EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics
type: Ontology
next id: 3424
date: 06:10:2014 23:58
remark: EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.
version: 1.4
creator: Jon Ison
creator: Matúš Kalaš
creator: Hervé Ménager
saved by: Jon Ison, Matus Kalas, Herve Menager
remark: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.
has subset: operations "EDAM operations"
has subset: edam "EDAM"
has subset: relations "EDAM relations"
has subset: bioinformatics "Bioinformatics"
has subset: data "EDAM types of data"
has subset: identifiers "EDAM types of identifiers"
has subset: formats "EDAM data formats"
has subset: topics "EDAM topics"
has subset: concept_properties "EDAM concept properties"
default-relationship-id-prefix: EDAM
idspace: EDAM_operation http://edamontology.org/operation_ "EDAM operations"
idspace: EDAM_topic http://edamontology.org/topic_ "EDAM topics"
idspace: EDAM_data http://edamontology.org/data_ "EDAM types of data"
idspace: EDAM_format http://edamontology.org/format_ "EDAM data formats"
idspace: EDAM http://edamontology.org/ "EDAM relations and concept properties"
format: application/rdf+xml

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

Example
type: AnnotationProperty
in subset: concept_properties
is metadata tag: true
has definition: 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.

Regular expression
type: AnnotationProperty
is metadata tag: true
in subset: concept_properties
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.

Documentation
type: AnnotationProperty
in subset: concept_properties
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

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

has format
type: ObjectProperty
is anti symmetric: false
has definition: 'A has_format B' defines for the subject A, that it has the object B as its data format.
in subset: edam
is symmetric: false
is reflexive: false
in subset: relations
in subset: bioinformatics
transitive over: OBO_REL:is_a
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'.
domain: Data
range: Format
has related synonym: OBI_0000298
has related synonym: has-quality

Axiom
comment: 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject.
annotated source: has format
annotated target: OBI_0000298
annotated property: hasRelatedSynonym

has function
type: ObjectProperty
is reflexive: false
in subset: relations
has definition: 'A has_function B' defines for the subject A, that it has the object B as its function.
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.
is symmetric: false
in subset: edam
has related synonym: OBO_REL:bearer_of
in subset: bioinformatics
transitive over: OBO_REL:is_a
is anti symmetric: false
range: Operation
has narrow synonym: OBI_0000306
has exact synonym: has function
has related synonym: has-quality

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

Axiom
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.
annotated source: has function
annotated property: hasRelatedSynonym

Axiom
comment: 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject.
annotated source: has function
annotated target: OBI_0000306
annotated property: hasNarrowSynonym

has identifier
type: ObjectProperty
is symmetric: false
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 definition: 'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
in subset: edam
transitive over: OBO_REL:is_a
in subset: bioinformatics
in subset: relations
is anti symmetric: false
is reflexive: false
domain: Data
range: Identifier

has input
type: ObjectProperty
in subset: edam
is cyclic: true
in subset: bioinformatics
is reflexive: false
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.
is symmetric: false
transitive over: OBO_REL:is_a
in subset: relations
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.
is anti symmetric: false
has related synonym: OBO_REL:has_participant
range: Data
domain: Operation
has narrow synonym: OBI_0000293
has exact synonym: has input

Axiom
comment: 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant).
annotated source: has input
annotated target: OBI_0000293
annotated property: hasNarrowSynonym

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

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

has output
type: ObjectProperty
is anti symmetric: false
is reflexive: false
is symmetric: false
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.
is cyclic: true
has related synonym: OBO_REL:has_participant
in subset: relations
transitive over: OBO_REL:is_a
in subset: bioinformatics
in subset: edam
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.
range: Data
domain: Operation
has narrow synonym: OBI_0000299
has exact synonym: has output

Axiom
comment: 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant).
annotated source: has output
annotated target: OBI_0000299
annotated property: hasNarrowSynonym

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

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

has topic
type: ObjectProperty
is reflexive: false
in subset: bioinformatics
is anti symmetric: false
transitive over: OBO_REL:is_a
in subset: edam
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).
is symmetric: 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 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.
in subset: relations
is cyclic: true
has related synonym: hasTopic
range: Topic
has related synonym: IAO_0000136
has related synonym: OBI_0000298
has related synonym: has-quality
domain: Class
  union of: Data
  union of: Operation

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

Axiom
comment: 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject.
annotated source: has topic
annotated target: OBI_0000298
annotated property: hasRelatedSynonym

Axiom
comment: 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource.
annotated target: hasTopic
annotated source: has topic
annotated property: hasRelatedSynonym

