction
in subset: bio
in subset: operations
comment: The terms and synyonyms here reflect that for practical intents and purposes, "pathway" and "network" can be treated the same.

SNP annotation
type: Class
subclass of: Sequence annotation
Created in: 1.12
has definition: Predict the effect or function of an individual single nucleotide polymorphism (SNP).
in subset: bio
in subset: operations

Ab-initio gene prediction
type: Class
subclass of: Gene prediction
Created in: 1.12
has definition: Prediction of genes or gene components from first principles, i.e. without reference to existing genes.
has exact synonym: Gene prediction (ab-initio)
in subset: bio
in subset: operations

Homology-based gene prediction
type: Class
subclass of: Gene prediction
Created in: 1.12
has definition: Prediction of genes or gene components by reference to homologous genes.
has exact synonym: Empirical gene finding
has exact synonym: Empirical gene prediction
has exact synonym: Evidence-based gene prediction
has exact synonym: Gene prediction (homology-based)
has exact synonym: Similarity-based gene prediction
has narrow synonym: Homology prediction
has narrow synonym: Orthology prediction
in subset: bio
in subset: operations

Statistical modelling
type: Class
subclass of: Statistical calculation
Created in: 1.12
has definition: 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.
in subset: bio
in subset: operations

Molecular surface comparison
type: Class
subclass of: Structure comparison
subclass of: Molecular surface analysis
Created in: 1.12
has definition: Compare two or more molecular surfaces.
in subset: bio
in subset: operations

Gene functional annotation
type: Class
subclass of: Sequence annotation
Created in: 1.12
has definition: 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).
has exact synonym: Sequence functional annotation
in subset: bio
in subset: operations

Variant filtering
type: Class
subclass of: Sequencing quality control
Created in: 1.12
has definition: Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info.
in subset: bio
in subset: operations

Differential binding analysis
type: Class
subclass of: Nucleic acid feature detection
Created in: 1.12
has definition: Identify binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups.
in subset: bio
in subset: operations

RNA-Seq analysis
type: Class
subclass of: Expression analysis
subclass of: Sequence read processing
Created in: 1.13
has definition: Analyze data from RNA-seq experiments.
in subset: bio
in subset: operations

Mass spectrum visualisation
type: Class
subclass of: Visualisation
Created in: 1.13
has definition: Visualise, format or render a mass spectrum.
in subset: bio
in subset: operations

Data filtering
type: Class
subclass of: Data handling
Created in: 1.13
has definition: Filter a set of files or data items according to some property.
has narrow synonym: Sequence filtering
has narrow synonym: rRNA filtering
in subset: bio
in subset: operations

Reference identification
type: Class
subclass of: Genetic variation analysis
Created in: 1.14
has definition: Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis.
in subset: bio
in subset: operations

Ion counting
type: Class
subclass of: Label-free quantification
Created in: 1.14
has definition: Label-free quantification by integration of ion current (ion counting).
has exact synonym: Ion current integration
in subset: bio
in subset: operations

Isotope-coded protein label
type: Class
subclass of: Labeled quantification
Created in: 1.14
has definition: Chemical tagging free amino groups of intact proteins with stable isotopes.
has exact synonym: ICPL
in subset: bio
in subset: operations

Metabolic labeling
type: Class
subclass of: Labeled quantification
Created in: 1.14
has definition: Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed.
has narrow synonym: C-13 metabolic labeling
has narrow synonym: N-15 metabolic labeling
in subset: bio
in subset: operations
comment: 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).

Cross-assembly
type: Class
subclass of: Sequence assembly
Created in: 1.15
has definition: Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis.
has exact synonym: Sequence assembly (cross-assembly)
in subset: bio
in subset: operations

Sample comparison
type: Class
subclass of: Comparison
Created in: 1.15
has definition: 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.
in subset: bio
in subset: operations

Differential protein expression profiling
type: Class
subclass of: Gene expression profiling
subclass of: Protein comparison
Created in: 1.15
has broad synonym: Differential protein analysis
has definition: The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup.
has exact synonym: Differential protein expression analysis
in subset: bio
in subset: operations

Differential gene expression analysis
type: Class
subclass of: DeprecatedClass
Created in: 1.15
Obsolete since: 1.17
Old parent: Comparison
has definition: The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup.
in subset: obsolete
replaced by: Differential gene expression profiling
deprecated: true

Multiple sample visualisation
type: Class
subclass of: Visualisation
Created in: 1.15
has definition: Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment.
in subset: bio
in subset: operations

Ancestral reconstruction
type: Class
subclass of: Phylogenetic analysis
Created in: 1.15
has definition: The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors.
has exact synonym: Ancestral sequence reconstruction
has exact synonym: Character mapping
has exact synonym: Character optimisation
in subset: bio
in subset: operations
comment: Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms.

PTM localisation
type: Class
subclass of: PTM identification
Created in: 1.16
has definition: Site localisation of post-translational modifications in peptide or protein mass spectra.
has exact synonym: PTM scoring
has exact synonym: Site localisation
in subset: bio
in subset: operations

Service management
type: Class
subclass of: Operation
Created in: 1.16
has definition: Operations concerning the handling and use of other tools.
has narrow synonym: Endpoint management
in subset: bio
in subset: operations

Service discovery
type: Class
subclass of: Service management
Created in: 1.16
has definition: An operation supporting the browsing or discovery of other tools and services.
in subset: bio
in subset: operations

Service composition
type: Class
subclass of: Service management
Created in: 1.16
has definition: An operation supporting the aggregation of other services (at least two) into a functional unit, for the automation of some task.
in subset: bio
in subset: operations

Service invocation
type: Class
subclass of: Service management
Created in: 1.16
has definition: An operation supporting the calling (invocation) of other tools and services.
in subset: bio
in subset: operations

Weighted correlation network analysis
type: Class
subclass of: Network analysis
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
Created in: 1.16
has definition: A data mining method typically used for studying biological networks based on pairwise correlations between variables.
has exact synonym: WGCNA
has exact synonym: Weighted gene co-expression network analysis
in subset: bio
in subset: operations

Protein identification
type: Class
subclass of: Prediction and recognition
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.16
has definition: Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry.
has exact synonym: Protein inference
in subset: bio
in subset: operations

Text annotation
type: Class
subclass of: Annotation
subclass of: Restriction
  on property: has input
  some values from: Text
subclass of: Restriction
  on property: has output
  some values from: Annotated text
subclass of: Restriction
  on property: has topic
  some values from: Literature and language
Created in: 1.16
has definition: 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).
has narrow synonym: Article annotation
has narrow synonym: Literature annotation
in subset: bio
in subset: operations

Collapsing methods
type: Class
subclass of: Genetic variation analysis
Created in: 1.17
has definition: A method whereby data on several variants are "collapsed" into a single covariate based on regions such as genes.
in subset: bio
in subset: operations
comment: 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.

miRNA expression analysis
type: Class
subclass of: Expression analysis
Created in: 1.17
has broad synonym: miRNA analysis
has definition: The analysis of microRNAs (miRNAs) : short, highly conserved small noncoding RNA molecules that are naturally occurring plant and animal genomes.
has exact synonym: miRNA expression profiling
in subset: bio
in subset: operations

Read summarisation
type: Class
subclass of: Sequence read processing
Created in: 1.17
has definition: Counting and summarising the number of short sequence reads that map to genomic features.
in subset: bio
in subset: operations

In vitro selection
type: Class
subclass of: Nucleic acid design
Created in: 1.17
has definition: 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 subset: bio
in subset: operations

Rarefaction
type: Class
subclass of: Calculation
Created in: 1.17
has definition: 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).
has exact synonym: Species richness assessment
in subset: bio
in subset: operations

Read binning
type: Class
subclass of: Sequence read processing
Created in: 1.17
has definition: An operation which groups reads or contigs and assigns them to operational taxonomic units.
has exact synonym: Binning
has exact synonym: Binning shotgun reads
in subset: bio
in subset: operations
comment: Binning methods use one or a combination of compositional features or sequence similarity.

Quantification
type: Class
subclass of: Operation
Created in: 1.17
notRecommendedForAnnotation: true
has definition: Counting and measuring experimentally determined observations into quantities.
has exact synonym: Quantitation
in subset: bio
in subset: operations

RNA-Seq quantification
type: Class
subclass of: Quantification
Created in: 1.17
has definition: Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study.
has exact synonym: RNA-Seq quantitation
in subset: bio
in subset: operations

Spectral library search
type: Class
subclass of: Peptide identification
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.17
has definition: Match experimentally measured mass spectrum to a spectrum in a spectral library or database.
in subset: bio
in subset: operations

Data sorting
type: Class
subclass of: Data handling
Created in: 1.17
has definition: Sort a set of files or data items according to some property.
in subset: bio
in subset: operations

Natural product identification
type: Class
subclass of: Spectral analysis
Created in: 1.17
has definition: Mass spectra identification of compounds that are produced by living systems. Including polyketides, terpenoids, phenylpropanoids, alkaloids and antibiotics.
has narrow synonym: De novo metabolite identification
has narrow synonym: Fragmenation tree generation
has narrow synonym: Metabolite identification
in subset: bio
in subset: operations

DMR identification
type: Class
subclass of: Methylation analysis
Created in: 1.19
has definition: Identify and assess specific genes or regulatory regions of interest that are differentially methylated.
has exact synonym: Differentially-methylated region identification
in subset: bio
in subset: operations

Multilocus sequence typing
type: Class
subclass of: Genotyping
Created in: 1.21
has db xref: OBI_0000435
has db xref: MLST
has definition: Genotyping of multiple loci, typically characterizing microbial species isolates using internal fragments of multiple housekeeping genes.
has exact synonym: MLST
in subset: bio
in subset: operations

Spectrum calculation
type: Class
subclass of: Protein property calculation
subclass of: Spectral analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
Created in: 1.21
has definition: Calculate a theoretical mass spectrometry spectra for given sequences.
has exact synonym: Spectrum prediction
in subset: bio
in subset: operations

Trajectory visualization
type: Class
subclass of: Structure visualisation
subclass of: Restriction
  on property: has output
  some values from: Helical wheel
Created in: 1.22
has definition: 3D visualization of a molecular trajectory.
in subset: bio
in subset: operations

Essential dynamics
type: Class
subclass of: Simulation analysis
subclass of: Nucleic acid structure analysis
Created in: 1.22
has definition: Compute Essential Dynamics (ED) on a simulation trajectory: an analysis of molecule dynamics using PCA (Principal Component Analysis) applied to the atomic positional fluctuations.
has exact synonym: ED
has exact synonym: PCA
has exact synonym: Principal modes
in subset: bio
in subset: operations
comment: Principal Component Analysis (PCA) is a multivariate statistical analysis to obtain collective variables and reduce the dimensionality of the system.

Forcefield parameterisation
type: Class
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has output
  some values from: DNA substitution model
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: 1.22
has definition: Obtain force field parameters (charge, bonds, dihedrals, etc.) from a molecule, to be used in molecular simulations.
has exact synonym: Ligand parameterization
has exact synonym: Molecule parameterization
in subset: bio
in subset: operations

DNA profiling
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.22
has definition: Analyse DNA sequences in order to determine an individual's DNA characteristics, for example in criminal forensics, parentage testing and so on.
has exact synonym: DNA fingerprinting

Active site prediction
type: Class
subclass of: Binding site prediction
Created in: 1.22
has definition: Predict or detect active sites in proteins; the region of an enzyme which binds a substrate bind and catalyses a reaction.
has narrow synonym: Active site detection
in subset: bio
in subset: operations

Ligand-binding site prediction
type: Class
subclass of: Binding site prediction
Created in: 1.22
has definition: 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.
has narrow synonym: Ligand-binding site detection
has narrow synonym: Peptide-protein binding prediction
in subset: bio
in subset: operations

Metal-binding site prediction
type: Class
subclass of: Binding site prediction
Created in: 1.22
has definition: Predict or detect metal ion-binding sites in proteins.
has exact synonym: Metal-binding site detection
has exact synonym: Protein metal-binding site prediction
in subset: bio
in subset: operations

Protein-protein docking
type: Class
subclass of: Molecular docking
subclass of: Restriction
  on property: has output
  some values from: Protein-ligand complex
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: 1.22
has definition: Model or simulate protein-protein binding using comparative modelling or other techniques.
has exact synonym: Protein docking
in subset: bio
in subset: operations

DNA-binding protein prediction
type: Class
subclass of: Protein-nucleic acid interaction analysis
subclass of: Restriction
  on property: has output
  some values from: Protein interaction data
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: 1.22
has definition: Predict DNA-binding proteins.
has exact synonym: DNA-binding protein detection
has exact synonym: DNA-protein interaction prediction
has exact synonym: Protein-DNA interaction prediction
in subset: bio
in subset: operations

RNA-binding protein prediction
type: Class
subclass of: Protein-nucleic acid interaction analysis
subclass of: Restriction
  on property: has output
  some values from: Protein interaction data
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: 1.22
has definition: Predict RNA-binding proteins.
has exact synonym: Protein-RNA interaction prediction
has exact synonym: RNA-binding protein detection
has exact synonym: RNA-protein interaction prediction
in subset: bio
in subset: operations

RNA binding site prediction
type: Class
subclass of: Nucleic acids-binding site prediction
Created in: 1.22
has definition: Predict or detect RNA-binding sites in protein sequences.
has exact synonym: Protein-RNA binding site detection
has exact synonym: Protein-RNA binding site prediction
has exact synonym: RNA binding site detection
in subset: bio
in subset: operations

DNA binding site prediction
type: Class
subclass of: Nucleic acids-binding site prediction
Created in: 1.22
has definition: Predict or detect DNA-binding sites in protein sequences.
has exact synonym: Protein-DNA binding site detection
has exact synonym: Protein-DNA binding site prediction
has narrow synonym: DNA binding site detection
in subset: bio
in subset: operations

Protein disorder prediction
type: Class
subclass of: Prediction and recognition
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Microbiology
Created in: 1.22
has definition: Identify or predict intrinsically disordered regions in proteins.
in subset: bio
in subset: operations

Information extraction
type: Class
subclass of: Text mining
Created in: 1.22
has definition: Extract structured information from unstructured ("free") or semi-structured textual documents.
has exact synonym: IE
in subset: bio
in subset: operations

Information retrieval
type: Class
subclass of: Text mining
Created in: 1.22
has definition: Retrieve resources from information systems matching a specific information need.
in subset: bio
in subset: operations

Genome analysis
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Genomics
Created in: 1.24
has exact synonym: Genomic analysis
has definition: Study of genomic feature structure, variation, function and evolution at a genomic scale.

Methylation calling
type: Class
subclass of: Methylation analysis
Created in: 1.24
has definition: The determination of cytosine methylation status of specific positions in a nucleic acid sequences (usually reads from a bisulfite sequencing experiment).
in subset: bio
in subset: operations

DNA testing
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Genomics
Created in: 1.24
has definition: 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.
has exact synonym: Genetic testing
in subset: bio
in subset: operations
comment: 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.

Sequence read processing
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.24
has definition: The processing of reads from high-throughput sequencing machines.
in subset: bio
in subset: operations

Network visualisation
type: Class
subclass of: Visualisation
subclass of: Network analysis
subclass of: Restriction
  on property: has input
  some values from: Pathway or network
Created in: 1.24
has definition: Render (visualise) a network - typically a biological network of some sort.
has exact synonym: Network rendering
has narrow synonym: Protein interaction network rendering
has narrow synonym: Protein interaction network visualisation

Pathway visualisation
type: Class
subclass of: Visualisation
subclass of: Pathway analysis
subclass of: Restriction
  on property: has input
  some values from: Pathway or network
Created in: 1.24
has definition: Render (visualise) a biological pathway.
has exact synonym: Pathway rendering
in subset: bio
in subset: operations

Network analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
subclass of: Restriction
  on property: has topic
  some values from: Systems biology
Created in: 1.24
has definition: Generate, process or analyse a biological network.
has exact synonym: Biological network analysis
has narrow synonym: Biological network modelling
has narrow synonym: Biological network prediction
has narrow synonym: Network comparison
has narrow synonym: Network modelling
has narrow synonym: Network prediction
has narrow synonym: Network simulation
has narrow synonym: Network topology simulation
in subset: bio
in subset: operations

Pathway analysis
type: Class
subclass of: Data analysis
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
subclass of: Restriction
  on property: has topic
  some values from: Systems biology
Created in: 1.24
has definition: Generate, process or analyse a biological pathway.
has exact synonym: Biological pathway analysis
has narrow synonym: Biological pathway modelling
has narrow synonym: Biological pathway prediction
has narrow synonym: Functional pathway analysis
has narrow synonym: Pathway comparison
has narrow synonym: Pathway modelling
has narrow synonym: Pathway prediction
has narrow synonym: Pathway simulation
in subset: bio
in subset: operations

Metabolic pathway prediction
type: Class
subclass of: Prediction and recognition
subclass of: Pathway analysis
Created in: 1.24
has definition: Predict a metabolic pathway.
in subset: bio
in subset: operations

Demultiplexing
type: Class
subclass of: Sequence read processing
Created in: 1.24
has definition: Assigning sequence reads to separate groups / files based on their index tag (sample origin).
has exact synonym: Sequence demultiplexing
in subset: bio
in subset: operations
comment: 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.

Dimensionality reduction
type: Class
subclass of: Calculation
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.24
has definition: A process used in statistics, machine learning, and information theory that reduces the number of random variables by obtaining a set of principal variables.
has exact synonym: Dimension reduction
in subset: bio
in subset: operations

Feature selection
type: Class
subclass of: Dimensionality reduction
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.24
has definition: A dimensionality reduction process that selects a subset of relevant features (variables, predictors) for use in model construction.
has exact synonym: Attribute selection
has exact synonym: Variable selection
has exact synonym: Variable subset selection
in subset: bio
in subset: operations

Feature extraction
type: Class
subclass of: Dimensionality reduction
subclass of: Restriction
  on property: has input
  some values from: Mass spectrum
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: 1.24
has definition: 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.
has exact synonym: Feature projection
in subset: bio
in subset: operations

Virtual screening
type: Class
subclass of: Protein-ligand docking
subclass of: Small molecule design
subclass of: Restriction
  on property: has output
  some values from: Protein-ligand complex
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: 1.24
has definition: 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).
has narrow synonym: Ligand-based screening
has narrow synonym: Ligand-based virtual screening
has narrow synonym: Structure-based screening
has narrow synonym: Structured-based virtual screening
has narrow synonym: Virtual ligand screening
in subset: bio
in subset: operations
comment: Virtual screening is widely used for lead identification, lead optimization, and scaffold hopping during drug design and discovery.