Axiom
comment: 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object.
annotated source: has topic
annotated target: IAO_0000136
annotated property: hasRelatedSynonym

is format of
type: ObjectProperty
has related synonym: OBO_REL:quality_of
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.
in subset: relations
in subset: edam
has definition: 'A is_format_of B' defines for the subject A, that it is a data format of the object B.
is cyclic: false
is symmetric: false
is reflexive: false
transitive over: OBO_REL:is_a
in subset: bioinformatics
is anti symmetric: false
range: Data
domain: Format
inverse of: has format
has related synonym: inherent-in

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

is function of
type: ObjectProperty
in subset: bioinformatics
is symmetric: false
is anti symmetric: false
in subset: relations
in subset: edam
has narrow synonym: OBO_REL:function_of
has definition: 'A is_function_of B' defines for the subject A, that it is a function of the object B.
is reflexive: false
is cyclic: true
transitive over: OBO_REL:is_a
has related synonym: OBO_REL:inheres_in
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.
inverse of: has function
domain: Operation
has exact synonym: is function of
has related synonym: inherent-in

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

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

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

is identifier of
type: ObjectProperty
is symmetric: false
has definition: 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B.
transitive over: OBO_REL:is_a
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.
in subset: relations
is cyclic: false
in subset: edam
in subset: bioinformatics
is reflexive: false
is anti symmetric: false
range: Data
domain: Identifier
inverse of: has identifier

is input of
type: ObjectProperty
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.
is symmetric: 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 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'.
in subset: edam
transitive over: OBO_REL:is_a
is reflexive: false
has related synonym: OBO_REL:participates_in
in subset: bioinformatics
is cyclic: true
in subset: relations
is anti symmetric: false
domain: Data
inverse of: has input
range: Operation
has narrow synonym: OBI_0000295
has exact synonym: is input of

Axiom
comment: 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011).
annotated source: is input of
annotated target: OBI_0000295
annotated property: hasNarrowSynonym

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

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

is output of
type: ObjectProperty
in subset: relations
is cyclic: true
has related synonym: OBO_REL:participates_in
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.
is anti symmetric: 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 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'.
in subset: edam
is symmetric: false
in subset: bioinformatics
is reflexive: false
transitive over: OBO_REL:is_a
domain: Data
inverse of: has output
range: Operation
has narrow synonym: OBI_0000312
has exact synonym: is output of

Axiom
comment: 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011).
annotated source: is output of
annotated target: OBI_0000312
annotated property: hasNarrowSynonym

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

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

is topic of
type: ObjectProperty
in subset: edam
is symmetric: false
transitive over: OBO_REL:is_a
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'.
is anti symmetric: false
is cyclic: true
is reflexive: false
in subset: bioinformatics
has related synonym: OBO_REL:quality_of
in subset: relations
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).
inverse of: has topic
domain: Topic
has related synonym: inherent-in
range: Class
  union of: Data
  union of: Operation

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

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

Resource type
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: A type of computational resource used in bioinformatics.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
in subset: bioinformatics
in subset: obsolete

Data
type: Class
disjoint with: Format
disjoint with: Operation
disjoint with: Topic
disjoint with: DeprecatedClass
has narrow synonym: Datum
Created in: beta12orEarlier
has narrow synonym: Data set
has exact synonym: Data record
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 related synonym: IAO_0000027
has related synonym: IAO_0000030
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: DigitalEntity
has related synonym: SIO_000069
has related synonym: SIO_000088
has exact synonym: data_002
has broad synonym: Continuant
has related synonym: Perpetuant

Axiom
comment: IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something.
annotated source: Data
annotated target: IAO_0000027
annotated property: hasRelatedSynonym

Axiom
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).
annotated source: Data
annotated property: hasExactSynonym

Axiom
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).
annotated source: Data
annotated property: hasNarrowSynonym

Axiom
comment: IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity.
annotated source: Data
annotated target: IAO_0000030
annotated property: hasRelatedSynonym

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

Axiom
comment: Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019).
annotated source: Data
annotated target: SIO_000069
annotated property: hasRelatedSynonym

Axiom
comment: Data does however not necessarily contain statements and not necessarily about an entity.
annotated source: Data
annotated target: SIO_000088
annotated property: hasRelatedSynonym

Axiom
comment: GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual.
annotated source: Data
annotated property: hasRelatedSynonym
annotated target: Perpetuant

Tool
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: A bioinformatics package or tool, e.g. a standalone application or web service.
Created in: beta12orEarlier
in subset: obsolete

Database
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
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

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

Directory metadata
type: Class
subclass of: System metadata
Created in: beta12orEarlier
has definition: A directory on disk from which files are read.
in subset: bioinformatics
in subset: data
in subset: edam

MeSH vocabulary
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
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.
Created in: beta12orEarlier
deprecated: true
consider: Ontology
in subset: obsolete

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

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

Identifier
type: Class
subclass of: Data
subclass of: Restriction
  on property: is identifier of
  some values from: Data
disjoint with: Report
disjoint with: Parameter
disjoint with: Core data
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
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers
has narrow synonym: identifier
has exact synonym: SIO_000115
has exact synonym: data_005

Axiom
comment: Almost exact but limited to identifying resources.
annotated source: Identifier
annotated target: identifier
annotated property: hasNarrowSynonym

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

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

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

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: bioinformatics
in subset: data
in subset: edam

QSAR descriptor
type: Class
subclass of: Molecular property (general)
Created in: beta12orEarlier
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.
has definition: A QSAR quantitative descriptor (name-value pair) of chemical structure.
in subset: bioinformatics
in subset: data
in subset: edam

Raw sequence
type: Class
subclass of: Sequence
comment: Non-sequence characters may be used for example for gaps and translation stop.
has definition: A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record
type: Class
subclass of: Sequence
has definition: A molecular sequence and associated metadata.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence set
type: Class
subclass of: Sequence report
has related synonym: SO:0001260
Created in: beta12orEarlier
comment: This concept may be used for arbitrary sequence sets and associated data arising from processing.
has definition: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence mask character
type: Class
subclass of: Sequence mask parameter
has definition: A character used to replace (mask) other characters in a molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence mask type
type: Class
subclass of: Sequence mask parameter
subclass of: Type
Created in: beta12orEarlier
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.
has definition: A label (text token) describing the type of sequence masking to perform.
in subset: bioinformatics
in subset: data
in subset: edam

DNA sense specification
type: Class
subclass of: Sequence parameter
subclass of: Sequence features metadata
Created in: beta12orEarlier
has exact synonym: DNA strand specification
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.
has definition: The strand of a DNA sequence (forward or reverse).
has exact synonym: Strand
in subset: bioinformatics
in subset: data
in subset: edam

Sequence length specification
type: Class
subclass of: Sequence parameter
Created in: beta12orEarlier
has definition: A specification of sequence length(s).
in subset: bioinformatics
in subset: data
in subset: edam

Sequence metadata
type: Class
subclass of: Sequence property
subclass of: Metadata
subclass of: Sequence report
comment: This is used for such things as a report including the sequence identifier, type and length.
has definition: Basic or general information concerning molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence feature source
type: Class
subclass of: Evidence
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.
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).
in subset: bioinformatics
in subset: data
in subset: edam

Database hits (sequence)
type: Class
subclass of: Database hits
has definition: A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Database hits (secondary)
type: Class
subclass of: Database hits
has definition: A report of hits from a search of a protein secondary or domain database.
Created in: beta12orEarlier
comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence signature model
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Data files used by motif or profile methods.
consider: Biological model
in subset: obsolete

Sequence signature
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A classifier of sequences such as a sequence motif, profile or other diagnostic element.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Sequence motif
consider: Sequence profile
in subset: obsolete

Sequence alignment (words)
type: Class
subclass of: Sequence alignment
has definition: Alignment of exact matches between subsequences (words) within two or more molecular sequences.
has exact synonym: Sequence word alignment
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Sequence alignment
type: Class
subclass of: Alignment
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
has definition: Alignment of multiple molecular sequences.
Created in: beta12orEarlier
has exact synonym: Sequence alignment
has exact synonym: D016415
in subset: bioinformatics
in subset: data
in subset: edam
has exact synonym: SIO_010066

Sequence alignment parameter
type: Class
subclass of: Sequence parameter
Created in: beta12orEarlier
has definition: Some simple value controlling a sequence alignment (or similar 'match') operation.
in subset: bioinformatics
in subset: data
in subset: edam

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

Sequence alignment metadata
type: Class
subclass of: Sequence alignment report
subclass of: Metadata
Created in: beta12orEarlier
has definition: Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence alignment report
type: Class
subclass of: Alignment report
Created in: beta12orEarlier
has definition: An informative report of molecular sequence alignment-derived data or metadata.
comment: This is a broad data type and is used a placeholder for other, more specific types.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence profile alignment
type: Class
subclass of: Alignment
has definition: A profile-profile alignment (each profile typically representing a sequence alignment).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence-profile alignment
type: Class
subclass of: Alignment
comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.
has definition: Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Phylogenetic tree
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
has db xref: Moby:myTree
Created in: beta12orEarlier
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 db xref: Moby:phylogenetic_tree
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'.
has db xref: Moby:Tree
has exact synonym: Phylogeny
has related synonym: D010802
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: Tree

Comparison matrix
type: Class
subclass of: Matrix
has exact synonym: Substitution matrix
has definition: Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.
Created in: beta12orEarlier
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).
in subset: bioinformatics
in subset: data
in subset: edam

Protein topology
type: Class
subclass of: Obsolete concept (EDAM)
comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated.
deprecated: true
has definition: Predicted or actual protein topology represented as a string of protein secondary structure elements.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Protein features (secondary structure)
in subset: obsolete