Tree dating
type: Class
subclass of: Phylogenetic analysis
Created in: 1.24
has definition: The application of phylogenetic and other methods to estimate paleogeographical events such as speciation.
has exact synonym: Biogeographic dating
has exact synonym: Speciation dating
has exact synonym: Species tree dating
has exact synonym: Tree-dating
in subset: bio
in subset: operations

Ecological modelling
type: Class
subclass of: Codon usage analysis
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has output
  some values from: DNA substitution model
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
Created in: 1.24
has definition: 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.
in subset: bio
in subset: operations

Phylogenetic tree reconciliation
type: Class
subclass of: Phylogenetic tree comparison
Created in: 1.24
has definition: 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.
has exact synonym: Gene tree / species tree reconciliation
in subset: bio
in subset: operations
comment: Methods typically test for topological similarity between trees using for example a congruence index.

Selection detection
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.24
has definition: 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.
in subset: bio
in subset: operations

Principal component analysis
type: Class
subclass of: Statistical calculation
Created in: 1.25
has definition: 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.
in subset: bio
in subset: operations

Copy number variation detection
type: Class
subclass of: Structural variation detection
Created in: 1.25
has definition: Identify where sections of the genome are repeated and the number of repeats in the genome varies between individuals.
has exact synonym: CNV detection
in subset: bio
in subset: operations

Deletion detection
type: Class
subclass of: Copy number variation detection
Created in: 1.25
has definition: Identify deletion events causing the number of repeats in the genome to vary between individuals.
in subset: bio
in subset: operations

Duplication detection
type: Class
subclass of: Copy number variation detection
Created in: 1.25
has definition: Identify duplication events causing the number of repeats in the genome to vary between individuals.
in subset: bio
in subset: operations

Complex CNV detection
type: Class
subclass of: Copy number variation detection
Created in: 1.25
has definition: 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.
in subset: bio
in subset: operations

Amplification detection
type: Class
subclass of: Copy number variation detection
Created in: 1.25
has definition: Identify amplification events causing the number of repeats in the genome to vary between individuals.
in subset: bio
in subset: operations

Adhesin prediction
type: Class
subclass of: Mapping
subclass of: Protein feature detection
subclass of: Restriction
  on property: has topic
  some values from: Immunology
Created in: 1.25
has definition: Predict adhesins in protein sequences.
in subset: bio
in subset: operations
comment: 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.

Protein design
type: Class
subclass of: Design
Created in: 1.25
has definition: Design new protein molecules with specific structural or functional properties.
has narrow synonym: Protein redesign
has narrow synonym: Rational protein design
has narrow synonym: de novo protein design
in subset: bio
in subset: operations

Small molecule design
type: Class
subclass of: Design
Created in: 1.25
has definition: 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.
has narrow synonym: Drug design
has narrow synonym: Ligand-based drug design
has narrow synonym: Structure-based drug design
has narrow synonym: Structure-based small molecule design
comment: Small molecule design can involve assessment of target druggability and flexibility, molecular docking, in silico fragment screening, molecular dynamics, and homology modeling.
comment: 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.

Power test
type: Class
subclass of: Statistical calculation
subclass of: Restriction
  on property: has input
  some values from: Evidence
subclass of: Restriction
  on property: has output
  some values from: Statistical estimate score
subclass of: Restriction
  on property: has topic
  some values from: Data quality management
subclass of: Restriction
  on property: has topic
  some values from: Data architecture, analysis and design
subclass of: Restriction
  on property: has topic
  some values from: Statistics and probability
Created in: 1.26
has definition: The estimation of the power of a test; that is the probability of correctly rejecting the null hypothesis when it is false.
has exact synonym: Estimation of statistical power
has exact synonym: Power analysis
in subset: bio
in subset: operations

DNA modification prediction
type: Class
subclass of: Nucleic acid feature detection
subclass of: Restriction
  on property: has input
  some values from: DNA sequence
subclass of: Restriction
  on property: has output
  some values from: Score
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features
subclass of: Restriction
  on property: has topic
  some values from: Epigenetics
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: 1.26
has definition: The prediction of DNA modifications (e.g. N4-methylcytosine and N6-Methyladenine) using, for example, statistical models.
in subset: bio
in subset: operations

Disease transmission analysis
type: Class
subclass of: Data analysis
subclass of: Statistical modelling
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has output
  some values from: Report
subclass of: Restriction
  on property: has topic
  some values from: Infectious disease
subclass of: Restriction
  on property: has topic
  some values from: Public health and epidemiology
Created in: 1.26
has definition: The analysis and simulation of disease transmission using, for example, statistical methods such as the SIR-model.
in subset: bio
in subset: operations

Multiple testing correction
type: Class
subclass of: Statistical calculation
subclass of: Restriction
  on property: has input
  some values from: P-value
subclass of: Restriction
  on property: has output
  some values from: Q-value
subclass of: Restriction
  on property: has topic
  some values from: Statistics and probability
Created in: 1.26
has definition: The correction of p-values from multiple statistical tests to correct for false positives.
has exact synonym: False discovery rate estimation
has exact synonym: FDR estimation
in subset: bio
in subset: operations

Data management planning
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has output
  some values from: Data management plan
subclass of: Restriction
  on property: has topic
  some values from: Data management
Created in: 1.26
has definition: Data management planning is the process of creating and updating a data management plan (DMP) for a project or an organisation.
in subset: bio
in subset: operations
comment: Good data management planning prevents unexpected legal issues or extra costs related to usage, sharing, storage, or archival of data.
comment: 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 digitisation
type: Class
subclass of: Data handling
subclass of: Restriction
  on property: has topic
  some values from: Data rescue
Created in: 1.26
Related term: Digital preservation
has definition: Data digitisation is the process of converting analog data, text, or information into a digital format, appropriate for computational analysis and preservation.
has exact synonym: Data digitalisation
has exact synonym: Data digitalization
has narrow synonym: Digital reformatting
in subset: bio
in subset: operations
editorial note: Data digitization
related match: Q632897

Topic
type: Class
disjoint with: DeprecatedClass
Created in: beta12orEarlier
notRecommendedForAnnotation: true
has definition: 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.
has related synonym: sumo:FieldOfStudy
in subset: bio
in subset: topics
broad match: Method
related match: Quality
broad match: BFO_0000002
related match: BFO_0000019
related match: quality
broad match: Category
broad match: Perpetuant

Nucleic acids
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: The processing and analysis of nucleic acid sequence, structural and other data.
has exact synonym: Nucleic acid bioinformatics
has exact synonym: Nucleic acid informatics
has human readable id: Nucleic_acids
has narrow synonym: Nucleic acid physicochemistry
has narrow synonym: Nucleic acid properties
in subset: bio
in subset: topics

Proteins
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: Archival, processing and analysis of protein data, typically molecular sequence and structural data.
has exact synonym: Protein bioinformatics
has exact synonym: Protein informatics
has human readable id: Proteins
has narrow synonym: Protein databases
in subset: bio
in subset: topics

Metabolites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.
in subset: obsolete
replaced by: Small molecules
deprecated: true

Sequence analysis
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.
has human readable id: Sequence_analysis
has narrow synonym: Biological sequences
has narrow synonym: Sequence databases
in subset: bio
in subset: events
in subset: topics

Structure analysis
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: The curation, processing, analysis and prediction of data about the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.
has exact synonym: Biomolecular structure
has exact synonym: Structural bioinformatics
has human readable id: Structure_analysis
has narrow synonym: Computational structural biology
has narrow synonym: Molecular structure
has narrow synonym: Structure data resources
has narrow synonym: Structure databases
has narrow synonym: Structures
in subset: bio
in subset: events
in subset: topics
comment: This includes related concepts such as structural properties, alignments and structural motifs.

Structure prediction
type: Class
subclass of: Structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Structure_prediction
has narrow synonym: DNA structure prediction
has narrow synonym: Nucleic acid design
has narrow synonym: Nucleic acid folding
has narrow synonym: Nucleic acid structure prediction
has narrow synonym: Protein fold recognition
has narrow synonym: Protein structure prediction
has narrow synonym: RNA structure prediction
in subset: bio
in subset: topics
comment: 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).

Alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence analysis
consider: Structure analysis
has definition: The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).
in subset: obsolete
deprecated: true

Phylogeny
type: Class
subclass of: Evolutionary biology
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: The study of evolutionary relationships amongst organisms.
has human readable id: Phylogeny
has narrow synonym: Phylogenetic clocks
has narrow synonym: Phylogenetic dating
has narrow synonym: Phylogenetic simulation
has narrow synonym: Phylogenetic stratigraphy
has narrow synonym: Phylogeny reconstruction
in subset: bio
in subset: events
in subset: topics
comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.

Functional genomics
type: Class
subclass of: Genomics
subclass of: Function analysis
Created in: beta12orEarlier
isdebtag: true
has definition: The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.
has human readable id: Functional_genomics
in subset: bio
in subset: events
in subset: topics

Ontology and terminology
type: Class
subclass of: Informatics
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Ontology_and_terminology
has narrow synonym: Applied ontology
has narrow synonym: Ontologies
has narrow synonym: Ontology
has narrow synonym: Ontology relations
has narrow synonym: Terminology
has narrow synonym: Upper ontology
in subset: bio
in subset: events
in subset: topics

Information retrieval
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information.
in subset: obsolete
consider: Database management
consider: Data management
deprecated: true

Bioinformatics
type: Class
subclass of: Informatics
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.5.6 Bioinformatics
has definition: The archival, curation, processing and analysis of complex biological data.
has human readable id: Bioinformatics
in subset: bio
in subset: events
in subset: topics
comment: This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation.

Data visualisation
type: Class
subclass of: Computer science
Created in: beta12orEarlier
isdebtag: true
has broad synonym: Computer graphics
has db xref: VT 1.2.5 Computer graphics
has definition: Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.
has exact synonym: Data rendering
has human readable id: Data_visualisation
in subset: bio
in subset: topics

Nucleic acid thermodynamics
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Nucleic acid structure analysis
has definition: The study of the thermodynamic properties of a nucleic acid.
in subset: obsolete
deprecated: true

Nucleic acid structure analysis
type: Class
subclass of: Nucleic acids
subclass of: Structure analysis
Created in: beta12orEarlier
has definition: The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.
has exact synonym: Nucleic acid structure
has human readable id: Nucleic_acid_structure_analysis
has narrow synonym: DNA melting
has narrow synonym: DNA structure
has narrow synonym: Nucleic acid denaturation
has narrow synonym: Nucleic acid thermodynamics
has narrow synonym: RNA alignment
has narrow synonym: RNA structure
has narrow synonym: RNA structure alignment
in subset: bio
in subset: topics
comment: Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.

RNA
type: Class
subclass of: Nucleic acids
Created in: beta12orEarlier
has definition: RNA sequences and structures.
has human readable id: RNA
has narrow synonym: Small RNA
in subset: bio
in subset: topics

Nucleic acid restriction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Enzymes
has definition: Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.
in subset: obsolete
deprecated: true

Mapping
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
isdebtag: true
has definition: 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).
has human readable id: Mapping
has narrow synonym: Genetic linkage
has narrow synonym: Linkage
has narrow synonym: Linkage mapping
has narrow synonym: Synteny
in subset: bio
in subset: topics
comment: 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.

Genetic codes and codon usage
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene expression
has definition: The study of codon usage in nucleotide sequence(s), genetic codes and so on.
in subset: obsolete
deprecated: true

Protein expression
type: Class
subclass of: Proteins
Created in: beta12orEarlier
has definition: The translation of mRNA into protein and subsequent protein processing in the cell.
has human readable id: Protein_expression
has narrow synonym: Translation
in subset: bio
in subset: events
in subset: topics

Gene finding
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene structure
has definition: Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.
in subset: obsolete
comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
deprecated: true

Transcription
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene expression
has definition: The transcription of DNA into mRNA.
in subset: obsolete
deprecated: true

Promoters
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Transcription factors and regulatory sites
has definition: Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).
in subset: obsolete
deprecated: true

Nucleic acid folding
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: The folding (in 3D space) of nucleic acid molecules.
in subset: obsolete
replaced by: Nucleic acid structure analysis
deprecated: true

Gene structure
type: Class
subclass of: Molecular genetics
Created in: beta12orEarlier
isdebtag: true
has definition: Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
has exact synonym: Gene features
has human readable id: Gene_structure
has narrow synonym: Fusion genes
in subset: bio
in subset: topics
comment: This includes the study of promoters, coding regions etc.
comment: 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.

Proteomics
type: Class
subclass of: Omics
Created in: beta12orEarlier
isdebtag: true
has definition: Protein and peptide identification, especially in the study of whole proteomes of organisms.
has human readable id: Proteomics
has narrow synonym: Bottom-up proteomics
has narrow synonym: Discovery proteomics
has narrow synonym: MS-based targeted proteomics
has narrow synonym: MS-based untargeted proteomics
has narrow synonym: Metaproteomics
has narrow synonym: Peptide identification
has narrow synonym: Protein and peptide identification
has narrow synonym: Quantitative proteomics
has narrow synonym: Targeted proteomics
has narrow synonym: Top-down proteomics
in subset: bio
in subset: events
in subset: topics
comment: Includes metaproteomics: proteomics analysis of an environmental sample.
comment: 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.

Structural genomics
type: Class
subclass of: Genomics
subclass of: Structural biology
Created in: beta12orEarlier
isdebtag: true
has definition: The elucidation of the three dimensional structure for all (available) proteins in a given organism.
has human readable id: Structural_genomics
in subset: bio
in subset: events
in subset: topics

Protein properties
type: Class
subclass of: Proteins
Created in: beta12orEarlier
isdebtag: true
has definition: The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.
has exact synonym: Protein physicochemistry
has human readable id: Protein_properties
has narrow synonym: Protein hydropathy
in subset: bio
in subset: topics

Protein interactions
type: Class
subclass of: Proteins
subclass of: Molecular interactions, pathways and networks
Created in: beta12orEarlier
isdebtag: true
has definition: Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.
has human readable id: Protein_interactions
has narrow synonym: Protein interaction map
has narrow synonym: Protein interaction networks
has narrow synonym: Protein interactome
has narrow synonym: Protein-DNA interaction
has narrow synonym: Protein-DNA interactions
has narrow synonym: Protein-RNA interaction
has narrow synonym: Protein-RNA interactions
has narrow synonym: Protein-ligand interactions
has narrow synonym: Protein-nucleic acid interactions
has narrow synonym: Protein-protein interactions
in subset: bio
in subset: topics
comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.

Protein folding, stability and design
type: Class
subclass of: Protein structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Protein_folding_stability_and_design
has narrow synonym: Protein design
has narrow synonym: Protein folding
has narrow synonym: Protein residue interactions
has narrow synonym: Protein stability
has narrow synonym: Rational protein design
in subset: bio
in subset: topics

Two-dimensional gel electrophoresis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Proteomics
has definition: Two-dimensional gel electrophoresis image and related data.
in subset: obsolete
deprecated: true

Mass spectrometry
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase.
in subset: obsolete
replaced by: Proteomics experiment
deprecated: true

Protein microarrays
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Proteomics
has definition: Protein microarray data.
in subset: obsolete
deprecated: true

Protein hydropathy
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein properties
has definition: The study of the hydrophobic, hydrophilic and charge properties of a protein.
in subset: obsolete
deprecated: true

Protein targeting and localisation
type: Class
subclass of: Protein expression
Created in: beta12orEarlier
has definition: The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export.
has human readable id: Protein_targeting_and_localisation
has narrow synonym: Protein localisation
has narrow synonym: Protein sorting
has narrow synonym: Protein targeting
in subset: bio
in subset: topics

Protein cleavage sites and proteolysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Proteomics
has definition: Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.
in subset: obsolete
deprecated: true

Protein structure comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: The comparison of two or more protein structures.
in subset: obsolete
replaced by: Structure analysis
comment: Use this concept for methods that are exclusively for protein structure.
deprecated: true

Protein residue interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein folding, stability and design
has definition: The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.
in subset: obsolete
deprecated: true

Protein-protein interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein interactions
has definition: Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.
in subset: obsolete
deprecated: true

Protein-ligand interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein interactions
has definition: Protein-ligand (small molecule) interactions.
in subset: obsolete
deprecated: true

Protein-nucleic acid interactions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein interactions
has definition: Protein-DNA/RNA interactions.
in subset: obsolete
deprecated: true

Protein design
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein folding, stability and design
has definition: The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
in subset: obsolete
deprecated: true

G protein-coupled receptors (GPCR)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Membrane and lipoproteins
has definition: G-protein coupled receptors (GPCRs).
in subset: obsolete
deprecated: true

Carbohydrates
type: Class
subclass of: Structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: Carbohydrates, typically including structural information.
has human readable id: Carbohydrates
in subset: bio
in subset: topics

Lipidomics
type: Class
subclass of: Structure analysis
subclass of: Metabolomics
Created in: beta12orEarlier
isdebtag: true
Related term: Lipidome
Related term: Lipids
has definition: Lipids and their structures.
has human readable id: Lipids
in subset: bio
in subset: topics

Small molecules
type: Class
subclass of: Structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.
has human readable id: Small_molecules
has narrow synonym: Amino acids
has narrow synonym: Chemical structures
has narrow synonym: Drug structures
has narrow synonym: Drug targets
has narrow synonym: Drugs and target structures
has narrow synonym: Metabolite structures
has narrow synonym: Peptides
has narrow synonym: Peptides and amino acids
has narrow synonym: Target structures
has narrow synonym: Targets
has narrow synonym: Toxins
has narrow synonym: Toxins and targets
has related synonym: CHEBI:23367
in subset: bio
in subset: topics
comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included.
comment: This concept excludes macromolecules such as proteins and nucleic acids.
comment: 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.

Sequence editing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence analysis
consider: Bioinformatics
has definition: Edit, convert or otherwise change a molecular sequence, either randomly or specifically.
in subset: obsolete
deprecated: true

Sequence composition, complexity and repeats
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Sequence_composition_complexity_and_repeats
has narrow synonym: Low complexity sequences
has narrow synonym: Nucleic acid repeats
has narrow synonym: Protein repeats
has narrow synonym: Protein sequence repeats
has narrow synonym: Repeat sequences
has narrow synonym: Sequence complexity
has narrow synonym: Sequence composition
has narrow synonym: Sequence repeats
in subset: bio
in subset: topics
comment: 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.
comment: This includes short repetitive subsequences (repeat sequences) in a protein sequence.

Sequence motifs
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
has definition: Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.
in subset: obsolete
deprecated: true

Sequence comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: The comparison of two or more molecular sequences, for example sequence alignment and clustering.
in subset: obsolete
replaced by: Sequence analysis
comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
deprecated: true

Sequence sites, features and motifs
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Sequence_sites_features_and_motifs
has narrow synonym: Functional sites
has narrow synonym: HMMs
has narrow synonym: Sequence features
has narrow synonym: Sequence motifs
has narrow synonym: Sequence profiles
has narrow synonym: Sequence sites
in subset: bio
in subset: topics

Sequence database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence analysis
has definition: Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).
in subset: obsolete
comment: The query is a sequence-based entity such as another sequence, a motif or profile.
deprecated: true

Sequence clustering
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: The comparison and grouping together of molecular sequences on the basis of their similarities.
in subset: obsolete
replaced by: Sequence analysis
comment: This includes systems that generate, process and analyse sequence clusters.
deprecated: true

Protein structural motifs and surfaces
type: Class
subclass of: Protein structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.
has exact synonym: Protein 3D motifs
has human readable id: Protein_structural_motifs_and_surfaces
has narrow synonym: Protein structural features
has narrow synonym: Protein structural motifs
has narrow synonym: Protein surfaces
has narrow synonym: Structural motifs
in subset: bio
in subset: topics
comment: 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.