Protein features (secondary structure)
type: Class
subclass of: Protein features
subclass of: Secondary structure
subclass of: Restriction
  on property: has topic
  some values from: Protein secondary structure
Created in: beta12orEarlier
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).
has exact synonym: Protein secondary structure
has definition: Secondary structure assignment (predicted or real) of a protein.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (super-secondary)
type: Class
subclass of: Protein features
subclass of: Protein structure report
has exact synonym: Protein structure report (super-secondary)
Created in: beta12orEarlier
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
has definition: A report of predicted or actual super-secondary structure of protein sequence(s).
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

Structure
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
has definition: 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.
has exact synonym: Structure data
comment: The coordinate data may be predicted or real.
Created in: beta12orEarlier
has exact synonym: Coordinate model
has related synonym: D015394
in subset: bioinformatics
in subset: data
in subset: edam

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

Database hits (structure)
type: Class
subclass of: Database hits
comment: This includes alignment and score data.
Created in: beta12orEarlier
has definition: Results (hits) from searching a database of tertiary structure.
in subset: bioinformatics
in subset: data
in subset: edam

Structure alignment
type: Class
subclass of: Structure
subclass of: Alignment
subclass of: Restriction
  on property: has topic
  some values from: Structure alignment
Created in: beta12orEarlier
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.
has definition: Alignment (superimposition) of molecular tertiary (3D) structures.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

Sequence-3D profile alignment
type: Class
subclass of: Sequence-structure alignment
Created in: beta12orEarlier
has definition: An alignment of a sequence to a 3D profile (representing structures or a structure alignment).
has exact synonym: Sequence-structural profile alignment
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Amino acid annotation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.4
deprecated: true
has definition: An informative report about a specific amino acid.
consider: Small molecule report
in subset: obsolete

Peptide annotation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: An informative report about a specific peptide.
deprecated: true
Obsolete since: 1.4
consider: Small molecule report
in subset: obsolete

Protein report
type: Class
subclass of: Molecule report
subclass of: Restriction
  on property: has topic
  some values from: Proteins
has exact synonym: Gene product annotation
Created in: beta12orEarlier
has definition: An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.
in subset: bioinformatics
in subset: data
in subset: edam

Protein property
type: Class
subclass of: Protein report
subclass of: Molecular property
comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.
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
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (3D motif)
type: Class
subclass of: Protein features
subclass of: Protein structure report
subclass of: Restriction
  on property: has topic
  some values from: Protein structural motifs and surfaces
Created in: beta12orEarlier
has exact synonym: Protein structure report (3D motif)
has definition: An informative report on the 3D structural motifs in a protein.
comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc.
in subset: bioinformatics
in subset: data
in subset: edam

Protein domain classification
type: Class
subclass of: Protein classification
subclass of: Restriction
  on property: has topic
  some values from: Protein domains and folds
Created in: beta12orEarlier
has definition: Data concerning the classification of the sequences and/or structures of protein structural domain(s).
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (domains)
type: Class
subclass of: Protein features
subclass of: Restriction
  on property: has topic
  some values from: Protein domains and folds
has exact synonym: Protein structural domains
comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.
Created in: beta12orEarlier
has exact synonym: Protein domain assignment
has definition: Summary of structural domains or 3D folds in a protein or polypeptide chain.
in subset: bioinformatics
in subset: data
in subset: edam

Protein architecture report
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has exact synonym: Protein structure report (architecture)
has exact synonym: Protein property (architecture)
has definition: An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.
Obsolete since: 1.4
consider: Protein structure report
in subset: obsolete

Protein folding report
type: Class
subclass of: Protein property
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.
has exact synonym: Protein property (folding)
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 stabilization centers etc.
has exact synonym: Protein report (folding)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (mutation)
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Protein report (mutation)
Obsolete since: beta13
has exact synonym: Protein structure report (mutation)
has exact synonym: Protein property (mutation)
Created in: beta12orEarlier
deprecated: true
has definition: Data on the effect of (typically point) mutation on protein folding, stability, structure and function.
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.
consider: Protein report
in subset: obsolete

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.
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.
in subset: bioinformatics
in subset: data
in subset: edam

Protein interaction
type: Class
subclass of: Protein report
subclass of: Molecular interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
has exact synonym: Protein report (interaction)
Created in: beta12orEarlier
has definition: An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand.
in subset: bioinformatics
in subset: data
in subset: edam

Protein family
type: Class
subclass of: Protein classification
subclass of: Restriction
  on property: has topic
  some values from: Protein families
has exact synonym: Protein family annotation
Created in: beta12orEarlier
has definition: An informative report on a specific protein family or other group of classified proteins.
in subset: bioinformatics
in subset: data
in subset: edam

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

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: bioinformatics
in subset: data
in subset: edam

Nucleotide base annotation
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.4
has definition: An informative report about a specific nucleotide base.
deprecated: true
Created in: beta12orEarlier
consider: Small molecule report
in subset: obsolete