Structural (3D) profiles
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Structure analysis
has definition: 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.
in subset: obsolete
deprecated: true

Protein structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Nucleic acid structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
in subset: obsolete
replaced by: Nucleic acid structure analysis
deprecated: true

Ab initio structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Homology modelling
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.4
Old parent: Thing
consider: Molecular modelling
has definition: The modelling of the three-dimensional structure of a protein using known sequence and structural data.
in subset: obsolete
deprecated: true

Molecular dynamics
type: Class
subclass of: Structure prediction
subclass of: Biomolecular simulation
Created in: beta12orEarlier
isdebtag: true
has broad synonym: Molecular flexibility
has broad synonym: Molecular motions
has definition: The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
has human readable id: Molecular_dynamics
has narrow synonym: Protein dynamics
in subset: bio
in subset: topics
comment: 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 docking
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
isdebtag: true
Obsolete since: 1.12
Old parent: Thing
has definition: The modelling the structure of proteins in complex with small molecules or other macromolecules.
in subset: obsolete
replaced by: Molecular modelling
deprecated: true

Protein secondary structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: The prediction of secondary or supersecondary structure of protein sequences.
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Protein tertiary structure prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: The prediction of tertiary structure of protein sequences.
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Protein fold recognition
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: The alignment of molecular sequences or sequence profiles (representing sequence alignments).
in subset: obsolete
replaced by: Sequence analysis
comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
deprecated: true

Structure alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.7
Old parent: Thing
has definition: The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).
in subset: obsolete
replaced by: Structure analysis
comment: This includes the generation, storage, analysis, rendering etc. of structure alignments.
deprecated: true

Threading
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
in subset: obsolete
replaced by: Structure prediction
deprecated: true

Sequence profiles and HMMs
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
has definition: Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.
in subset: obsolete
comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
deprecated: true

Phylogeny reconstruction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Phylogenetics
has definition: The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.
in subset: obsolete
comment: Currently too specific for the topic sub-ontology (but might be unobsoleted).
deprecated: true

Phylogenomics
type: Class
subclass of: Sequence analysis
subclass of: Genomics
Created in: beta12orEarlier
isdebtag: true
has definition: The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.
has human readable id: Phylogenomics
in subset: bio
in subset: events
in subset: topics

Virtual PCR
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Nucleic acids
has definition: Simulated polymerase chain reaction (PCR).
in subset: obsolete
deprecated: true

Sequence assembly
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
isdebtag: true
has definition: The assembly of fragments of a DNA sequence to reconstruct the original sequence.
has human readable id: Sequence_assembly
has narrow synonym: Assembly
in subset: bio
in subset: topics
comment: 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'.

Genetic variation
type: Class
subclass of: Molecular genetics
subclass of: Genomics
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has exact synonym: DNA variation
has human readable id: Genetic_variation
has narrow synonym: Genomic variation
has narrow synonym: Mutation
has narrow synonym: Polymorphism
has narrow synonym: Somatic mutations
in subset: bio
in subset: topics

Microarrays
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene expression
has definition: Microarrays, for example, to process microarray data or design probes and experiments.
in subset: obsolete
deprecated: true

Pharmacology
type: Class
subclass of: Biomedical science
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.1.7 Pharmacology and pharmacy
has definition: The study of drugs and their effects or responses in living systems.
has human readable id: Pharmacology
has narrow synonym: Computational pharmacology
has narrow synonym: Pharmacoinformatics
in subset: bio
in subset: events
in subset: topics

Gene expression
type: Class
subclass of: Molecular genetics
Created in: beta12orEarlier
isdebtag: true
has alternative id: http://edamontology.org/topic_0197
has definition: The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.
has exact synonym: Expression
has human readable id: Gene_expression
has narrow synonym: Codon usage
has narrow synonym: DNA chips
has narrow synonym: DNA microarrays
has narrow synonym: Gene expression profiling
has narrow synonym: Gene transcription
has narrow synonym: Gene translation
has narrow synonym: Transcription
in subset: bio
in subset: events
in subset: topics
comment: 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.
comment: This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.

Gene regulation
type: Class
subclass of: Gene expression
Created in: beta12orEarlier
isdebtag: true
has definition: The regulation of gene expression.
has narrow synonym: Regulatory genomics
in subset: bio
in subset: topics

Pharmacogenomics
type: Class
subclass of: Pharmacology
subclass of: Genomics
Created in: beta12orEarlier
isdebtag: true
has definition: The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
has human readable id: Pharmacogenomics
has narrow synonym: Pharmacogenetics
in subset: bio
in subset: events
in subset: topics

Medicinal chemistry
type: Class
subclass of: Drug discovery
subclass of: Synthetic chemistry
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.1.4 Medicinal chemistry
has definition: The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.
has exact synonym: Drug design
has human readable id: Medicinal_chemistry
in subset: bio
in subset: events
in subset: topics
comment: This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.

Fish
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Model organisms
has definition: Information on a specific fish genome including molecular sequences, genes and annotation.
in subset: obsolete
deprecated: true

Flies
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Model organisms
has definition: Information on a specific fly genome including molecular sequences, genes and annotation.
in subset: obsolete
deprecated: true

Mice or rats
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Vertebrates
consider: Model organisms
has definition: Information on a specific mouse or rat genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a group of mice / rats or all mice / rats.
deprecated: true

Worms
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Model organisms
has definition: Information on a specific worm genome including molecular sequences, genes and annotation.
in subset: obsolete
deprecated: true

Literature analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.
in subset: obsolete
replaced by: Natural language processing
deprecated: true

Natural language processing
type: Class
subclass of: Literature and language
subclass of: Computer science
Created in: beta12orEarlier
has definition: 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.
has exact synonym: NLP
has human readable id: Natural_language_processing
has narrow synonym: BioNLP
has narrow synonym: Literature mining
has narrow synonym: Text analytics
has narrow synonym: Text data mining
has narrow synonym: Text mining
in subset: bio
in subset: events
in subset: topics

Data curation and archival
type: Class
subclass of: Data management
Created in: beta12orEarlier
Related term: Data archive
Related term: Data library
Related term: Data provenance
Related term: Data registry
Related term: Data repository
Related term: Data storage
Related term: Deposition database
Related term: Research data archive
Related term: Research data repository
has definition: 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.
has exact synonym: Data archival
has exact synonym: Data archiving
has exact synonym: Data curation
has exact synonym: Data preservation
has narrow synonym: Database curation
has narrow synonym: Research data archiving
in subset: bio
in subset: events
in subset: topics
comment: Note that biocuration is a more specific concept than simply curation and archival of bioscientific data.
comment: 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).
narrow match: Q17155735
related match: Q5227240

Document, record and content management
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The management and manipulation of digital documents, including database records, files and reports.
in subset: obsolete
replaced by: Database management
deprecated: true

Sequence annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data curation and archival
has definition: Annotation of a molecular sequence.
in subset: obsolete
deprecated: true

Genome annotation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Data curation and archival
consider: Model organisms
consider: Genomics
has definition: Annotation of a genome.
in subset: obsolete
deprecated: true

NMR
type: Class
subclass of: Structural biology
subclass of: Imaging
Created in: beta12orEarlier
has broad synonym: Spectroscopy
has definition: 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.
has exact synonym: NMR spectroscopy
has exact synonym: Nuclear magnetic resonance spectroscopy
has human readable id: NMR
has narrow synonym: HOESY
has narrow synonym: Heteronuclear Overhauser Effect Spectroscopy
has narrow synonym: NOESY
has narrow synonym: Nuclear Overhauser Effect Spectroscopy
has narrow synonym: ROESY
has narrow synonym: Rotational Frame Nuclear Overhauser Effect Spectroscopy
in subset: bio
in subset: events
in subset: topics

Sequence classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.12
Old parent: Thing
has definition: The classification of molecular sequences based on some measure of their similarity.
in subset: obsolete
replaced by: Sequence analysis
comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
deprecated: true

Protein classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene and protein families
has definition: primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.
in subset: obsolete
deprecated: true

Sequence motif or profile
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Sequence sites, features and motifs
has definition: Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.
in subset: obsolete
comment: This includes comparison, discovery, recognition etc. of sequence motifs.
deprecated: true

Protein modifications
type: Class
subclass of: Protein expression
Created in: beta12orEarlier
isdebtag: true
has definition: Protein chemical modifications, e.g. post-translational modifications.
has exact synonym: PTMs
has exact synonym: Post-translational modifications
has exact synonym: Protein post-translational modification
has human readable id: Protein_modifications
has narrow synonym: Post-translation modifications
has narrow synonym: Protein chemical modifications
has narrow synonym: Protein post-translational modifications
has related synonym: GO:0006464
has related synonym: MOD:00000
in subset: bio
in subset: topics
comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)

Molecular interactions, pathways and networks
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has alternative id: http://edamontology.org/topic_3076
has definition: Molecular interactions, biological pathways, networks and other models.
has human readable id: Molecular_interactions_pathways_and_networks
has narrow synonym: Biological models
has narrow synonym: Biological networks
has narrow synonym: Biological pathways
has narrow synonym: Cellular process pathways
has narrow synonym: Disease pathways
has narrow synonym: Environmental information processing pathways
has narrow synonym: Gene regulatory networks
has narrow synonym: Genetic information processing pathways
has narrow synonym: Interactions
has narrow synonym: Interactome
has narrow synonym: Metabolic pathways
has narrow synonym: Molecular interactions
has narrow synonym: Networks
has narrow synonym: Pathways
has narrow synonym: Signal transduction pathways
has narrow synonym: Signaling pathways
in subset: bio
in subset: events
in subset: topics

Informatics
type: Class
subclass of: Topic
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.3 Information sciences
has db xref: VT 1.3.3 Information retrieval
has db xref: VT 1.3.4 Information management
has db xref: VT 1.3.5 Knowledge management
has db xref: VT 1.3.99 Other
has definition: The study and practice of information processing and use of computer information systems.
has exact synonym: Information management
has exact synonym: Information science
has exact synonym: Knowledge management
has human readable id: Informatics
in subset: bio
in subset: topics

Literature data resources
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.
in subset: obsolete
replaced by: Literature and language
deprecated: true

Laboratory information management
type: Class
subclass of: Informatics
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has human readable id: Laboratory_Information_management
has narrow synonym: Laboratory resources
in subset: bio
in subset: events
in subset: topics

Cell and tissue culture
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Cell biology
has definition: General cell culture or data on a specific cell lines.
in subset: obsolete
deprecated: true

Ecology
type: Class
subclass of: Biosciences
subclass of: Environmental sciences
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.5.15 Ecology
has definition: The ecological and environmental sciences and especially the application of information technology (ecoinformatics).
has human readable id: Ecology
has narrow synonym: Computational ecology
has narrow synonym: Ecoinformatics
has narrow synonym: Ecological informatics
has narrow synonym: Ecosystem science
in subset: bio
in subset: events
in subset: topics

Electron microscopy
type: Class
subclass of: Structural biology
subclass of: Imaging
Created in: beta12orEarlier
has broad synonym: Electron diffraction experiment
has definition: 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.
has human readable id: Electron_microscopy
has narrow synonym: Electron crystallography
has narrow synonym: SEM
has narrow synonym: Scanning electron microscopy
has narrow synonym: Single particle electron microscopy
has narrow synonym: TEM
has narrow synonym: Transmission electron microscopy
in subset: bio
in subset: events
in subset: topics

Cell cycle
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Cell biology
has definition: The cell cycle including key genes and proteins.
in subset: obsolete
deprecated: true

Peptides and amino acids
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The physicochemical, biochemical or structural properties of amino acids or peptides.
in subset: obsolete
replaced by: Small molecules
deprecated: true

Organelles
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Cell biology
has definition: A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).
in subset: obsolete
deprecated: true

Ribosomes
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Cell biology
has definition: Ribosomes, typically of ribosome-related genes and proteins.
in subset: obsolete
deprecated: true

Scents
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Small molecules
has definition: A database about scents.
in subset: obsolete
deprecated: true

Drugs and target structures
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The structures of drugs, drug target, their interactions and binding affinities.
in subset: obsolete
replaced by: Small molecules
deprecated: true

Model organisms
type: Class
subclass of: Biology
Created in: beta12orEarlier
isdebtag: true
has definition: A specific organism, or group of organisms, used to study a particular aspect of biology.
has exact synonym: Organisms
has human readable id: Model_organisms
in subset: bio
in subset: events
in subset: topics
comment: 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.

Genomics
type: Class
subclass of: Omics
Created in: beta12orEarlier
isdebtag: true
has definition: Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
has human readable id: Genomics
has narrow synonym: Exomes
has narrow synonym: Genome annotation
has narrow synonym: Genomes
has narrow synonym: Personal genomics
has narrow synonym: Synthetic genomics
has narrow synonym: Viral genomics
has narrow synonym: Whole genomes
in subset: bio
in subset: events
in subset: topics

Gene and protein families
type: Class
subclass of: Proteins
subclass of: Molecular genetics
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has exact synonym: Genes, gene family or system
has human readable id: Gene_and protein_families
has narrow synonym: Gene families
has narrow synonym: Gene family
has narrow synonym: Gene system
has narrow synonym: Protein families
has narrow synonym: Protein sequence classification
in subset: bio
in subset: events
in subset: topics
comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.

Chromosomes
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Study of chromosomes.
in subset: obsolete
replaced by: DNA
deprecated: true

Genotype and phenotype
type: Class
subclass of: Genetics
Created in: beta12orEarlier
isdebtag: true
has definition: 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.
has exact synonym: Genotype and phenotype resources
has exact synonym: Genotype-phenotype
has exact synonym: Genotype-phenotype analysis
has human readable id: Genotype_and_phenotype
has narrow synonym: Genotype
has narrow synonym: Genotyping
has narrow synonym: Phenotype
has narrow synonym: Phenotyping
in subset: bio
in subset: events
in subset: topics

Gene expression and microarray
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Gene expression
has definition: Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.
in subset: obsolete
deprecated: true

Probes and primers
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
isdebtag: true
has definition: Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence.
has human readable id: Probes_and_primers
has narrow synonym: Primer quality
has narrow synonym: Primers
has narrow synonym: Probes
in subset: bio
in subset: topics
comment: This includes the design of primers for PCR and DNA amplification or the design of molecular probes.

Pathology
type: Class
subclass of: Medicine
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.1.6 Pathology
has definition: Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.
has exact synonym: Disease
has human readable id: Pathology
in subset: bio
in subset: events
in subset: topics

Specific protein resources
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene and protein families
has definition: A particular protein, protein family or other group of proteins.
in subset: obsolete
deprecated: true

Taxonomy
type: Class
subclass of: Evolutionary biology
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.5.25 Taxonomy
has definition: Organism classification, identification and naming.
has human readable id: Taxonomy
in subset: bio
in subset: topics

Protein sequence analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Nucleic acid sequence analysis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Repeat sequences
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence composition, complexity and repeats
has definition: The repetitive nature of molecular sequences.
in subset: obsolete
deprecated: true

Low complexity sequences
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence composition, complexity and repeats
has definition: The (character) complexity of molecular sequences, particularly regions of low complexity.
in subset: obsolete
deprecated: true

Proteome
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequence analysis
has definition: A specific proteome including protein sequences and annotation.
in subset: obsolete
deprecated: true

DNA
type: Class
subclass of: Nucleic acids
Created in: beta12orEarlier
has definition: DNA sequences and structure, including processes such as methylation and replication.
has exact synonym: DNA analysis
has human readable id: DNA
has narrow synonym: Ancient DNA
has narrow synonym: Chromosomes
in subset: bio
in subset: topics
comment: The DNA sequences might be coding or non-coding sequences.

Coding RNA
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

Functional, regulatory and non-coding RNA
type: Class
subclass of: RNA
subclass of: Gene structure
Created in: beta12orEarlier
isdebtag: true
has definition: Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).
has human readable id: Functional_regulatory_and_non-coding_RNA
has narrow synonym: Functional RNA
has narrow synonym: Long ncRNA
has narrow synonym: Long non-coding RNA
has narrow synonym: Non-coding RNA
has narrow synonym: Regulatory RNA
has narrow synonym: Small and long non-coding RNAs
has narrow synonym: Small interfering RNA
has narrow synonym: Small ncRNA
has narrow synonym: Small non-coding RNA
has narrow synonym: Small nuclear RNA
has narrow synonym: Small nucleolar RNA
has narrow synonym: lncRNA
has narrow synonym: miRNA
has narrow synonym: microRNA
has narrow synonym: ncRNA
has narrow synonym: piRNA
has narrow synonym: piwi-interacting RNA
has narrow synonym: siRNA
has narrow synonym: snRNA
has narrow synonym: snoRNA
in subset: bio
in subset: topics
comment: 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).

rRNA
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Functional, regulatory and non-coding RNA
has definition: One or more ribosomal RNA (rRNA) sequences.
in subset: obsolete
deprecated: true

tRNA
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Functional, regulatory and non-coding RNA
has definition: One or more transfer RNA (tRNA) sequences.
in subset: obsolete
deprecated: true

Protein secondary structure
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Protein secondary structure or secondary structure alignments.
in subset: obsolete
replaced by: Protein structure analysis
comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
deprecated: true

RNA structure
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Nucleic acid structure analysis
has definition: RNA secondary or tertiary structure and alignments.
in subset: obsolete
deprecated: true

Protein tertiary structure
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.8
Old parent: Thing
has definition: Protein tertiary structures.
in subset: obsolete
replaced by: Protein structure analysis
deprecated: true

Nucleic acid classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Gene and protein families
has definition: Classification of nucleic acid sequences and structures.
in subset: obsolete
deprecated: true

Protein families
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.14
Old parent: Thing
has definition: 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.
in subset: obsolete
replaced by: Gene and protein families
deprecated: true

Protein folds and structural domains
type: Class
subclass of: Protein structure analysis
Created in: beta12orEarlier
isdebtag: true
has definition: Protein tertiary structural domains and folds in a protein or polypeptide chain.
has human readable id: Protein_folds_and_structural_domains
has narrow synonym: Intramembrane regions
has narrow synonym: Protein domains
has narrow synonym: Protein folds
has narrow synonym: Protein membrane regions
has narrow synonym: Protein structural domains
has narrow synonym: Protein topological domains
has narrow synonym: Protein transmembrane regions
has narrow synonym: Transmembrane regions
in subset: bio
in subset: topics
comment: This includes topological domains such as cytoplasmic regions in a protein.
comment: 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.

Nucleic acid sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
has definition: Nucleotide sequence alignments.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Protein sequence alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence analysis
has definition: Protein sequence alignments.
in subset: obsolete
comment: A sequence profile typically represents a sequence alignment.
deprecated: true

Nucleic acid sites and features
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
consider: Nucleic acid sequence analysis
has definition: The archival, detection, prediction and analysis ofpositional features such as functional sites in nucleotide sequences.
in subset: obsolete
deprecated: true

Protein sites and features
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
consider: Protein sequence analysis
has definition: The detection, identification and analysis of positional features in proteins, such as functional sites.
in subset: obsolete
deprecated: true

Transcription factors and regulatory sites
type: Class
subclass of: Proteins
subclass of: Gene expression
subclass of: DNA binding sites
Created in: beta12orEarlier
has definition: 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.
has human readable id: Transcription_factors_and_regulatory_sites
has narrow synonym: -10 signals
has narrow synonym: -35 signals
has narrow synonym: Attenuators
has narrow synonym: CAAT signals
has narrow synonym: CAT box
has narrow synonym: CCAAT box
has narrow synonym: CpG islands
has narrow synonym: Enhancers
has narrow synonym: GC signals
has narrow synonym: Isochores
has narrow synonym: Promoters
has narrow synonym: TATA signals
has narrow synonym: TFBS
has narrow synonym: Terminators
has narrow synonym: Transcription factor binding sites
has narrow synonym: Transcription factors
has narrow synonym: Transcriptional regulatory sites
in subset: bio
in subset: topics
comment: This includes CpG rich regions (isochores) in a nucleotide sequence.
comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
comment: 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.

Phosphorylation sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: Protein modifications
consider: Protein sites and features
has definition: Protein phosphorylation and phosphorylation sites in protein sequences.
in subset: obsolete
deprecated: true

Metabolic pathways
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Metabolic pathways.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Signaling pathways
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Signaling pathways.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Protein and peptide identification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Proteomics
has definition: Protein and peptide identification.
in subset: obsolete
deprecated: true

Workflows
type: Class
subclass of: Data management
Created in: beta12orEarlier
has definition: Biological or biomedical analytical workflows or pipelines.
has exact synonym: Pipelines
has human readable id: Workflows
has narrow synonym: Software integration
has narrow synonym: Tool integration
has narrow synonym: Tool interoperability
in subset: bio
in subset: topics

Data types and objects
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.0
Old parent: Thing
consider: Bioinformatics
has definition: Structuring data into basic types and (computational) objects.
in subset: obsolete
deprecated: true

Theoretical biology
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Computational biology
has definition: Theoretical biology.
in subset: obsolete
deprecated: true

Mitochondria
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Cell biology
has definition: Mitochondria, typically of mitochondrial genes and proteins.
in subset: obsolete
deprecated: true

Plant biology
type: Class
subclass of: Biology
Created in: beta12orEarlier
has db xref: VT 1.5.10 Botany
has db xref: VT 1.5.22 Plant science
has definition: Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.
has exact synonym: Botany
has exact synonym: Plant
has exact synonym: Plant science
has exact synonym: Plants
has human readable id: Plant_biology
has narrow synonym: Plant anatomy
has narrow synonym: Plant cell biology
has narrow synonym: Plant ecology
has narrow synonym: Plant genetics
has narrow synonym: Plant physiology
in subset: bio
in subset: topics
comment: The resource may be specific to a plant, a group of plants or all plants.

Virology
type: Class
subclass of: Biology
Created in: beta12orEarlier
has db xref: VT 1.5.28
has definition: Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.
has human readable id: Virology
in subset: bio
in subset: topics

Fungi
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Eukaryotes
consider: Model organisms
has definition: Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a fungus, a group of fungi or all fungi.
deprecated: true

Pathogens
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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.
Obsolete since: 1.17
Old parent: Model organisms
consider: Model organisms
has definition: Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens.
deprecated: true

Arabidopsis
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Plant biology
has definition: Arabidopsis-specific data.
in subset: obsolete
deprecated: true

Rice
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Plant biology
has definition: Rice-specific data.
in subset: obsolete
deprecated: true

Genetic mapping and linkage
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Mapping
has definition: 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.
in subset: obsolete
deprecated: true

Comparative genomics
type: Class
subclass of: Genomics
Created in: beta12orEarlier
isdebtag: true
has definition: The study (typically comparison) of the sequence, structure or function of multiple genomes.
has human readable id: Comparative_genomics
in subset: bio
in subset: events
in subset: topics

Mobile genetic elements
type: Class
subclass of: Gene structure
Created in: beta12orEarlier
has definition: Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.
has human readable id: Mobile_genetic_elements
has narrow synonym: Transposons
in subset: bio
in subset: topics

Human disease
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Pathology
has definition: Human diseases, typically describing the genes, mutations and proteins implicated in disease.
in subset: obsolete
deprecated: true

Immunology
type: Class
subclass of: Biomedical science
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.1.3 Immunology
has definition: The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.
has human readable id: Immunology
in subset: bio
in subset: events
in subset: topics

Membrane and lipoproteins
type: Class
subclass of: Proteins
Created in: beta12orEarlier
isdebtag: true
has definition: Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.
has human readable id: Membrane_and_lipoproteins
has narrow synonym: Lipoproteins
has narrow synonym: Membrane proteins
has narrow synonym: Transmembrane proteins
in subset: bio
in subset: topics

Enzymes
type: Class
subclass of: Proteins
Created in: beta12orEarlier
isdebtag: true
has definition: Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.
has exact synonym: Enzymology
has human readable id: Enzymes
in subset: bio
in subset: topics

Primers
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: PCR primers and hybridisation oligos in a nucleic acid sequence.
in subset: obsolete
replaced by: Probes and primers
deprecated: true

PolyA signal or sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

CpG island and isochores
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: CpG rich regions (isochores) in a nucleotide sequence.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

Restriction sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.
in subset: obsolete
replaced by: DNA binding sites
deprecated: true

Splice sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
consider: RNA splicing
consider: Gene transcripts
has definition: Splice sites in a nucleotide sequence or alternative RNA splicing events.
in subset: obsolete
deprecated: true

Matrix/scaffold attachment sites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.
in subset: obsolete
replaced by: DNA binding sites
deprecated: true

Operon
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Operons (operators, promoters and genes) from a bacterial genome.
in subset: obsolete
replaced by: Gene structure
deprecated: true

Promoters
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.
in subset: obsolete
replaced by: Transcription factors and regulatory sites
deprecated: true

Structural biology
type: Class
subclass of: Biology
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.5.24 Structural biology
has definition: The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.
has human readable id: Structural_biology
has narrow synonym: Structural assignment
has narrow synonym: Structural determination
has narrow synonym: Structure determination
in subset: bio
in subset: events
in subset: topics
comment: 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.

Protein membrane regions
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.
in subset: obsolete
replaced by: Protein folds and structural domains
deprecated: true

Structure comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: The comparison of two or more molecular structures, for example structure alignment and clustering.
in subset: obsolete
replaced by: Structure analysis
comment: This might involve comparison of secondary or tertiary (3D) structural information.
deprecated: true

Function analysis
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
isdebtag: true
has definition: The study of gene and protein function including the prediction of functional properties of a protein.
has exact synonym: Functional analysis
has human readable id: Function_analysis
has narrow synonym: Protein function analysis
has narrow synonym: Protein function prediction
in subset: bio
in subset: events
in subset: topics

Prokaryotes and Archaea
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Model organisms
consider: Model organisms
has definition: Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
deprecated: true

Protein databases
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Proteins
has definition: Protein data resources.
in subset: obsolete
deprecated: true

Structure determination
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Structural biology
has definition: 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.
in subset: obsolete
deprecated: true

Cell biology
type: Class
subclass of: Biology
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 1.5.11 Cell biology
has definition: Cells, such as key genes and proteins involved in the cell cycle.
has human readable id: Cell_biology
has narrow synonym: Cells
has narrow synonym: Cellular processes
has narrow synonym: Protein subcellular localization
in subset: bio
in subset: topics

Classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Ontology and terminology
has definition: Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.
in subset: obsolete
deprecated: true

Lipoproteins
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Membrane and lipoproteins
has definition: Lipoproteins (protein-lipid assemblies).
in subset: obsolete
deprecated: true

Phylogeny visualisation
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Phylogeny
has definition: Visualise a phylogeny, for example, render a phylogenetic tree.
in subset: obsolete
deprecated: true

Cheminformatics
type: Class
subclass of: Informatics
Created in: beta12orEarlier
isdebtag: true
has definition: The application of information technology to chemistry in biological research environment.
has exact synonym: Chemical informatics
has exact synonym: Chemoinformatics
has human readable id: Cheminformatics
in subset: bio
in subset: events
in subset: topics

Systems biology
type: Class
subclass of: Biology
Created in: beta12orEarlier
isdebtag: true
has definition: The holistic modelling and analysis of complex biological systems and the interactions therein.
has human readable id: Systems_biology
has narrow synonym: Biological modelling
has narrow synonym: Biological system modelling
has narrow synonym: Systems modelling
in subset: bio
in subset: events
in subset: topics
comment: This includes databases of models and methods to construct or analyse a model.

Statistics and probability
type: Class
subclass of: Mathematics
Created in: beta12orEarlier
has definition: The application of statistical methods to biological problems.
has human readable id: Statistics_and_probability
has narrow synonym: Bayesian methods
has narrow synonym: Biostatistics
has narrow synonym: Descriptive statistics
has narrow synonym: Gaussian processes
has narrow synonym: Inferential statistics
has narrow synonym: Markov processes
has narrow synonym: Multivariate statistics
has narrow synonym: Probabilistic graphical model
has narrow synonym: Probability
has narrow synonym: Statistics
in subset: bio
in subset: events
in subset: topics

Structure database search
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure analysis
has definition: Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).
in subset: obsolete
comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
deprecated: true

Molecular modelling
type: Class
subclass of: Structure prediction
Created in: beta12orEarlier
isdebtag: true
has definition: 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).
has human readable id: Molecular_modelling
has narrow synonym: Comparative modelling
has narrow synonym: Docking
has narrow synonym: Homology modeling
has narrow synonym: Homology modelling
has narrow synonym: Molecular docking
in subset: bio
in subset: topics

Protein function prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.2
Old parent: Thing
consider: Function analysis
has definition: The prediction of functional properties of a protein.
in subset: obsolete
deprecated: true

SNP
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.
in subset: obsolete
replaced by: DNA polymorphism
deprecated: true

Transmembrane protein prediction
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Structure prediction
consider: Membrane and lipoproteins
has definition: Predict transmembrane domains and topology in protein sequences.
in subset: obsolete
deprecated: true

Nucleic acid structure comparison
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Nucleic acid structure analysis
consider: Structure comparison
has definition: The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.
in subset: obsolete
comment: Use this concept for methods that are exclusively for nucleic acid structures.
deprecated: true

Exons
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Exons in a nucleotide sequences.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

Gene transcription
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Transcription of DNA into RNA including the regulation of transcription.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

DNA mutation
type: Class
subclass of: Genetic variation
subclass of: DNA
Created in: beta12orEarlier
has definition: DNA mutation.
has human readable id: DNA_mutation
in subset: bio
in subset: topics

Oncology
type: Class
subclass of: Medicine
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.2.16 Oncology
has definition: The study of cancer, for example, genes and proteins implicated in cancer.
has exact synonym: Cancer biology
has human readable id: Oncology
has narrow synonym: Cancer
has narrow synonym: Neoplasm
has narrow synonym: Neoplasms
in subset: bio
in subset: events
in subset: topics

Toxins and targets
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Structural and associated data for toxic chemical substances.
in subset: obsolete
replaced by: Small molecules
deprecated: true

Introns
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Introns in a nucleotide sequences.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

Tool topic
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.
in subset: obsolete
replaced by: Topic
deprecated: true

Study topic
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
has definition: A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.
in subset: obsolete
replaced by: Topic
deprecated: true

Nomenclature
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Ontology and terminology
has definition: Biological nomenclature (naming), symbols and terminology.
in subset: obsolete
deprecated: true

Disease genes and proteins
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Pathology
has definition: The genes, gene variations and proteins involved in one or more specific diseases.
in subset: obsolete
deprecated: true

Protein structure analysis
type: Class
subclass of: Proteins
subclass of: Structure analysis
Created in: beta12orEarlier
isdebtag: true
has alternative id: http://edamontology.org/topic_3040
has definition: Protein secondary or tertiary structural data and/or associated annotation.
has exact synonym: Protein structure
has human readable id: Protein_structure_analysis
has narrow synonym: Protein tertiary structure
in subset: bio
in subset: events
in subset: topics

Human biology
type: Class
subclass of: Biology
Created in: beta12orEarlier
has definition: The study of human beings in general, including the human genome and proteome.
has exact synonym: Humans
has human readable id: Human_biology
in subset: bio
in subset: topics

Gene resources
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Genetics
has definition: Informatics resource (typically a database) primarily focused on genes.
in subset: obsolete
deprecated: true

Yeast
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Model organisms
has definition: Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.
in subset: obsolete
deprecated: true

Eukaryotes
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Model organisms
consider: Model organisms
has definition: Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
deprecated: true

Invertebrates
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Zoology
consider: Model organisms
has definition: Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
deprecated: true

Vertebrates
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Zoology
consider: Model organisms
has definition: Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
deprecated: true

Unicellular eukaryotes
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
deprecation_comment: (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).
Obsolete since: 1.17
Old parent: Eukaryotes
consider: Model organisms
has definition: Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.
in subset: obsolete
comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
deprecated: true

Protein structure alignment
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Protein structure analysis
has definition: Protein secondary or tertiary structure alignments.
in subset: obsolete
deprecated: true

X-ray diffraction
type: Class
subclass of: Structural biology
subclass of: Imaging
Created in: beta12orEarlier
has definition: 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.
has exact synonym: Crystallography
has human readable id: X-ray_diffraction
has narrow synonym: X-ray crystallography
has narrow synonym: X-ray microscopy
in subset: bio
in subset: events
in subset: topics

Ontologies, nomenclature and classification
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Ontology and terminology
has definition: Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.
in subset: obsolete
deprecated: true

Immunoproteins and antigens
type: Class
subclass of: Gene and protein families
subclass of: Immunology
Created in: beta12orEarlier
has definition: Immunity-related proteins and their ligands.
has human readable id: Immunoproteins_and_antigens
has narrow synonym: Antigens
has narrow synonym: Immunopeptides
has narrow synonym: Immunoproteins
has narrow synonym: Therapeutic antibodies
in subset: bio
in subset: events
in subset: topics
comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."

Molecules
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Molecular biology
has definition: Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.
has related synonym: CHEBI:23367
in subset: obsolete
deprecated: true

Toxicology
type: Class
subclass of: Medicine
subclass of: Safety sciences
Created in: beta12orEarlier
isdebtag: true
has db xref: VT 3.1.9 Toxicology
has definition: Toxins and the adverse effects of these chemical substances on living organisms.
has human readable id: Toxicology
has narrow synonym: Computational toxicology
has narrow synonym: Toxicoinformatics
in subset: bio
in subset: events
in subset: topics

High-throughput sequencing
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta13
Old parent: Thing
consider: Sequencing
has definition: Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously.
in subset: obsolete
deprecated: true

Gene regulatory networks
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Gene regulatory networks.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Disease (specific)
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Old parent: Thing
consider: Pathology
has definition: Informatics resources dedicated to one or more specific diseases (not diseases in general).
in subset: obsolete
deprecated: true

VNTR
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has definition: Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.
in subset: obsolete
replaced by: DNA polymorphism
deprecated: true

Microsatellites
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has alternative id: data 2868
has definition: Microsatellite polymorphism in a DNA sequence.
in subset: obsolete
replaced by: DNA polymorphism
deprecated: true

RFLP
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.13
Old parent: Thing
has alternative id: data 2869
has definition: Restriction fragment length polymorphisms (RFLP) in a DNA sequence.
in subset: obsolete
replaced by: DNA polymorphism
deprecated: true

DNA polymorphism
type: Class
subclass of: Genetic variation
subclass of: DNA
Created in: beta12orEarlier
isdebtag: true
has definition: DNA polymorphism.
has human readable id: DNA_polymorphism
has narrow synonym: Microsatellites
has narrow synonym: RFLP
has narrow synonym: SNP
has narrow synonym: Single nucleotide polymorphism
has narrow synonym: VNTR
has narrow synonym: Variable number of tandem repeat polymorphism
has narrow synonym: snps
in subset: bio
in subset: topics
comment: 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.
comment: 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.
comment: 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.
comment: 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.

Nucleic acid design
type: Class
subclass of: DeprecatedClass
Created in: beta12orEarlier
Obsolete since: 1.3
Old parent: Thing
consider: Nucleic acid structure analysis
has definition: Topic for the design of nucleic acid sequences with specific conformations.
in subset: obsolete
deprecated: true

Primer or probe design
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Probes and primers
has definition: The design of primers for PCR and DNA amplification or the design of molecular probes.
in subset: obsolete
deprecated: true

Structure databases
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.2
Old parent: Thing
consider: Structure analysis
has definition: Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.
in subset: obsolete
deprecated: true

Nucleic acid structure
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.2
Old parent: Thing
consider: Nucleic acid structure analysis
has definition: Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.
in subset: obsolete
deprecated: true

Sequence databases
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Sequence analysis
has definition: Molecular sequence data resources, including sequence sites, alignments, motifs and profiles.
in subset: obsolete
deprecated: true

Nucleic acid sequences
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Sequence analysis
has definition: Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
in subset: obsolete
deprecated: true

Protein sequences
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
has definition: Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Protein interaction networks
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Protein interactions
has definition: Protein interaction networks.
in subset: obsolete
deprecated: true

Molecular biology
type: Class
subclass of: Biology
Created in: beta13
isdebtag: true
has db xref: VT 1.5.4 Biochemistry and molecular biology
has definition: The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.
has human readable id: Molecular_biology
has narrow synonym: Biological processes
in subset: bio
in subset: events
in subset: topics

Mammals
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Model organisms
has definition: Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.
in subset: obsolete
deprecated: true

Biodiversity
type: Class
subclass of: Ecology
Created in: beta13
isdebtag: true
has db xref: VT 1.5.5 Biodiversity conservation
has definition: The degree of variation of life forms within a given ecosystem, biome or an entire planet.
has human readable id: Biodiversity
in subset: bio
in subset: events
in subset: topics

Sequence clusters and classification
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Sequence analysis
has definition: The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.
in subset: obsolete
comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
deprecated: true

Genetics
type: Class
subclass of: Biology
Created in: beta13
isdebtag: true
has definition: The study of genes, genetic variation and heredity in living organisms.
has human readable id: Genetics
has narrow synonym: Genes
has narrow synonym: Heredity
in subset: bio
in subset: events
in subset: topics

Quantitative genetics
type: Class
subclass of: Genotype and phenotype
Created in: beta13
isdebtag: true
has definition: The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).
has human readable id: Quantitative_genetics
in subset: bio
in subset: topics

Population genetics
type: Class
subclass of: Genetics
Created in: beta13
isdebtag: true
has definition: 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.
has human readable id: Population_genetics
in subset: bio
in subset: events
in subset: topics

Regulatory RNA
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
has definition: Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).
in subset: obsolete
replaced by: Functional, regulatory and non-coding RNA
deprecated: true

Documentation and help
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.13
Old parent: Thing
has definition: The documentation of resources such as tools, services and databases and how to get help.
in subset: obsolete
replaced by: Literature and language
deprecated: true

Genetic organisation
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Gene structure
has definition: The structural and functional organisation of genes and other genetic elements.
in subset: obsolete
deprecated: true

Medical informatics
type: Class
subclass of: Informatics
Created in: beta13
isdebtag: true
has definition: The application of information technology to health, disease and biomedicine.
has exact synonym: Biomedical informatics
has exact synonym: Clinical informatics
has exact synonym: Health and disease
has exact synonym: Health informatics
has exact synonym: Healthcare informatics
has human readable id: Medical_informatics
in subset: bio
in subset: events
in subset: topics

Developmental biology
type: Class
subclass of: Biology
Created in: beta13
isdebtag: true
has db xref: VT 1.5.14 Developmental biology
has definition: How organisms grow and develop.
has human readable id: Developmental_biology
has narrow synonym: Development
in subset: bio
in subset: events
in subset: topics

Embryology
type: Class
subclass of: Developmental biology
Created in: beta13
isdebtag: true
has definition: The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.
has human readable id: Embryology
in subset: bio
in subset: events
in subset: topics

Anatomy
type: Class
subclass of: Biomedical science
Created in: beta13
isdebtag: true
has db xref: VT 3.1.1 Anatomy and morphology
has definition: The form and function of the structures of living organisms.
has human readable id: Anatomy
in subset: bio
in subset: events
in subset: topics

Literature and language
type: Class
subclass of: Topic
Created in: beta13
isdebtag: true
has definition: The scientific literature, language processing, reference information, and documentation.
has exact synonym: Language
has exact synonym: Literature
has human readable id: Literature_and_language
has narrow synonym: Bibliography
has narrow synonym: Citations
has narrow synonym: Documentation
has narrow synonym: References
has narrow synonym: Scientific literature
in subset: bio
in subset: events
in subset: topics
comment: This includes the documentation of resources such as tools, services and databases, user support, how to get help etc.