Nucleic acid property
type: Class
subclass of: Nucleic acid report
subclass of: Molecular property
Created in: beta12orEarlier
has exact synonym: Nucleic acid physicochemical property
comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.
has definition: A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.
in subset: bioinformatics
in subset: data
in subset: edam

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

Gene annotation
type: Class
subclass of: Nucleic acid features
subclass of: Restriction
  on property: has topic
  some values from: Gene families
has exact synonym: Gene annotation (functional)
has db xref: Moby:GeneInfo
has db xref: Moby_namespace:Human_Readable_Description
Created in: beta12orEarlier
comment: 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).
has db xref: Moby:gene
has exact synonym: Gene report
has definition: An informative report on a particular locus, gene, gene system or groups of genes.
in subset: bioinformatics
in subset: data
in subset: edam

Gene classification
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.
deprecated: true
Created in: beta12orEarlier
consider: Gene annotation
in subset: obsolete

Nucleic acid features (variation)
type: Class
subclass of: Nucleic acid features (difference and change)
subclass of: Restriction
  on property: has topic
  some values from: Genetic variation
Created in: beta12orEarlier
has definition: A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.
has exact synonym: Sequence variation annotation
has related synonym: SO:0001059
in subset: bioinformatics
in subset: data
in subset: edam

Gene annotation (chromosome)
type: Class
subclass of: Gene annotation
subclass of: Restriction
  on property: has topic
  some values from: Chromosomes
comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
has definition: An informative report on a specific chromosome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Genotype/phenotype annotation
type: Class
subclass of: Report
Created in: beta12orEarlier
has definition: An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (primers)
type: Class
subclass of: Nucleic acid features (replication and recombination)
subclass of: Restriction
  on property: has topic
  some values from: Sequence design
Created in: beta12orEarlier
has definition: Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation (PCR assay data)
type: Class
subclass of: Experiment annotation
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
has exact synonym: PCR assay data
Created in: beta12orEarlier
has definition: Data on a PCR assay or electronic / virtual PCR.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence trace
type: Class
subclass of: Sequence record (nucleic acid)
subclass of: Experimental measurement
Created in: beta12orEarlier
comment: This is the raw data produced by a DNA sequencing machine.
has definition: Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence assembly
type: Class
subclass of: Sequence set (nucleic acid)
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.
has exact synonym: SO:0000353
has narrow synonym: SO:0001248
has definition: An assembly of fragments of a (typically genomic) DNA sequence.
Created in: beta12orEarlier
has exact synonym: Sequence assembly
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Gene annotation (linkage)
type: Class
subclass of: Gene annotation
has definition: An informative report on the linkage of alleles.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Experiment annotation (microarray)
type: Class
subclass of: Experiment annotation
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
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.
has exact synonym: Experimental design annotation
has definition: Information on a microarray experiment such as conditions, protocol, sample:data relationships etc.
in subset: bioinformatics
in subset: data
in subset: edam

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

SAGE experimental data
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: Serial analysis of gene expression (SAGE) experimental data
has definition: Output from a serial analysis of gene expression (SAGE) experiment.
deprecated: true
Obsolete since: beta12orEarlier
consider: Sequence tag profile
in subset: obsolete

MPSS experimental data
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has exact synonym: Massively parallel signature sequencing (MPSS) experimental data
Obsolete since: beta12orEarlier
has definition: Massively parallel signature sequencing (MPSS) data.
Created in: beta12orEarlier
consider: Sequence tag profile
in subset: obsolete

SBS experimental data
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Sequencing by synthesis (SBS) experimental data
has definition: Sequencing by synthesis (SBS) data.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Sequence tag profile
in subset: obsolete

Sequence tag profile (with gene assignment)
type: Class
subclass of: Sequence tag profile
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein X-ray crystallographic data
type: Class
subclass of: Protein structure raw data
Created in: beta12orEarlier
has definition: X-ray crystallography data.
in subset: bioinformatics
in subset: data
in subset: edam

Protein NMR data
type: Class
subclass of: Protein structure raw data
Created in: beta12orEarlier
has definition: Protein nuclear magnetic resonance (NMR) raw data.
in subset: bioinformatics
in subset: data
in subset: edam

Protein circular dichroism (CD) spectroscopic data
type: Class
subclass of: Protein structure raw data
has definition: Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Electron microscopy model
type: Class
subclass of: Electron microscopy volume map
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
comment: This might include the location in the model of the known features of a particular macromolecule.
has definition: Annotation on a structural 3D model (volume map) from electron microscopy.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

2D PAGE image
type: Class
subclass of: Image
subclass of: Experimental measurement
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
has definition: Two-dimensional gel electrophoresis image.
Created in: beta12orEarlier
has exact synonym: Two-dimensional gel electrophoresis image
in subset: bioinformatics
in subset: data
in subset: edam