Biology
type: Class
subclass of: Biosciences
Created in: beta13
isdebtag: true
has db xref: VT 1.5 Biological sciences
has db xref: VT 1.5.1 Aerobiology
has db xref: VT 1.5.13 Cryobiology
has db xref: VT 1.5.23 Reproductive biology
has db xref: VT 1.5.3 Behavioural biology
has db xref: VT 1.5.7 Biological rhythm
has db xref: VT 1.5.8 Biology
has db xref: VT 1.5.99 Other
has definition: The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on.
has exact synonym: Biological science
has human readable id: Biology
has narrow synonym: Aerobiology
has narrow synonym: Behavioural biology
has narrow synonym: Biological rhythms
has narrow synonym: Chronobiology
has narrow synonym: Cryobiology
has narrow synonym: Reproductive biology
in subset: bio
in subset: events
in subset: topics

Data management
type: Class
subclass of: Topic
Created in: beta13
isdebtag: true
Related term: Data life cycle
Related term: Data lifecycle
has db xref: VT 1.3.1 Data management
has definition: 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.
has narrow synonym: Metadata management
has narrow synonym: Research data management (RDM)
in subset: bio
in subset: events
in subset: topics
comment: 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.
narrow match: Q30089794
narrow match: Q6822246

Sequence feature detection
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
has definition: The detection of the positional features, such as functional and other key sites, in molecular sequences.
in subset: obsolete
deprecated: true

Nucleic acid feature detection
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Nucleic acid sites, features and motifs
has definition: The detection of positional features such as functional sites in nucleotide sequences.
in subset: obsolete
deprecated: true

Protein feature detection
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Sequence sites, features and motifs
has definition: The detection, identification and analysis of positional protein sequence features, such as functional sites.
in subset: obsolete
deprecated: true

Biological system modelling
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.2
Old parent: Thing
consider: Systems biology
has definition: Topic for modelling biological systems in mathematical terms.
in subset: obsolete
deprecated: true

Data acquisition
type: Class
subclass of: Topic
Created in: beta13
has definition: The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means.
has exact synonym: Data collecting
has exact synonym: Data collection
has exact synonym: Data gathering
has narrow synonym: Experimental techniques
has narrow synonym: Experiments
has narrow synonym: Lab method
has narrow synonym: Lab techniques
has narrow synonym: Laboratory experiments
has narrow synonym: Laboratory method
has narrow synonym: Laboratory techniques
in subset: bio
in subset: topics

Genes and proteins resources
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.3
Old parent: Thing
consider: Gene and protein families
has definition: Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.
in subset: obsolete
deprecated: true

Protein topological domains
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.13
Old parent: Thing
has definition: Topological domains such as cytoplasmic regions in a protein.
in subset: obsolete
replaced by: Protein folds and structural domains
deprecated: true

Protein variants
type: Class
subclass of: Protein expression
Created in: beta13
isdebtag: true
has alternative id: data 3120
has definition: Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
has human readable id: Protein_variants
in subset: bio
in subset: topics

Expression signals
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.12
Old parent: Thing
consider: Transcription factors and regulatory sites
has definition: Regions within a nucleic acid sequence containing a signal that alters a biological function.
in subset: obsolete
deprecated: true

DNA binding sites
type: Class
subclass of: DNA
subclass of: Nucleic acid sites, features and motifs
Created in: beta13
has alternative id: data 3125
has definition: Nucleic acids binding to some other molecule.
has human readable id: DNA_binding_sites
has narrow synonym: Matrix-attachment region
has narrow synonym: Matrix/scaffold attachment region
has narrow synonym: Nucleosome exclusion sequences
has narrow synonym: Restriction sites
has narrow synonym: Ribosome binding sites
has narrow synonym: Scaffold-attachment region
in subset: bio
in subset: topics
comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc.
comment: 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).

Nucleic acid repeats
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.13
Old parent: Thing
has definition: Repetitive elements within a nucleic acid sequence.
in subset: obsolete
replaced by: Sequence composition, complexity and repeats
comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit.
deprecated: true

DNA replication and recombination
type: Class
subclass of: DNA
Created in: beta13
isdebtag: true
has definition: DNA replication or recombination.
has human readable id: DNA_replication_and_recombination
in subset: bio
in subset: topics

Signal or transit peptide
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.13
Old parent: Thing
has definition: Coding sequences for a signal or transit peptide.
in subset: obsolete
replaced by: Gene transcripts
deprecated: true

Sequence tagged sites
type: Class
subclass of: DeprecatedClass
Created in: beta13
Obsolete since: 1.13
Old parent: Thing
has definition: Sequence tagged sites (STS) in nucleic acid sequences.
in subset: obsolete
replaced by: Nucleic acid sites, features and motifs
deprecated: true

Sequencing
type: Class
subclass of: Data acquisition
Created in: 1.1
isdebtag: true
has definition: The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
has exact synonym: DNA-Seq
has human readable id: Sequencing
has narrow synonym: Chromosome walking
has narrow synonym: Clone verification
has narrow synonym: DNase-Seq
has narrow synonym: High throughput sequencing
has narrow synonym: High-throughput sequencing
has narrow synonym: NGS
has narrow synonym: NGS data analysis
has narrow synonym: Next gen sequencing
has narrow synonym: Next generation sequencing
has narrow synonym: Panels
has narrow synonym: Primer walking
has narrow synonym: Sanger sequencing
has narrow synonym: Targeted next-generation sequencing panels
in subset: bio
in subset: events
in subset: topics

ChIP-seq
type: Class
subclass of: Sequencing
subclass of: Immunoprecipitation experiment
Created in: 1.1
has definition: 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.
has exact synonym: ChIP-sequencing
has exact synonym: Chip Seq
has exact synonym: Chip sequencing
has exact synonym: Chip-sequencing
has human readable id: ChIP-seq
has narrow synonym: ChIP-exo
in subset: bio
in subset: topics

RNA-Seq
type: Class
subclass of: Sequencing
Created in: 1.1
has definition: 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.
has exact synonym: RNA sequencing
has exact synonym: RNA-Seq analysis
has exact synonym: Small RNA sequencing
has exact synonym: Small RNA-Seq
has exact synonym: Small-Seq
has exact synonym: Transcriptome profiling
has exact synonym: WTSS
has exact synonym: Whole transcriptome shotgun sequencing
has human readable id: RNA-Seq
has narrow synonym: MicroRNA sequencing
has narrow synonym: miRNA-seq
in subset: bio
in subset: topics
comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.

DNA methylation
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.3
Old parent: Thing
has definition: DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.
in subset: obsolete
replaced by: Epigenetics
deprecated: true

Metabolomics
type: Class
subclass of: Omics
Created in: 1.1
isdebtag: true
has definition: 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.
has human readable id: Metabolomics
has narrow synonym: Exometabolomics
has narrow synonym: LC-MS-based metabolomics
has narrow synonym: MS-based metabolomics
has narrow synonym: MS-based targeted metabolomics
has narrow synonym: MS-based untargeted metabolomics
has narrow synonym: Mass spectrometry-based metabolomics
has narrow synonym: Metabolites
has narrow synonym: Metabolome
has narrow synonym: Metabonomics
has narrow synonym: NMR-based metabolomics
in subset: bio
in subset: events
in subset: topics

Epigenomics
type: Class
subclass of: Genomics
subclass of: Epigenetics
Created in: 1.1
isdebtag: true
has definition: The study of the epigenetic modifications of a whole cell, tissue, organism etc.
has human readable id: Epigenomics
in subset: bio
in subset: events
in subset: topics
comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.

Metagenomics
type: Class
subclass of: Ecology
subclass of: Genomics
Created in: 1.1
isdebtag: true
has broad synonym: Biome sequencing
has broad synonym: Community genomics
has broad synonym: Ecogenomics
has broad synonym: Environmental genomics
has broad synonym: Environmental omics
Related term: Environmental sequencing
Related term: Environmental DNA (eDNA)
has definition: The study of genetic material recovered from environmental samples, and associated environmental data.
has human readable id: Metagenomics
has narrow synonym: Shotgun metagenomics
in subset: bio
in subset: events
in subset: topics

Structural variation
type: Class
subclass of: Genetic variation
subclass of: DNA
Created in: 1.1
has definition: Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
has exact synonym: DNA structural variation
has exact synonym: Genomic structural variation
has human readable id: DNA_structural_variation
has narrow synonym: Deletion
has narrow synonym: Duplication
has narrow synonym: Insertion
has narrow synonym: Inversion
has narrow synonym: Translocation
in subset: bio
in subset: topics

DNA packaging
type: Class
subclass of: DNA
Created in: 1.1
has definition: DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.
has human readable id: DNA_packaging
has narrow synonym: Nucleosome positioning
in subset: bio
in subset: topics

DNA-Seq
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.3
Old parent: Thing
consider: Sequencing
has definition: 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.
in subset: obsolete
deprecated: true

RNA-Seq alignment
type: Class
subclass of: DeprecatedClass
Created in: 1.1
Obsolete since: 1.3
Old parent: Thing
consider: Sequence assembly
has definition: 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.
in subset: obsolete
deprecated: true

ChIP-on-chip
type: Class
subclass of: Immunoprecipitation experiment
Created in: 1.1
has definition: Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions.
has exact synonym: ChIP-chip
has human readable id: ChIP-on-chip
has narrow synonym: ChiP
in subset: bio
in subset: topics

Data security
type: Class
subclass of: DeprecatedClass
Created in: 1.3
obsolete: true
Obsolete since: 1.26
Old parent: Data management
consider: Data protection
consider: Cybersecurity
has definition: The protection of data, such as patient health data, from damage or unwanted access from unauthorised users.
has exact synonym: Data privacy
has human readable id: Data_security
in subset: bio
in subset: obsolete
in subset: topics
comment: The concept of data security was ambiguous, and therefore replaced by two distinct concepts: data protection (incl. sensitive data etc.), and cybersecurity.
deprecated: true

Sample collections
type: Class
subclass of: Biomedical science
Created in: 1.3
has definition: Biological samples and specimens.
has exact synonym: Specimen collections
has human readable id: Sample_collections
has narrow synonym: biosamples
has narrow synonym: samples
in subset: bio
in subset: events
in subset: topics

Biochemistry
type: Class
subclass of: Biology
subclass of: Chemistry
Created in: 1.3
isdebtag: true
has db xref: VT 1.5.4 Biochemistry and molecular biology
has definition: Chemical substances and physico-chemical processes and that occur within living organisms.
has exact synonym: Biological chemistry
has human readable id: Biochemistry
has narrow synonym: Glycomics
has narrow synonym: Pathobiochemistry
has narrow synonym: Phytochemistry
in subset: bio
in subset: events
in subset: topics

Phylogenetics
type: Class
subclass of: Sequence analysis
subclass of: Phylogeny
Created in: 1.3
isdebtag: true
has definition: The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).
has human readable id: Phylogenetics
in subset: bio
in subset: topics

Epigenetics
type: Class
subclass of: Genetics
Created in: 1.3
isdebtag: true
has definition: Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.
has human readable id: Epigenetics
has narrow synonym: DNA methylation
has narrow synonym: Histone modification
has narrow synonym: Methylation profiles
in subset: bio
in subset: events
in subset: topics
comment: 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.)

Biotechnology
type: Class
subclass of: Biology
Created in: 1.3
isdebtag: true
has definition: The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.
has human readable id: Biotechnology
has narrow synonym: Applied microbiology
in subset: bio
in subset: events
in subset: topics

Phenomics
type: Class
subclass of: Genotype and phenotype
subclass of: Evolutionary biology
subclass of: Omics
Created in: 1.3
isdebtag: true
has definition: Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
has human readable id: Phenomics
in subset: bio
in subset: events
in subset: topics

Evolutionary biology
type: Class
subclass of: Biology
Created in: 1.3
isdebtag: true
has db xref: VT 1.5.16 Evolutionary biology
has definition: The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.
has exact synonym: Evolution
has human readable id: Evolutionary_biology
in subset: bio
in subset: events
in subset: topics

Physiology
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has db xref: VT 3.1.8 Physiology
has definition: The functions of living organisms and their constituent parts.
has human readable id: Physiology
has narrow synonym: Electrophysiology
in subset: bio
in subset: events
in subset: topics

Microbiology
type: Class
subclass of: Biology
Created in: 1.3
isdebtag: true
has db xref: VT 1.5.20 Microbiology
has definition: The biology of microorganisms.
has human readable id: Microbiology
has narrow synonym: Antimicrobial stewardship
has narrow synonym: Medical microbiology
has narrow synonym: Microbial genetics
has narrow synonym: Microbial physiology
has narrow synonym: Microbial surveillance
has narrow synonym: Microbiological surveillance
has narrow synonym: Molecular infection biology
has narrow synonym: Molecular microbiology
in subset: bio
in subset: events
in subset: topics

Parasitology
type: Class
subclass of: Biomedical science
Created in: 1.3
isdebtag: true
has definition: The biology of parasites.
has human readable id: Parasitology
in subset: bio
in subset: events
in subset: topics

Medicine
type: Class
subclass of: Biosciences
Created in: 1.3
isdebtag: true
has db xref: VT 3.1 Basic medicine
has db xref: VT 3.2 Clinical medicine
has db xref: VT 3.2.9 General and internal medicine
has definition: Research in support of healing by diagnosis, treatment, and prevention of disease.
has exact synonym: Biomedical research
has exact synonym: Clinical medicine
has exact synonym: Experimental medicine
has human readable id: Medicine
has narrow synonym: General medicine
has narrow synonym: Internal medicine
in subset: bio
in subset: events
in subset: topics

Neurobiology
type: Class
subclass of: Biomedical science
Created in: 1.3
isdebtag: true
has broad synonym: Neuroscience
has db xref: VT 3.1.5 Neuroscience
has definition: The study of the nervous system and brain; its anatomy, physiology and function.
has human readable id: Neurobiology
has narrow synonym: Molecular neuroscience
has narrow synonym: Neurophysiology
has narrow synonym: Systemetic neuroscience
in subset: bio
in subset: events
in subset: topics

Public health and epidemiology
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has db xref: VT 3.3.1 Epidemiology
has definition: Topic concerning the the patterns, cause, and effect of disease within populations.
has human readable id: Public_health_and_epidemiology
has narrow synonym: Epidemiology
has narrow synonym: Public health
in subset: bio
in subset: events
in subset: topics

Biophysics
type: Class
subclass of: Biology
subclass of: Physics
Created in: 1.3
isdebtag: true
has db xref: VT 1.5.9 Biophysics
has definition: The use of physics to study biological system.
has human readable id: Biophysics
has narrow synonym: Medical physics
in subset: bio
in subset: events
in subset: topics

Computational biology
type: Class
subclass of: Biosciences
Created in: 1.3
isdebtag: true
has db xref: VT 1.5.12 Computational biology
has db xref: VT 1.5.19 Mathematical biology
has db xref: VT 1.5.26 Theoretical biology
has definition: The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.
has human readable id: Computational_biology
has narrow synonym: Biomathematics
has narrow synonym: Mathematical biology
has narrow synonym: Theoretical biology
in subset: bio
in subset: events
in subset: topics
comment: This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).

Transcriptomics
type: Class
subclass of: Gene expression
subclass of: Genomics
Created in: 1.3
isdebtag: true
has definition: The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.
has human readable id: Transcriptomics
has narrow synonym: Comparative transcriptomics
has narrow synonym: Transcriptome
in subset: bio
in subset: events
in subset: topics

Chemistry
type: Class
subclass of: Topic
Created in: 1.3
has broad synonym: Chemical science
has broad synonym: Polymer science
has broad synonym: VT 1.7.10 Polymer science
has db xref: VT 1.7 Chemical sciences
has db xref: VT 1.7.2 Chemistry
has db xref: VT 1.7.3 Colloid chemistry
has db xref: VT 1.7.5 Electrochemistry
has db xref: VT 1.7.6 Inorganic and nuclear chemistry
has db xref: VT 1.7.7 Mathematical chemistry
has db xref: VT 1.7.8 Organic chemistry
has db xref: VT 1.7.9 Physical chemistry
has definition: The composition and properties of matter, reactions, and the use of reactions to create new substances.
has human readable id: Chemistry
has narrow synonym: Inorganic chemistry
has narrow synonym: Mathematical chemistry
has narrow synonym: Nuclear chemistry
has narrow synonym: Organic chemistry
has narrow synonym: Physical chemistry
in subset: bio
in subset: events
in subset: topics

Mathematics
type: Class
subclass of: Topic
Created in: 1.3
has db xref: VT 1.1.99 Other
has db xref: VT:1.1 Mathematics
has definition: The study of numbers (quantity) and other topics including structure, space, and change.
has exact synonym: Maths
has human readable id: Mathematics
has narrow synonym: Dynamic systems
has narrow synonym: Dynamical systems
has narrow synonym: Dynymical systems theory
has narrow synonym: Graph analytics
has narrow synonym: Monte Carlo methods
has narrow synonym: Multivariate analysis
in subset: bio
in subset: events
in subset: topics

Computer science
type: Class
subclass of: Topic
Created in: 1.3
has db xref: VT 1.2 Computer sciences
has db xref: VT 1.2.99 Other
has definition: The theory and practical use of computer systems.
has human readable id: Computer_science
has narrow synonym: Cloud computing
has narrow synonym: HPC
has narrow synonym: High performance computing
has narrow synonym: High-performance computing
in subset: bio
in subset: events
in subset: topics

Physics
type: Class
subclass of: Topic
Created in: 1.3
has definition: The study of matter, space and time, and related concepts such as energy and force.
has human readable id: Physics
in subset: bio
in subset: events
in subset: topics

RNA splicing
type: Class
subclass of: RNA
subclass of: Gene expression
Created in: 1.3
isdebtag: true
has definition: RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.
has exact synonym: Alternative splicing
has human readable id: RNA_splicing
has narrow synonym: Splice sites
in subset: bio
in subset: topics
comment: This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc..