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

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: Protein fingerprint
has exact synonym: Peak list
in subset: bioinformatics
in subset: data
in subset: edam

Peptide identification
type: Class
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, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Data resource definition
type: Class
subclass of: 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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Biological model
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Computational biology
Created in: beta12orEarlier
has definition: A biological model which can be represented in mathematical terms.
in subset: bioinformatics
in subset: data
in subset: edam

Statistical estimate score
type: Class
subclass of: Score or penalty
subclass of: Sequence features metadata
has definition: A value representing estimated statistical significance of some observed data; typically sequence database hits.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

EMBOSS database resource definition
type: Class
subclass of: Database metadata
Created in: beta12orEarlier
has definition: Resource definition for an EMBOSS database.
in subset: bioinformatics
in subset: data
in subset: edam

Version information
type: Class
subclass of: Metadata
Created in: beta12orEarlier
has definition: Information on a version of software or data, for example name, version number and release date.
comment: Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
has narrow synonym: IAO_0000129
in subset: bioinformatics
in subset: data
in subset: edam
has narrow synonym: SIO_000653
has exact synonym: Version
has narrow synonym: SWO_9000061

Axiom
comment: Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
annotated source: Version information
annotated target: SWO_9000061
annotated property: hasNarrowSynonym

Database cross-mapping
type: Class
subclass of: Data reference
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.
has definition: A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Data index
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Data processing and validation
Created in: beta12orEarlier
has definition: An index of data of biological relevance.
in subset: bioinformatics
in subset: data
in subset: edam

Data index report
type: Class
subclass of: Report
subclass of: Restriction
  on property: has topic
  some values from: Data processing and validation
Created in: beta12orEarlier
has exact synonym: Database index annotation
has definition: A report of an analysis of an index of biological data.
in subset: bioinformatics
in subset: data
in subset: edam

Database metadata
type: Class
subclass of: System 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: bioinformatics
in subset: data
in subset: edam

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

Job metadata
type: Class
subclass of: System metadata
has definition: Textual metadata on a submitted or completed job.
has db xref: Moby:PDGJOB
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Small molecule report
type: Class
subclass of: Structure report
subclass of: Molecule report
subclass of: Restriction
  on property: has topic
  some values from: Small molecules
has definition: An informative report on a specific chemical compound.
has exact synonym: Small molecule report
has exact synonym: Chemical compound annotation
Created in: beta12orEarlier
has exact synonym: Small molecule annotation
in subset: bioinformatics
in subset: data
in subset: edam

Cell line report
type: Class
subclass of: Organism report
Created in: beta12orEarlier
has definition: Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.
has exact synonym: Cell line annotation
has exact synonym: Organism strain data
in subset: bioinformatics
in subset: data
in subset: edam

Scent annotation
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.4
has definition: An informative report about a specific scent.
Created in: beta12orEarlier
consider: Small molecule report
in subset: obsolete

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

Ontology concept metadata
type: Class
subclass of: Metadata
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
has definition: Data concerning or derived from a concept from a biological ontology.
has exact synonym: Ontology term metadata
Created in: beta12orEarlier
has exact synonym: Ontology class metadata
in subset: bioinformatics
in subset: data
in subset: edam

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

Citation
type: Class
subclass of: Data reference
subclass of: Article metadata
Created in: beta12orEarlier
has db xref: Moby:Publication
has exact synonym: Bibliographic reference
has exact synonym: Reference
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.
has definition: Bibliographic data that uniquely identifies a scientific article, book or other published material.
has db xref: Moby:GCP_SimpleCitation
in subset: bioinformatics
in subset: data
in subset: edam

Article
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Literature and reference
has definition: A body of scientific text, typically a full text article from a scientific journal.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Text mining report
type: Class
subclass of: Article report
comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.
Created in: beta12orEarlier
has definition: An abstract of the results of text mining.
in subset: bioinformatics
in subset: data
in subset: edam

Entity identifier
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An identifier of a biological entity or phenomenon.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: Identifier
in subset: obsolete

Data resource identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: An identifier of a data resource.
deprecated: true
consider: Identifier
in subset: obsolete

Identifier (typed)
type: Class
subclass of: Identifier
has definition: An identifier that identifies a particular type of data.
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'.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

Entity feature identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
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).
Created in: beta12orEarlier
deprecated: true
consider: Identifier
in subset: obsolete

Entity collection identifier
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name or other identifier of a collection of discrete biological entities.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: Identifier
in subset: obsolete

Phenomenon identifier
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name or other identifier of a physical, observable biological occurrence or event.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Identifier
in subset: obsolete

Molecule identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Molecule report
Created in: beta12orEarlier
has definition: Name or other identifier of a molecule.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Atom ID
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: Identifier (e.g. character symbol) of a specific atom.
has exact synonym: Atom identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Molecule type
type: Class
subclass of: Type
Example: Protein|DNA|RNA
Created in: beta12orEarlier
has definition: A label (text token) describing the type a molecule.
comment: For example, 'Protein', 'DNA', 'RNA' etc.
in subset: bioinformatics
in subset: data
in subset: edam

Chemical identifier
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Unique identifier of a chemical compound.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Compound identifier
in subset: obsolete

Chromosome name
type: Class
subclass of: Molecule name
subclass of: Nucleic acid identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Gene annotation (chromosome)
has definition: Name of a chromosome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

Ligand identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Code word for a ligand, for example from a PDB file.
Created in: beta12orEarlier
deprecated: true
consider: Compound identifier
in subset: obsolete

Drug identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Drug structure
has definition: Identifier of a drug.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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
has exact synonym: Residue identifier
Created in: beta12orEarlier
has definition: Identifier of an amino acid.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

Chemical name (ChEBI)
type: Class
subclass of: Compound name
comment: This is the recommended chemical name for use for example in database annotation.
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

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

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

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

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

Nucleotide code
type: Class
subclass of: Compound name
subclass of: Nucleotide identifier
has definition: String of one or more ASCII characters representing a nucleotide.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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
has exact synonym: Polypeptide chain identifier
comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
has exact synonym: PDB chain identifier
has exact synonym: Protein chain identifier
has exact synonym: PDB strand id
has db xref: PDBML:pdbx_PDB_strand_id
has definition: Identifier of a polypeptide chain from a protein.
has exact synonym: Chain identifier
has db xref: WHATIF: chain
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Enzyme identifier
type: Class
subclass of: Protein identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Enzyme property
has definition: Name or other identifier of an enzyme or record from a database of enzymes.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Restriction enzyme name
type: Class
subclass of: Enzyme name
subclass of: Restriction
  on property: is identifier of
  some values from: Restriction enzyme property
Created in: beta12orEarlier
has definition: Name of a restriction enzyme.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence position specification
type: Class
subclass of: Sequence parameter
Created in: beta12orEarlier
has definition: A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence feature ID
type: Class
subclass of: Accession
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Sequence range
type: Class
subclass of: Sequence position specification
has definition: Specification of range(s) of sequence positions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid feature identifier
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Name or other identifier of an nucleic acid feature.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Sequence feature ID
in subset: obsolete

Protein feature identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: Name or other identifier of a protein feature.
consider: Sequence feature ID
in subset: obsolete

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

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

Sequence feature label
type: Class
subclass of: Sequence features metadata
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.
Created in: beta12orEarlier
has definition: Typically an EMBL or Swiss-Prot feature label.
has exact synonym: Sequence feature name
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

Gene symbol
type: Class
subclass of: Gene name
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.
has db xref: Moby_namespace:Global_GeneCommonName
Created in: beta12orEarlier
has db xref: Moby_namespace:Global_GeneSymbol
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

Gene identifier (Entrez)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Regular expression: [0-9]+
Created in: beta12orEarlier
deprecated: true
has definition: An Entrez unique identifier of a gene.
consider: Gene ID (NCBI)
in subset: obsolete

Gene ID (CGD)
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

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

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

SCOP domain identifier
type: Class
subclass of: Protein domain ID
subclass of: Restriction
  on property: is identifier of
  some values from: SCOP node
Created in: beta12orEarlier
has definition: Identifier of a protein domain (or other node) from the SCOP database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

SCOP sunid
type: Class
subclass of: SCOP domain identifier
Example: 33229
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.
has exact synonym: SCOP unique identifier
has exact synonym: sunid
has definition: Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

URI
type: Class
subclass of: Identifier
Created in: beta12orEarlier
has definition: A string of characters that name or otherwise identify a resource on the Internet.
in subset: bioinformatics
in subset: data
in subset: edam

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

Directory name
type: Class
subclass of: Name
has definition: The name of a directory.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
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
has definition: Name of an ontology of biological or bioinformatics concepts and relations.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence database name
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
has definition: The name of a molecular sequence database.
consider: Database name
in subset: bioinformatics
in subset: obsolete

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

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

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

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
has definition: Name of a QSAR descriptor.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Database entry identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
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.
Created in: beta12orEarlier
comment: This concept is required for completeness. It should never have child concepts.
deprecated: true
consider: Identifier
in subset: obsolete

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

Sequence set ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence set
Created in: beta12orEarlier
has definition: An identifier of a set of molecular sequence(s).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

Phylogenetic distance matrix identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Identifier of a phylogenetic distance matrix.
Created in: beta12orEarlier
consider: Identifier (typed)
in subset: obsolete