Molecular genetics
type: Class
subclass of: Genetics
subclass of: Computational biology
Created in: 1.3
isdebtag: true
has definition: The structure and function of genes at a molecular level.
has human readable id: Molecular_genetics
in subset: bio
in subset: events
in subset: topics

Respiratory medicine
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has db xref: VT 3.2.25 Respiratory systems
has definition: The study of respiratory system.
has exact synonym: Pulmonary medicine
has exact synonym: Pulmonology
has human readable id: Respiratory_medicine
has narrow synonym: Pulmonary disorders
has narrow synonym: Respiratory disease
in subset: bio
in subset: events
in subset: topics

Metabolic disease
type: Class
subclass of: DeprecatedClass
Created in: 1.3
Obsolete since: 1.4
Old parent: Thing
consider: Endocrinology and metabolism
has definition: The study of metabolic diseases.
in subset: obsolete
deprecated: true

Infectious disease
type: Class
subclass of: Pathology
Created in: 1.3
has db xref: VT 3.3.4 Infectious diseases
has definition: 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).
has exact synonym: Communicable disease
has exact synonym: Transmissible disease
has human readable id: Infectious_disease
in subset: bio
in subset: events
in subset: topics

Rare diseases
type: Class
subclass of: Pathology
Created in: 1.3
has definition: The study of rare diseases.
has human readable id: Rare_diseases
in subset: bio
in subset: events
in subset: topics

Computational chemistry
type: Class
subclass of: Chemistry
subclass of: Computer science
Created in: 1.3
isdebtag: true
has db xref: VT 1.7.4 Computational chemistry
has definition: Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.
has human readable id: Computational_chemistry
in subset: bio
in subset: events
in subset: topics

Neurology
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has definition: The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.
has human readable id: Neurology
has narrow synonym: Neurological disorders
in subset: bio
in subset: events
in subset: topics

Cardiology
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has db xref: VT 3.2.22 Peripheral vascular disease
has db xref: VT 3.2.4 Cardiac and Cardiovascular systems
has definition: The diseases and abnormalities of the heart and circulatory system.
has exact synonym: Cardiovascular medicine
has human readable id: Cardiology
has narrow synonym: Cardiovascular disease
has narrow synonym: Heart disease
in subset: bio
in subset: events
in subset: topics

Drug discovery
type: Class
subclass of: Chemistry
subclass of: Medicines research and development
Created in: 1.3
isdebtag: true
has definition: The discovery and design of drugs or potential drug compounds.
has human readable id: Drug_discovery
in subset: bio
in subset: events
in subset: topics
comment: This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.

Biobank
type: Class
subclass of: Sample collections
Created in: 1.3
isdebtag: true
has definition: Repositories of biological samples, typically human, for basic biological and clinical research.
has exact synonym: Tissue collection
has exact synonym: biobanking
has human readable id: Biobank
in subset: bio
in subset: events
in subset: topics

Mouse clinic
type: Class
subclass of: Sample collections
Created in: 1.3
has definition: Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.
has exact synonym: Laboratory mouse
has human readable id: Mouse_clinic
in subset: bio
in subset: events
in subset: topics

Microbial collection
type: Class
subclass of: Sample collections
Created in: 1.3
has definition: Collections of microbial cells including bacteria, yeasts and moulds.
has human readable id: Microbial_collection
in subset: bio
in subset: events
in subset: topics

Cell culture collection
type: Class
subclass of: Sample collections
Created in: 1.3
has definition: Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.
has human readable id: Cell_culture_collection
in subset: bio
in subset: events
in subset: topics

Clone library
type: Class
subclass of: Sample collections
Created in: 1.3
has definition: Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.
has human readable id: Clone_library
in subset: bio
in subset: events
in subset: topics

Translational medicine
type: Class
subclass of: Medicine
Created in: 1.3
isdebtag: true
has definition: 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.
has human readable id: Translational_medicine
in subset: bio
in subset: events
in subset: topics

Compound libraries and screening
type: Class
subclass of: Drug discovery
Created in: 1.3
has definition: Collections of chemicals, typically for use in high-throughput screening experiments.
has human readable id: Compound_libraries_and_screening
has narrow synonym: Chemical library
has narrow synonym: Chemical screening
has narrow synonym: Compound library
has narrow synonym: Small chemical compounds libraries
has narrow synonym: Small compounds libraries
has narrow synonym: Target identification and validation
in subset: bio
in subset: events
in subset: topics

Biomedical science
type: Class
subclass of: Biosciences
Created in: 1.3
isdebtag: true
has db xref: VT 3.3 Health sciences
has definition: Topic concerning biological science that is (typically) performed in the context of medicine.
has exact synonym: Biomedical sciences
has exact synonym: Health science
has human readable id: Biomedical_science
in subset: bio
in subset: events
in subset: topics

Data identity and mapping
type: Class
subclass of: Data management
Created in: 1.3
has definition: Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.
has human readable id: Data_identity_and_mapping
in subset: bio
in subset: events
in subset: topics

Sequence search
type: Class
subclass of: DeprecatedClass
Created in: 1.3
Obsolete since: 1.12
Old parent: Thing
has definition: The search and retrieval from a database on the basis of molecular sequence similarity.
in subset: obsolete
replaced by: Sequence analysis
deprecated: true

Biomarkers
type: Class
subclass of: Biology
Created in: 1.4
isdebtag: true
has definition: Objective indicators of biological state often used to assess health, and determinate treatment.
has exact synonym: Diagnostic markers
has human readable id: Biomarkers
in subset: bio
in subset: topics

Laboratory techniques
type: Class
subclass of: DeprecatedClass
Created in: 1.4
deprecation_comment: This was merged into Data acquisition.
has human readable id: Laboratory_techniques
Obsolete since: 1.26
Old parent: Topic
has definition: The procedures used to conduct an experiment.
has exact synonym: Experimental techniques
has exact synonym: Lab method
has exact synonym: Lab techniques
has exact synonym: Laboratory method
has narrow synonym: Experiments
has narrow synonym: Laboratory experiments
in subset: bio
in subset: events
in subset: obsolete
in subset: topics
replaced by: Data acquisition
deprecated: true

Data architecture, analysis and design
type: Class
subclass of: Data management
Created in: 1.4
has definition: 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.
has human readable id: Data_architecture_analysis_and_design
has narrow synonym: Data analysis
has narrow synonym: Data architecture
has narrow synonym: Data design
in subset: bio
in subset: events
in subset: topics

Data integration and warehousing
type: Class
subclass of: Data management
Created in: 1.4
has definition: 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.
has human readable id: Data_integration_and_warehousing
has narrow synonym: Data integration
has narrow synonym: Data warehousing
in subset: bio
in subset: events
in subset: topics

Biomaterials
type: Class
subclass of: Biotechnology
Created in: 1.4
has definition: Any matter, surface or construct that interacts with a biological system.
has human readable id: Biomaterials
in subset: bio
in subset: events
in subset: topics

Chemical biology
type: Class
subclass of: Biology
subclass of: Synthetic chemistry
Created in: 1.4
isdebtag: true
has definition: The use of synthetic chemistry to study and manipulate biological systems.
has human readable id: Chemical_biology
in subset: bio
in subset: events
in subset: topics

Analytical chemistry
type: Class
subclass of: Chemistry
Created in: 1.4
has db xref: VT 1.7.1 Analytical chemistry
has definition: The study of the separation, identification, and quantification of the chemical components of natural and artificial materials.
has human readable id: Analytical_chemistry
in subset: bio
in subset: events
in subset: topics

Synthetic chemistry
type: Class
subclass of: Chemistry
Created in: 1.4
has definition: The use of chemistry to create new compounds.
has human readable id: Synthetic_chemistry
has narrow synonym: Synthetic organic chemistry
in subset: bio
in subset: events
in subset: topics

Software engineering
type: Class
subclass of: Computer science
Created in: 1.4
has db xref: 1.2.12 Programming languages
has db xref: Software engineering
has db xref: VT 1.2.1 Algorithms
has db xref: VT 1.2.14 Software engineering
has db xref: VT 1.2.7 Data structures
has definition: The process that leads from an original formulation of a computing problem to executable programs.
has exact synonym: Computer programming
has exact synonym: Software development
has human readable id: Software_engineering
has narrow synonym: Algorithms
has narrow synonym: Data structures
has narrow synonym: Programming languages
in subset: bio
in subset: events
in subset: topics

Drug development
type: Class
subclass of: Medicines research and development
Created in: 1.4
isdebtag: true
has definition: The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.
has exact synonym: Drug development science
has exact synonym: Medicine development
has exact synonym: Medicines development
has human readable id: Drug_development
in subset: bio
in subset: events
in subset: topics

Biotherapeutics
type: Class
subclass of: Medicines research and development
Created in: 1.4
has broad synonym: Drug delivery
has broad synonym: Drug formulation
has broad synonym: Drug formulation and delivery
has definition: The process of formulating and administering a pharmaceutical compound to achieve a therapeutic effect.
has human readable id: Biotherapeutics
in subset: bio
in subset: events
in subset: topics

Drug metabolism
type: Class
subclass of: Medicines research and development
Created in: 1.4
isdebtag: true
has definition: The study of how a drug interacts with the body.
has human readable id: Drug_metabolism
has narrow synonym: ADME
has narrow synonym: Drug absorption
has narrow synonym: Drug distribution
has narrow synonym: Drug excretion
has narrow synonym: Pharmacodynamics
has narrow synonym: Pharmacokinetics
has narrow synonym: Pharmacokinetics and pharmacodynamics
in subset: bio
in subset: events
in subset: topics

Medicines research and development
type: Class
subclass of: Biomedical science
Created in: 1.4
has broad synonym: Health care research
has broad synonym: Health care science
has definition: The discovery, development and approval of medicines.
has exact synonym: Drug discovery and development
has human readable id: Medicines_research_and_development
in subset: bio
in subset: events
in subset: topics

Safety sciences
type: Class
subclass of: Medicines research and development
Created in: 1.4
has definition: The safety (or lack) of drugs and other medical interventions.
has exact synonym: Patient safety
has human readable id: Safety_sciences
has narrow synonym: Drug safety
in subset: bio
in subset: events
in subset: topics

Pharmacovigilance
type: Class
subclass of: Safety sciences
Created in: 1.4
has definition: The detection, assessment, understanding and prevention of adverse effects of medicines.
has human readable id: Pharmacovigilence
in subset: bio
in subset: events
in subset: topics
comment: Pharmacovigilence concerns safety once a drug has gone to market.

Preclinical and clinical studies
type: Class
subclass of: Medicines research and development
subclass of: Experimental design and studies
Created in: 1.4
has definition: The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.
has human readable id: Preclinical_and_clinical_studies
has narrow synonym: Clinical studies
has narrow synonym: Clinical study
has narrow synonym: Clinical trial
has narrow synonym: Drug trials
has narrow synonym: Preclinical studies
has narrow synonym: Preclinical study
in subset: bio
in subset: events
in subset: topics

Imaging
type: Class
subclass of: Data acquisition
Created in: 1.4
isdebtag: true
has definition: The visual representation of an object.
has human readable id: Imaging
has narrow synonym: Diffraction experiment
has narrow synonym: Microscopy
has narrow synonym: Microscopy imaging
has narrow synonym: Optical super resolution microscopy
has narrow synonym: Photonic force microscopy
has narrow synonym: Photonic microscopy
in subset: bio
in subset: events
in subset: topics
comment: 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.

Bioimaging
type: Class
subclass of: Imaging
Created in: 1.4
has definition: The use of imaging techniques to understand biology.
has exact synonym: Biological imaging
has human readable id: Biological_imaging
in subset: bio
in subset: events
in subset: topics

Medical imaging
type: Class
subclass of: Imaging
Created in: 1.4
has db xref: VT 3.2.13 Medical imaging
has db xref: VT 3.2.14 Nuclear medicine
has db xref: VT 3.2.24 Radiology
has definition: The use of imaging techniques for clinical purposes for medical research.
has human readable id: Medical_imaging
has narrow synonym: Neuroimaging
has narrow synonym: Nuclear medicine
has narrow synonym: Radiology
in subset: bio
in subset: events
in subset: topics

Light microscopy
type: Class
subclass of: Imaging
Created in: 1.4
has definition: The use of optical instruments to magnify the image of an object.
has human readable id: Light_microscopy
in subset: bio
in subset: events
in subset: topics

Laboratory animal science
type: Class
subclass of: Biomedical science
Created in: 1.4
has definition: The use of animals and alternatives in experimental research.
has exact synonym: Animal experimentation
has exact synonym: Animal research
has exact synonym: Animal testing
has exact synonym: In vivo testing
has human readable id: Laboratory_animal_science
in subset: bio
in subset: events
in subset: topics

Marine biology
type: Class
subclass of: Biology
Created in: 1.4
isdebtag: true
has db xref: VT 1.5.18 Marine and Freshwater biology
has definition: The study of organisms in the ocean or brackish waters.
has human readable id: Marine_biology
in subset: bio
in subset: events
in subset: topics

Molecular medicine
type: Class
subclass of: Translational medicine
Created in: 1.4
isdebtag: true
has definition: The identification of molecular and genetic causes of disease and the development of interventions to correct them.
has human readable id: Molecular_medicine
in subset: bio
in subset: events
in subset: topics

Nutritional science
type: Class
subclass of: Biomedical science
Created in: 1.4
has db xref: VT 3.3.7 Nutrition and Dietetics
has definition: 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.
has exact synonym: Nutrition
has exact synonym: Nutrition science
has human readable id: Nutritional_science
has narrow synonym: Dietetics
in subset: bio
in subset: events
in subset: topics

Omics
type: Class
subclass of: Biosciences
Created in: 1.4
isdebtag: true
has definition: The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
has human readable id: Omics
in subset: bio
in subset: events
in subset: topics

Quality affairs
type: Class
subclass of: Medicines research and development
Created in: 1.4
has definition: The processes that need to be in place to ensure the quality of products for human or animal use.
has exact synonym: Quality assurance
has human readable id: Quality_affairs
has narrow synonym: Good clinical practice
has narrow synonym: Good laboratory practice
has narrow synonym: Good manufacturing practice
in subset: bio
in subset: events
in subset: topics

Regulatory affairs
type: Class
subclass of: Medicines research and development
Created in: 1.4
has definition: 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.
has exact synonym: Healthcare RA
has human readable id: Regulatory_affairs
in subset: bio
in subset: events
in subset: topics

Regenerative medicine
type: Class
subclass of: Biomedical science
Created in: 1.4
isdebtag: true
has definition: Biomedical approaches to clinical interventions that involve the use of stem cells.
has exact synonym: Stem cell research
has human readable id: Regenerative_medicine
in subset: bio
in subset: events
in subset: topics

Systems medicine
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has definition: 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.
has human readable id: Systems_medicine
in subset: bio
in subset: events
in subset: topics

Veterinary medicine
type: Class
subclass of: Medicine
Created in: 1.4
has definition: Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.
has human readable id: Veterinary_medicine
has narrow synonym: Clinical veterinary medicine
in subset: bio
in subset: events
in subset: topics

Bioengineering
type: Class
subclass of: Biotechnology
Created in: 1.4
has definition: The application of biological concepts and methods to the analytical and synthetic methodologies of engineering.
has exact synonym: Biological engineering
has human readable id: Bioengineering
in subset: bio
in subset: events
in subset: topics

Geriatric medicine
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has broad synonym: Ageing
has broad synonym: Aging
has broad synonym: Gerontology
has db xref: VT 3.2.10 Geriatrics and gerontology
has definition: The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.
has exact synonym: Geriatrics
has human readable id: Geriatric_medicine
in subset: bio
in subset: events
in subset: topics

Allergy, clinical immunology and immunotherapeutics
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has db xref: VT 3.2.1 Allergy
has definition: Health issues related to the immune system and their prevention, diagnosis and management.
has human readable id: Allergy_clinical_immunology_and_immunotherapeutics
has narrow synonym: Allergy
has narrow synonym: Clinical immunology
has narrow synonym: Immune disorders
has narrow synonym: Immunomodulators
has narrow synonym: Immunotherapeutics
in subset: bio
in subset: events
in subset: topics

Pain medicine
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has definition: The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.
has exact synonym: Algiatry
has exact synonym: Pain management
has human readable id: Pain_medicine
in subset: bio
in subset: events
in subset: topics

Anaesthesiology
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.2 Anaesthesiology
has definition: Anaesthesia and anaesthetics.
has exact synonym: Anaesthetics
has human readable id: Anaesthesiology
in subset: bio
in subset: events
in subset: topics

Critical care medicine
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.5 Critical care/Emergency medicine
has definition: The multidisciplinary that cares for patients with acute, life-threatening illness or injury.
has exact synonym: Acute medicine
has exact synonym: Emergency medicine
has exact synonym: Intensive care medicine
has human readable id: Critical_care_medicine
in subset: bio
in subset: events
in subset: topics

Dermatology
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.7 Dermatology and venereal diseases
has definition: The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.
has human readable id: Dermatology
has narrow synonym: Dermatological disorders
in subset: bio
in subset: events
in subset: topics

Dentistry
type: Class
subclass of: Medicine
Created in: 1.4
has definition: The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.
has human readable id: Dentistry
in subset: bio
in subset: events
in subset: topics

Ear, nose and throat medicine
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.20 Otorhinolaryngology
has definition: The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.
has exact synonym: Audiovestibular medicine
has exact synonym: Otolaryngology
has exact synonym: Otorhinolaryngology
has human readable id: Ear_nose_and_throat_medicine
has narrow synonym: Head and neck disorders
in subset: bio
in subset: events
in subset: topics

Endocrinology and metabolism
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has definition: 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.
has human readable id: Endocrinology_and_metabolism
has narrow synonym: Endocrine disorders
has narrow synonym: Endocrinology
has narrow synonym: Metabolic disorders
has narrow synonym: Metabolism
in subset: bio
in subset: events
in subset: topics

Haematology
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has db xref: VT 3.2.11 Hematology
has definition: The branch of medicine that deals with the blood, blood-forming organs and blood diseases.
has human readable id: Haematology
has narrow synonym: Blood disorders
has narrow synonym: Haematological disorders
in subset: bio
in subset: events
in subset: topics

Gastroenterology
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has db xref: VT 3.2.8 Gastroenterology and hepatology
has definition: The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.
has human readable id: Gastroenterology
has narrow synonym: Gastrointestinal disorders
in subset: bio
in subset: events
in subset: topics

Gender medicine
type: Class
subclass of: Medicine
Created in: 1.4
has definition: The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.
has human readable id: Gender_medicine
in subset: bio
in subset: events
in subset: topics

Gynaecology and obstetrics
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has db xref: VT 3.2.15 Obstetrics and gynaecology
has definition: The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.
has human readable id: Gynaecology_and_obstetrics
has narrow synonym: Gynaecological disorders
has narrow synonym: Gynaecology
has narrow synonym: Obstetrics
in subset: bio
in subset: events
in subset: topics

Hepatic and biliary medicine
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has definition: The branch of medicine that deals with the liver, gallbladder, bile ducts and bile.
has exact synonym: Hepatology
has human readable id: Hepatic_and_biliary_medicine
has narrow synonym: Liver disorders
in subset: bio
in subset: events
in subset: topics
see also: Hepatobiliary medicine

Infectious tropical disease
type: Class
subclass of: DeprecatedClass
Created in: 1.4
Obsolete since: 1.13
Old parent: Thing
has definition: The branch of medicine that deals with the infectious diseases of the tropics.
in subset: obsolete
replaced by: Infectious disease
deprecated: true

Trauma medicine
type: Class
subclass of: Medicine
Created in: 1.4
has definition: The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.
has exact synonym: Traumatology
has human readable id: Trauma_medicine
in subset: bio
in subset: events
in subset: topics

Medical toxicology
type: Class
subclass of: Medicine
Created in: 1.4
isdebtag: true
has definition: 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.
has human readable id: Medical_toxicology
in subset: bio
in subset: events
in subset: topics

Musculoskeletal medicine
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.19 Orthopaedics
has db xref: VT 3.2.26 Rheumatology
has definition: 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.
has human readable id: Musculoskeletal_medicine
has narrow synonym: Musculoskeletal disorders
has narrow synonym: Orthopaedics
has narrow synonym: Rheumatology
in subset: bio
in subset: events
in subset: topics

Ophthalmology
type: Class
subclass of: Medicine
Created in: 1.4
has broad synonym: Optometry
has db xref: VT 3.2.17 Ophthalmology
has db xref: VT 3.2.18 Optometry
has definition: The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.
has human readable id: Ophthalmology
has narrow synonym: Eye disoders
in subset: bio
in subset: events
in subset: topics

Paediatrics
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.21 Paediatrics
has definition: The branch of medicine that deals with the medical care of infants, children and adolescents.
has exact synonym: Child health
has human readable id: Paediatrics
in subset: bio
in subset: events
in subset: topics

Psychiatry
type: Class
subclass of: Medicine
Created in: 1.4
has broad synonym: Mental health
has db xref: VT 3.2.23 Psychiatry
has definition: The branch of medicine that deals with the management of mental illness, emotional disturbance and abnormal behaviour.
has human readable id: Psychiatry
has narrow synonym: Psychiatric disorders
in subset: bio
in subset: events
in subset: topics

Reproductive health
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.3 Andrology
has definition: The health of the reproductive processes, functions and systems at all stages of life.
has human readable id: Reproductive_health
has narrow synonym: Andrology
has narrow synonym: Family planning
has narrow synonym: Fertility medicine
has narrow synonym: Reproductive disorders
in subset: bio
in subset: events
in subset: topics

Surgery
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.28 Transplantation
has definition: 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.
has human readable id: Surgery
has narrow synonym: Transplantation
in subset: bio
in subset: events
in subset: topics

Urology and nephrology
type: Class
subclass of: Medicine
Created in: 1.4
has db xref: VT 3.2.29 Urology and nephrology
has definition: 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.
has human readable id: Urology_and_nephrology
has narrow synonym: Kidney disease
has narrow synonym: Nephrology
has narrow synonym: Urological disorders
has narrow synonym: Urology
in subset: bio
in subset: events
in subset: topics

Complementary medicine
type: Class
subclass of: Medicine
Created in: 1.4
has broad synonym: Alternative medicine
has broad synonym: Holistic medicine
has broad synonym: Integrative medicine
has db xref: VT 3.2.12 Integrative and Complementary medicine
has definition: Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.
has human readable id: Complementary_medicine
in subset: bio
in subset: events
in subset: topics

MRI
type: Class
subclass of: Imaging
Created in: 1.7
has definition: Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.
has exact synonym: MRT
has exact synonym: Magnetic resonance imaging
has exact synonym: Magnetic resonance tomography
has exact synonym: NMRI
has exact synonym: Nuclear magnetic resonance imaging
has human readable id: MRI
in subset: bio
in subset: topics

Neutron diffraction
type: Class
subclass of: Structural biology
subclass of: Imaging
Created in: 1.7
has definition: The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure.
has exact synonym: Neutron diffraction experiment
has human readable id: Neutron_diffraction
has narrow synonym: Elastic neutron scattering
has narrow synonym: Neutron microscopy
in subset: bio
in subset: topics

Tomography
type: Class
subclass of: Imaging
Created in: 1.7
has definition: Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram).
has exact synonym: CT
has exact synonym: Computed tomography
has exact synonym: TDM
has human readable id: Tomography
has narrow synonym: Electron tomography
has narrow synonym: PET
has narrow synonym: Positron emission tomography
has narrow synonym: X-ray tomography
in subset: bio
in subset: topics

Data mining
type: Class
subclass of: Computer science
Created in: 1.7
isdebtag: true
has broad synonym: KDD
has broad synonym: Knowledge discovery in databases
has db xref: VT 1.3.2 Data mining
has definition: The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.
has human readable id: Data_mining
has narrow synonym: Pattern recognition
in subset: bio
in subset: topics

Machine learning
type: Class
subclass of: Computer science
Created in: 1.7
has broad synonym: Artificial Intelligence
has db xref: VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)
has definition: 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.
has human readable id: Machine_learning
has narrow synonym: Active learning
has narrow synonym: Ensembl learning
has narrow synonym: Kernel methods
has narrow synonym: Knowledge representation
has narrow synonym: Neural networks
has narrow synonym: Recommender system
has narrow synonym: Reinforcement learning
has narrow synonym: Supervised learning
has narrow synonym: Unsupervised learning
in subset: bio
in subset: topics

Database management
type: Class
subclass of: Informatics
Created in: 1.8
has definition: The general handling of data stored in digital archives such as databases, databanks, web portals, and other data resources.
Related term: Database administration
has human readable id: Database_management
has broad synonym: Databases
Related term: Information systems
has narrow synonym: Content management
has narrow synonym: Document management
has narrow synonym: File management
has narrow synonym: Record management
in subset: bio
in subset: topics
comment: 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.

Zoology
type: Class
subclass of: Biology
Created in: 1.8
has db xref: VT 1.5.29 Zoology
has definition: Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.
has exact synonym: Animal
has exact synonym: Animal biology
has exact synonym: Animals
has exact synonym: Metazoa
has human readable id: Zoology
has narrow synonym: Animal genetics
has narrow synonym: Animal physiology
has narrow synonym: Entomology
in subset: bio
in subset: topics
comment: The study of the animal kingdom.

Protein sites, features and motifs
type: Class
subclass of: Proteins
subclass of: Sequence sites, features and motifs
Created in: 1.8
has definition: 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.
has human readable id: Protein_sites_features_and_motifs
has narrow synonym: Protein sequence features
has narrow synonym: Signal peptide cleavage sites
in subset: bio
in subset: topics
comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.

Nucleic acid sites, features and motifs
type: Class
subclass of: Nucleic acids
subclass of: Sequence sites, features and motifs
Created in: 1.8
has definition: 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.
has human readable id: Nucleic_acid_sites_features_and_motifs
has narrow synonym: Nucleic acid functional sites
has narrow synonym: Nucleic acid sequence features
has narrow synonym: Primer binding sites
has narrow synonym: Sequence tagged sites
in subset: bio
in subset: topics
comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.

Gene transcripts
type: Class
subclass of: RNA
subclass of: Gene structure
Created in: 1.8
has definition: Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.
has narrow synonym: mRNA features
has human readable id: Gene_transcripts
has narrow synonym: Coding RNA
has narrow synonym: EST
has narrow synonym: Exons
has narrow synonym: Fusion transcripts
has narrow synonym: Gene transcript features
has narrow synonym: Introns
has narrow synonym: PolyA signal
has narrow synonym: PolyA site
has narrow synonym: Signal peptide coding sequence
has narrow synonym: Transit peptide coding sequence
has narrow synonym: cDNA
has narrow synonym: mRNA
in subset: bio
in subset: topics
comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
comment: 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.
comment: 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.
comment: 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.

Protein-ligand interactions
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Protein-ligand (small molecule) interaction(s).
in subset: obsolete
replaced by: Protein interactions
deprecated: true

Protein-drug interactions
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Protein-drug interaction(s).
in subset: obsolete
replaced by: Protein interactions
deprecated: true

Genotyping experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
has human readable id: Genotyping_experiment
in subset: bio
in subset: topics

GWAS study
type: Class
subclass of: Experimental design and studies
Created in: 1.8
has definition: Genome-wide association study experiments.
has exact synonym: GWAS
has exact synonym: GWAS analysis
has exact synonym: Genome-wide association study
has human readable id: GWAS_study
in subset: bio
in subset: topics

Microarray experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: Microarray experiments including conditions, protocol, sample:data relationships etc.
has exact synonym: Microarrays
has human readable id: Microarray_experiment
has narrow synonym: Gene expression microarray
has narrow synonym: Genotyping array
has narrow synonym: Methylation array
has narrow synonym: MicroRNA array
has narrow synonym: Multichannel microarray
has narrow synonym: One channel microarray
has narrow synonym: Proprietary platform micoarray
has narrow synonym: RNA chips
has narrow synonym: RNA microarrays
has narrow synonym: Reverse phase protein array
has narrow synonym: SNP array
has narrow synonym: Tiling arrays
has narrow synonym: Tissue microarray
has narrow synonym: Two channel microarray
has narrow synonym: aCGH microarray
has narrow synonym: mRNA microarray
has narrow synonym: miRNA array
in subset: bio
in subset: topics
comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.

PCR experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: PCR experiments, e.g. quantitative real-time PCR.
has exact synonym: Polymerase chain reaction
has human readable id: PCR_experiment
has narrow synonym: Quantitative PCR
has narrow synonym: RT-qPCR
has narrow synonym: Real Time Quantitative PCR
in subset: bio
in subset: topics

Proteomics experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: Proteomics experiments.
has human readable id: Proteomics_experiment
has narrow synonym: 2D PAGE experiment
has narrow synonym: DIA
has narrow synonym: Data-independent acquisition
has narrow synonym: MS
has narrow synonym: MS experiments
has narrow synonym: Mass spectrometry
has narrow synonym: Mass spectrometry experiments
has narrow synonym: Northern blot experiment
has narrow synonym: Spectrum demultiplexing
in subset: bio
in subset: topics
comment: 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.

2D PAGE experiment
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Two-dimensional gel electrophoresis experiments, gels or spots in a gel.
in subset: obsolete
replaced by: Proteomics experiment
deprecated: true

Northern blot experiment
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Northern Blot experiments.
in subset: obsolete
replaced by: Proteomics experiment
deprecated: true

RNAi experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: RNAi experiments.
has human readable id: RNAi_experiment
in subset: bio
in subset: topics

Simulation experiment
type: Class
subclass of: Data acquisition
Created in: 1.8
has definition: Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.
has human readable id: Simulation_experiment
in subset: bio
in subset: topics

Protein-nucleic acid interactions
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Protein-DNA/RNA interaction(s).
in subset: obsolete
replaced by: Protein interactions
deprecated: true

Protein-protein interactions
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Protein-protein interaction(s), including interactions between protein domains.
in subset: obsolete
replaced by: Protein interactions
deprecated: true

Cellular process pathways
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Cellular process pathways.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Disease pathways
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Disease pathways, typically of human disease.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Environmental information processing pathways
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Environmental information processing pathways.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Genetic information processing pathways
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Genetic information processing pathways.
in subset: obsolete
replaced by: Molecular interactions, pathways and networks
deprecated: true

Protein super-secondary structure
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Super-secondary structure of protein sequence(s).
in subset: obsolete
replaced by: Protein secondary structure
deprecated: true

Protein active sites
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Catalytic residues (active site) of an enzyme.
in subset: obsolete
replaced by: Protein sites, features and motifs
deprecated: true

Protein binding sites
type: Class
subclass of: Protein sites, features and motifs
Created in: 1.8
has definition: 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.
has human readable id: Protein_binding_sites
has narrow synonym: Enzyme active site
has narrow synonym: Protein cleavage sites
has narrow synonym: Protein functional sites
has narrow synonym: Protein key folding sites
has narrow synonym: Protein-nucleic acid binding sites
in subset: bio
in subset: topics

Protein-nucleic acid binding sites
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: RNA and DNA-binding proteins and binding sites in protein sequences.
in subset: obsolete
replaced by: Protein binding sites
deprecated: true

Protein cleavage sites
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
in subset: obsolete
replaced by: Protein sites, features and motifs
deprecated: true

Protein chemical modifications
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Chemical modification of a protein.
in subset: obsolete
replaced by: Protein modifications
deprecated: true

Protein disordered structure
type: Class
subclass of: Protein structure analysis
Created in: 1.8
has definition: Disordered structure in a protein.
has exact synonym: Protein features (disordered structure)
has human readable id: Protein_disordered_structure
in subset: bio
in subset: topics

Protein domains
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Structural domains or 3D folds in a protein or polypeptide chain.
in subset: obsolete
replaced by: Protein folds and structural domains
deprecated: true

Protein key folding sites
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Key residues involved in protein folding.
in subset: obsolete
replaced by: Protein sites, features and motifs
deprecated: true

Protein post-translational modifications
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Post-translation modifications in a protein sequence, typically describing the specific sites involved.
in subset: obsolete
replaced by: Protein modifications
deprecated: true

Protein secondary structure
type: Class
subclass of: Protein structure analysis
Created in: 1.8
has definition: Secondary structure (predicted or real) of a protein, including super-secondary structure.
has exact synonym: Protein features (secondary structure)
has human readable id: Protein_secondary_structure
has narrow synonym: Protein super-secondary structure
in subset: bio
in subset: topics
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).

Protein sequence repeats
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Short repetitive subsequences (repeat sequences) in a protein sequence.
in subset: obsolete
replaced by: Sequence composition, complexity and repeats
deprecated: true

Protein signal peptides
type: Class
subclass of: DeprecatedClass
Created in: 1.8
Obsolete since: 1.13
Old parent: Thing
has definition: Signal peptides or signal peptide cleavage sites in protein sequences.
in subset: obsolete
replaced by: Protein sites, features and motifs
deprecated: true

Applied mathematics
type: Class
subclass of: Mathematics
Created in: 1.10
has db xref: VT 1.1.1 Applied mathematics
has definition: The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models.
has human readable id: Applied_mathematics
in subset: bio
in subset: topics

Pure mathematics
type: Class
subclass of: Mathematics
Created in: 1.10
has db xref: VT 1.1.1 Pure mathematics
has definition: The study of abstract mathematical concepts.
has human readable id: Pure_mathematics
has narrow synonym: Linear algebra
in subset: bio
in subset: topics

Data governance
type: Class
subclass of: Data management
Created in: 1.10
has definition: Data governance is the control of data entry and maintenance to ensure the data meets defined standards, qualities, or constraints.
has human readable id: Data_governance
has related synonym: Data stewardship
in subset: bio
in subset: topics
related match: Q1172231
related match: Q57450885

Data quality management
type: Class
subclass of: Data management
Created in: 1.10
has definition: The quality, integrity, and cleaning up of data.
has human readable id: Data_quality_management
has narrow synonym: Data clean-up
has narrow synonym: Data cleaning
has narrow synonym: Data integrity
has narrow synonym: Data quality
in subset: bio
in subset: topics

Freshwater biology
type: Class
subclass of: Biology
Created in: 1.10
has broad synonym: Freshwater science
has db xref: VT 1.5.18 Marine and Freshwater biology
has definition: The study of organisms in freshwater ecosystems.
has human readable id: Freshwater_biology
in subset: bio
in subset: events
in subset: topics

Human genetics
type: Class
subclass of: Genetics
Created in: 1.10
isdebtag: true
has db xref: VT 3.1.2 Human genetics
has definition: The study of inheritance in human beings.
has human readable id: Human_genetics
in subset: bio
in subset: events
in subset: topics

Tropical medicine
type: Class
subclass of: Medicine
Created in: 1.10
has db xref: VT 3.3.14 Tropical medicine
has definition: Health problems that are prevalent in tropical and subtropical regions.
has human readable id: Tropical_medicine
in subset: bio
in subset: events
in subset: topics

Medical biotechnology
type: Class
subclass of: Biotechnology
Created in: 1.10
isdebtag: true
has db xref: VT 3.3.14 Tropical medicine
has db xref: VT 3.4 Medical biotechnology
has db xref: VT 3.4.1 Biomedical devices
has db xref: VT 3.4.2 Health-related biotechnology
has definition: Biotechnology applied to the medical sciences and the development of medicines.
has human readable id: Medical_biotechnology
has narrow synonym: Pharmaceutical biotechnology
in subset: bio
in subset: events
in subset: topics

Personalised medicine
type: Class
subclass of: Medicine
Created in: 1.10
isdebtag: true
has db xref: VT 3.4.5 Molecular diagnostics
has definition: An approach to medicine whereby decisions, practices and are tailored to the individual patient based on their predicted response or risk of disease.
has exact synonym: Precision medicine
has human readable id: Personalised_medicine
has narrow synonym: Molecular diagnostics
in subset: bio
in subset: events
in subset: topics

Immunoprecipitation experiment
type: Class
subclass of: Data acquisition
Created in: 1.12
has definition: Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq.
has exact synonym: Chromatin immunoprecipitation
has human readable id: Immunoprecipitation_experiment
in subset: bio
in subset: topics

Whole genome sequencing
type: Class
subclass of: Sequencing
Created in: 1.12
has definition: Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time.
has exact synonym: Genome sequencing
has exact synonym: WGS
has human readable id: Whole_genome_sequencing
has narrow synonym: De novo genome sequencing
has narrow synonym: Whole genome resequencing
in subset: bio
in subset: topics

Methylated DNA immunoprecipitation
type: Class
subclass of: Immunoprecipitation experiment
Created in: 1.12
Documentation: Whole genome sequencing
has definition: Laboratory technique to sequence the methylated regions in DNA.
has exact synonym: MeDIP-chip
has exact synonym: MeDIP-seq
has exact synonym: mDIP
has human readable id: Methylated_DNA_immunoprecipitation
has narrow synonym: BS-Seq
has narrow synonym: Bisulfite sequencing
has narrow synonym: MeDIP
has narrow synonym: Methylated DNA immunoprecipitation (MeDIP)
has narrow synonym: Methylation sequencing
has narrow synonym: WGBS
has narrow synonym: Whole-genome bisulfite sequencing
has narrow synonym: methy-seq
has narrow synonym: methyl-seq
in subset: bio
in subset: topics

Exome sequencing
type: Class
subclass of: Sequencing
Created in: 1.12
has definition: Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome.
has exact synonym: Exome
has exact synonym: Exome analysis
has exact synonym: Exome capture
has exact synonym: Targeted exome capture
has exact synonym: WES
has exact synonym: Whole exome sequencing
has human readable id: Exome_sequencing
in subset: bio
in subset: topics
comment: Exome sequencing is considered a cheap alternative to whole genome sequencing.

Experimental design and studies
type: Class
subclass of: Topic
Created in: 1.12
Documentation: Design of experiments
isdebtag: true
has definition: The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions.
has exact synonym: Design of experiments
has exact synonym: Experimental design
has exact synonym: Studies
has human readable id: Experimental_design_and_studies
in subset: bio
in subset: topics

Animal study
type: Class
subclass of: Laboratory animal science
subclass of: Experimental design and studies
Created in: 1.12
has definition: The design of an experiment involving non-human animals.
has human readable id: Animal_study
has narrow synonym: Challenge study
in subset: bio
in subset: topics

Microbial ecology
type: Class
subclass of: Ecology
subclass of: Microbiology
Created in: 1.13
isdebtag: true
has definition: The ecology of microorganisms including their relationship with one another and their environment.
has exact synonym: Environmental microbiology
has human readable id: Microbial_ecology
has narrow synonym: Community analysis
has narrow synonym: Microbiome
has narrow synonym: Molecular community analysis
in subset: bio
in subset: topics

RNA immunoprecipitation
type: Class
subclass of: Immunoprecipitation experiment
Created in: 1.17
has definition: An antibody-based technique used to map in vivo RNA-protein interactions.
has exact synonym: RIP
has human readable id: RNA_immunoprecipitation
has narrow synonym: CLIP
has narrow synonym: CLIP-seq
has narrow synonym: HITS-CLIP
has narrow synonym: PAR-CLIP
has narrow synonym: iCLIP
in subset: bio
in subset: topics

Population genomics
type: Class
subclass of: Genomics
Created in: 1.17
has definition: Large-scale study (typically comparison) of DNA sequences of populations.
has human readable id: Population_genomics
in subset: bio
in subset: events
in subset: topics

Agricultural science
type: Class
subclass of: Biology
Created in: 1.20
has broad synonym: Agriculture
has broad synonym: Agroecology
has broad synonym: Agronomy
has definition: Multidisciplinary study, research and development within the field of agriculture.
has human readable id: Agricultural_science
has narrow synonym: Agricultural biotechnology
has narrow synonym: Agricultural economics
has narrow synonym: Animal breeding
has narrow synonym: Animal husbandry
has narrow synonym: Animal nutrition
has narrow synonym: Farming systems research
has narrow synonym: Food process engineering
has narrow synonym: Food security
has narrow synonym: Horticulture
has narrow synonym: Phytomedicine
has narrow synonym: Plant breeding
has narrow synonym: Plant cultivation
has narrow synonym: Plant nutrition
has narrow synonym: Plant pathology
has narrow synonym: Soil science
in subset: bio
in subset: topics

Metagenomic sequencing
type: Class
subclass of: Sequencing
Created in: 1.20
has definition: Approach which samples, in parallel, all genes in all organisms present in a given sample, e.g. to provide insight into biodiversity and function.
has exact synonym: Shotgun metagenomic sequencing
has human readable id: Metagenomic_sequencing
in subset: bio
in subset: topics

Environmental sciences
type: Class
subclass of: Topic
Created in: 1.21
has definition: 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.
Related term: Environment
has human readable id: Environmental_science
in subset: bio
in subset: topics

Biomolecular simulation
type: Class
subclass of: Computational biology
Created in: 1.22
has definition: The study and simulation of molecular conformations using a computational model and computer simulations.
in subset: bio
in subset: topics
comment: This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc.

Synthetic biology
type: Class
subclass of: Biology
subclass of: Biotechnology
Created in: 1.22
has definition: The application of multi-disciplinary science and technology for the construction of artificial biological systems for diverse applications.
has narrow synonym: Biomimeic chemistry
in subset: bio
in subset: topics

Genetic engineering
type: Class
subclass of: Genetics
subclass of: Biotechnology
Created in: 1.22
has definition: The application of biotechnology to directly manipulate an organism's genes.
has exact synonym: Genetic manipulation
has exact synonym: Genetic modification
has human readable id: Genetic_engineering
has narrow synonym: Genome editing
has narrow synonym: Genome engineering
in subset: bio
in subset: topics

Proteogenomics
type: Class
subclass of: Genomics
Created in: 1.24
has definition: A field of biological research focused on the discovery and identification of peptides, typically by comparing mass spectra against a protein database.
has human readable id: Proteogenomics
in subset: bio
in subset: topics

Genome resequencing
type: Class
subclass of: Sequencing
Created in: 1.24
has definition: 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.).
has broad synonym: Resequencing
Related term: Amplicon panels
has related synonym: Amplicon sequencing
has related synonym: Amplicon-based sequencing
has narrow synonym: Highly targeted resequencing
has narrow synonym: Whole genome resequencing (WGR)
has narrow synonym: Whole-genome re-sequencing (WGSR)
comment: 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.
has related synonym: Ultra-deep sequencing

Immunogenetics
type: Class
subclass of: Immunology
subclass of: Genetics
Created in: 1.24
has definition: A biomedical field that bridges immunology and genetics, to study the genetic basis of the immune system.
has exact synonym: Immune system genetics
has exact synonym: Immungenetics
has exact synonym: Immunology and genetics
has human readable id: Immunogenetics
has narrow synonym: Immunogenes
in subset: bio
in subset: topics
comment: 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.

Chemometrics
type: Class
subclass of: Cheminformatics
Created in: 1.24
has definition: Interdisciplinary science focused on extracting information from chemical systems by data analytical approaches, for example multivariate statistics, applied mathematics, and computer science.
has human readable id: Chemometrics
in subset: bio
in subset: topics

Cytometry
type: Class
subclass of: Data acquisition
Created in: 1.24
has definition: Cytometry is the measurement of the characteristics of cells.
has human readable id: Cytometry
has narrow synonym: Flow cytometry
has narrow synonym: Image cytometry
has narrow synonym: Mass cytometry
in subset: bio
in subset: topics

Metabolic engineering
type: Class
subclass of: Biotechnology
Created in: 1.24
has definition: Biotechnology approach that seeks to optimize cellular genetic and regulatory processes in order to increase the cells' production of a certain substance.
in subset: bio
in subset: topics

Chromosome conformation capture
type: Class
subclass of: Data acquisition
Created in: 1.24
has definition: Molecular biology methods used to analyze the spatial organization of chromatin in a cell.
has exact synonym: 3C technologies
has exact synonym: 3C-based methods
has exact synonym: Chromosome conformation analysis
has human readable id: Chromosome_conformation_capture
has narrow synonym: Chromatin accessibility
has narrow synonym: Chromatin accessibility assay

Metatranscriptomics
type: Class
subclass of: Gene expression
subclass of: Transcriptomics
Created in: 1.24
has definition: The study of microbe gene expression within natural environments (i.e. the metatranscriptome).
has human readable id: Metatranscriptomics
in subset: bio
in subset: topics
comment: Metatranscriptomics methods can be used for whole gene expression profiling of complex microbial communities.

Paleogenomics
type: Class
subclass of: Genomics
Created in: 1.24
has definition: The reconstruction and analysis of genomic information in extinct species.
has human readable id: Paleogenomics
has narrow synonym: Ancestral genomes
has narrow synonym: Paleogenetics

Cladistics
type: Class
subclass of: Sequence analysis
subclass of: Phylogeny
Created in: 1.24
has definition: The biological classification of organisms by categorizing them in groups ("clades") based on their most recent common ancestor.
has human readable id: Cladistics
has narrow synonym: Tree of life
in subset: bio
in subset: topics

Molecular evolution
type: Class
subclass of: Genotype and phenotype
subclass of: Evolutionary biology
subclass of: Omics
Created in: 1.24
has definition: The study of the process and mechanism of change of biomolecules such as DNA, RNA, and proteins across generations.
has human readable id: Molecular_evolution
in subset: bio
in subset: topics

Immunoinformatics
type: Class
subclass of: Informatics
subclass of: Immunology
Created in: 1.24
has definition: 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.
has exact synonym: Computational immunology
has human readable id: Immunoinformatics
comment: 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.

Echography
type: Class
subclass of: Imaging
Created in: 1.24
has definition: A diagnostic imaging technique based on the application of ultrasound.
has exact synonym: Standardized echography
has exact synonym: Ultrasound imaging
has human readable id: Echography
has narrow synonym: Diagnostic sonography
has narrow synonym: Medical ultrasound
has narrow synonym: Standard echography
has narrow synonym: Ultrasonography
in subset: bio
in subset: topics

Fluxomics
type: Class
subclass of: Omics
Created in: 1.24
has definition: Experimental approaches to determine the rates of metabolic reactions - the metabolic fluxes - within a biological entity.
has human readable id: Fluxomics
comment: The "fluxome" is the complete set of metabolic fluxes in a cell, and is a dynamic aspect of phenotype.

Protein interaction experiment
type: Class
subclass of: Data acquisition
Created in: 1.12
has definition: An experiment for studying protein-protein interactions.
has human readable id: Protein_interaction_experiment
has narrow synonym: Co-immunoprecipitation
has narrow synonym: Phage display
has narrow synonym: Yeast one-hybrid
has narrow synonym: Yeast two-hybrid
in subset: bio
in subset: topics
comment: 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.

Copy number variation
type: Class
subclass of: Structural variation
Created in: 1.25
has definition: 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.
has human readable id: Copy_number_variation
has narrow synonym: CNV deletion
has narrow synonym: CNV duplication
has narrow synonym: CNV insertion / amplification
has narrow synonym: Complex CNV
has narrow synonym: Copy number variant

Cytogenetics
type: Class
subclass of: Molecular genetics
Created in: 1.25
has definition: The branch of genetics concerned with the relationships between chromosomes and cellular behaviour, especially during mitosis and meiosis.
in subset: bio
in subset: topics

Vaccinology
type: Class
subclass of: Medicines research and development
Created in: 1.25
has definition: 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.
has human readable id: Vaccinology
has narrow synonym: Rational vaccine design
has narrow synonym: Reverse vaccinology
has narrow synonym: Structural vaccinology
has narrow synonym: Structure-based immunogen design
has narrow synonym: Vaccine design
in subset: bio
in subset: topics

Immunomics
type: Class
subclass of: Omics
Created in: 1.25
has definition: The study of immune system as a whole, its regulation and response to pathogens using genome-wide approaches.
in subset: bio
in subset: topics

Epistasis
type: Class
subclass of: Genotype and phenotype
Created in: 1.25
has exact synonym: Epistatic genetic interaction
has exact synonym: Epistatic interactions
in subset: bio
in subset: topics
has definition: 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...

Open science
type: Class
subclass of: Topic
Created in: 1.26
has broad synonym: Open and reliable science
has broad synonym: Open research
has broad synonym: Open, reliable, transparent, and trustable science
has definition: Open science encompasses the practices of making scientific research transparent and participatory, and its outputs publicly accessible.
in subset: bio
in subset: topics

Data rescue
type: Class
subclass of: Data management
Created in: 1.26
has definition: 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.
in subset: bio
in subset: topics

FAIR data
type: Class
subclass of: Data management
subclass of: Open science
Created in: 1.26
Related term: FAIR data principles
Related term: FAIR principles
Related term: FAIRification
has definition: FAIR data is scientific data that meets the principles of being findable, accessible, interoperable, and reusable.
has exact synonym: Findable, accessible, interoperable, reusable data
has related synonym: Open data
in subset: bio
in subset: topics
comment: 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).

Antimicrobial resistance
type: Class
Created in: 1.26
has exact synonym: AMR
has narrow synonym: Antibiotic resistance (ABR)
has narrow synonym: Antifungal resistance
has narrow synonym: Antiviral resistance
has narrow synonym: Antiprotozoal resistance
has narrow synonym: Multiple drug resistance (MDR)
has narrow synonym: Multidrug resistance
has narrow synonym: Multiresistance
has narrow synonym: Extensive drug resistance (XDR)
has narrow synonym: Pandrug resistance (PDR)
has narrow synonym: Total drug resistance (TDR)
in subset: bio
in subset: topics
has definition: Microbial mechanisms for protecting microorganisms against antimicrobial agents.
subclass of: Microbiology
subclass of: Infectious disease

Electroencephalography
type: Class
Created in: 1.26
has exact synonym: EEG
in subset: bio
in subset: topics
has definition: The monitoring method for measuring electrical activity in the brain.
subclass of: Physiology
subclass of: Imaging

Electrocardiography
type: Class
Created in: 1.26
has exact synonym: EKG
has exact synonym: ECG
in subset: bio
in subset: topics
has definition: The monitoring method for measuring electrical activity in the heart.
subclass of: Physiology
subclass of: Imaging

Cryogenic electron microscopy
type: Class
Created in: 1.26
has exact synonym: cryo-EM
in subset: bio
in subset: topics
has definition: A method for studying biomolecules and other structures at very low (cryogenic) temperature using electron microscopy.
subclass of: Electron microscopy

Biosciences
type: Class
subclass of: Topic
Created in: 1.26
Related term: Life
has definition: Biosciences, or life sciences, include fields of study related to life, living beings, and biomolecules.
has exact synonym: Life sciences
in subset: bio
in subset: topics

Carbon cycle
type: Class
subclass of: Environmental sciences
subclass of: Ecology
subclass of: Chemistry
subclass of: Physics
Created in: 1.26
has definition: 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.
has broad synonym: Biogeochemical cycle
in subset: bio
in subset: topics
comment: Note that the carbon-nitrogen-oxygen (CNO) cycle (https://en.wikipedia.org/wiki/CNO_cycle) is a completely different, thermonuclear reaction in stars.

Multiomics
type: Class
Created in: 1.26
has exact synonym: Panomics
has exact synonym: Pan-omics
has exact synonym: Integrative omics
has exact synonym: Multi-omics
in subset: bio
in subset: topics
has definition: Multiomics concerns integration of data from multiple omics (e.g. transcriptomics, proteomics, epigenomics).
subclass of: Omics

Ribosome Profiling
type: Class
Created in: 1.26
subclass of: Transcriptomics
has exact synonym: RIBO-seq
has exact synonym: ribo-seq
has exact synonym: RiboSeq
has exact synonym: Ribo-Seq
has exact synonym: ribosomal footprinting
has narrow synonym: translation footprinting
in subset: bio
in subset: topics
has definition: With ribosome profiling, ribosome-protected mRNA fragments are analyzed with RNA-seq techniques leading to a genome-wide measurement of the translation landscape.

Single-cell sequencing
type: Class
subclass of: Sequencing
Created in: 1.26
has definition: 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.
has narrow synonym: Single-cell genomics
in subset: bio
in subset: topics

Acoustics
type: Class
Created in: 1.26
subclass of: Physics
in subset: bio
in subset: topics
has definition: The study of mechanical waves in liquids, solids, and gases.

Microfluidics
type: Class
Created in: 1.26
subclass of: Physics
subclass of: Biochemistry
subclass of: Biotechnology
has narrow synonym: Fluidics
in subset: bio
in subset: topics
has definition: Interdisplinary study of behavior, precise control, and manipulation of low (microlitre) volume fluids in constrained space.

Genomic imprinting
type: Class
Created in: 1.26
has exact synonym: Gene imprinting
in subset: bio
in subset: topics
has definition: 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.
subclass of: Epigenetics

Metabarcoding
type: Class
subclass of: Sequence analysis
subclass of: Microbial ecology
subclass of: Restriction
  on property: related
  some values from: Genome resequencing
Created in: 1.26
Related term: Environmental DNA (eDNA)
Related term: Environmental RNA (eRNA)
Related term: Environmental sequencing
Related term: Taxonomic profiling
has definition: Metabarcoding is the barcoding of (environmental) DNA or RNA to identify multiple taxa from the same sample.
has narrow synonym: DNA metabarcoding
has narrow synonym: Environmental metabarcoding
has narrow synonym: RNA metabarcoding
has narrow synonym: eDNA metabarcoding
has narrow synonym: eRNA metabarcoding
in subset: bio
in subset: topics
comment: Typically, high-throughput sequencing is performed and the resulting sequence reads are matched to DNA barcodes in a reference database.
related match: Q25098939

Data protection
type: Class
subclass of: Data management
Created in: 1.26
Related term: Classified information
Related term: Confidential information
Related term: Data privacy
Related term: Information privacy
Related term: Information sensitivity
Related term: Personal data
Related term: Private data
Related term: Sensitive data
Related term: Sensitive human data
Related term: Sensitive information
Related term: Special category data
has definition: Data protection is a topic concerning data that should be protected from disclosure, damage, or unauthorised access, due to its sensitive nature.
has related synonym: Management of sensitive data
in subset: bio
in subset: topics
comment: Sensitive data includes not only personal and commercial data, but also information about e.g. localisation of endangered biological species that could be exploited.
comment: 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).
related match: Q1172506

Cybersecurity
type: Class
subclass of: Informatics
Created in: 1.26
has definition: 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.
has broad synonym: Cryptography
has broad synonym: Cryptology
has broad synonym: IT security
has broad synonym: System security
has narrow synonym: Data security
has narrow synonym: Computer security
in subset: bio
in subset: topics
comment: 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).
narrow match: Q3510521
narrow match: Q899388
related match: Q189900

Version control
type: Class
subclass of: Informatics
Created in: 1.26
has definition: 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.
has broad synonym: Version tracking
has narrow synonym: Source control
has related synonym: Version control system
has related synonym: Source control system
has related synonym: Versioning system
in subset: bio
in subset: topics
comment: Distributed version control is particularly useful for open, collaborative development of software and other creative work, enabling global communities to work cohesively.
comment: 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.

Software management
type: Class
subclass of: Informatics
Created in: 1.26
Related term: Code stewardship
Related term: Software stewardship
Related term: Service curation
Related term: Service registry
Related term: Software archive
Related term: Software curation
Related term: Software registry
Related term: Tool curation
Related term: Tool registry
Related term: Workflow curation
Related term: Workflow registry
has definition: 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.
has related synonym: Service management
in subset: bio
in subset: topics
comment: 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.
related match: Q947779

Obsolete concept (EDAM)
type: Class
subclass of: DeprecatedClass
Created in: 1.2
Old parent: Thing
has definition: An obsolete concept (redefined in EDAM).
replaced by: DeprecatedClass
comment: Needed for conversion to the OBO format.
deprecated: true