Phylogenetic tree ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Phylogenetic tree
has definition: Identifier of a phylogenetic tree for example from a phylogenetic tree database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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
has definition: An identifier of a comparison matrix.
has exact synonym: Substitution matrix identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Structural (3D) profile ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Structural (3D) profile
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Structure alignment ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Structure alignment
has definition: Identifier of an entry from a database of tertiary structure alignments.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Amino acid index ID
type: Class
subclass of: Accession
subclass of: Matrix identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Amino acid index
Created in: beta12orEarlier
has definition: Identifier of an index of amino acid physicochemical and biochemical property data.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein interaction ID
type: Class
subclass of: Molecular interaction ID
has definition: Identifier of a report of protein interactions from a protein interaction database (typically).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein family identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Protein family
Created in: beta12orEarlier
has definition: Identifier of a protein family.
has exact synonym: Protein secondary database record identifier
in subset: bioinformatics
in subset: data
in subset: edam
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: Genetic code
subclass of: Restriction
  on property: is identifier of
  some values from: Codon usage table
has definition: Unique name of a codon usage table.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Transcription factor identifier
type: Class
subclass of: Identifier (typed)
subclass of: Protein identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Gene features (TFBS)
Created in: beta12orEarlier
has definition: Identifier of a transcription factor (or a TF binding site).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Microarray experiment annotation ID
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Experiment annotation (microarray)
has definition: Identifier of an entry from a database of microarray data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Electron microscopy model ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Electron microscopy model
Created in: beta12orEarlier
has definition: Identifier of an entry from a database of electron microscopy data.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Genotype and phenotype annotation ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Genotype/phenotype annotation
Created in: beta12orEarlier
has definition: Identifier of an entry from a database of genotypes and phenotypes.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Workflow ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Workflow
has definition: Identifier of a biological or biomedical workflow, typically from a database of workflows.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Data resource definition ID
type: Class
subclass of: Identifier (typed)
has exact synonym: Data resource definition identifier
has definition: Identifier of a data type definition from some provider.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Biological model ID
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Biological model
Created in: beta12orEarlier
has definition: Identifier of a mathematical model, typically an entry from a database.
has exact synonym: Biological model identifier
in subset: bioinformatics
in subset: data
in subset: edam
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
has exact synonym: Small molecule identifier
has definition: Identifier of an entry from a database of chemicals.
has exact synonym: Chemical compound identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ontology concept ID
type: Class
subclass of: Accession
subclass of: Ontology concept identifier
has exact synonym: Ontology concept ID
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Article ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Article
has definition: Unique identifier of a scientific article.
Created in: beta12orEarlier
has exact synonym: Article identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

Sequence type
type: Class
subclass of: Type
subclass of: Sequence parameter
Created in: beta12orEarlier
has definition: A label (text token) describing a type of molecular sequence.
comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
in subset: bioinformatics
in subset: data
in subset: edam

EMBOSS Uniform Sequence Address
type: Class
subclass of: Sequence identifier
subclass of: Name
has definition: The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.
Created in: beta12orEarlier
has exact synonym: EMBOSS USA
in subset: bioinformatics
in subset: data
in subset: edam
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
has exact synonym: Protein sequence accession number
has definition: Accession number of a protein sequence database entry.
in subset: bioinformatics
in subset: data
in subset: edam
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
has exact synonym: Nucleotide sequence accession number
Created in: beta12orEarlier
has definition: Accession number of a nucleotide sequence database entry.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

UniProt accession (extended)
type: Class
subclass of: Obsolete concept (EDAM)
Example: Q7M1G0|P43353-2|P01012.107
Obsolete since: 1.0
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]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+
has definition: Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.
deprecated: true
consider: UniProt accession
in subset: obsolete

PIR identifier
type: Class
subclass of: Sequence accession (protein)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
has exact synonym: PIR ID
Created in: beta12orEarlier
has definition: An identifier of PIR sequence database entry.
has exact synonym: PIR accession number
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TREMBL accession
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.2
deprecated: true
has definition: Identifier of a TREMBL sequence database entry.
Created in: beta12orEarlier
replaced by: UniProt accession
in subset: obsolete

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

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

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

dbEST accession
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

EMBOSS listfile
type: Class
subclass of: ID list
Created in: beta12orEarlier
has definition: List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).
in subset: bioinformatics
in subset: data
in subset: edam

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
has definition: An identifier of a cluster of molecular sequence(s).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

Sequence profile ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence profile
comment: A sequence profile typically represents a sequence alignment.
has definition: Identifier of a sequence profile.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

HMMER hidden Markov model ID
type: Class
subclass of: Sequence profile ID
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Sequence alignment type
type: Class
subclass of: Sequence alignment parameter
subclass of: Type
has definition: A label (text token) describing the type of a sequence alignment.
comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

BLAST sequence alignment type
type: Class
subclass of: Obsolete concept (EDAM)
has definition: The type of a BLAST sequence alignment.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Sequence alignment type
in subset: obsolete

Phylogenetic tree type
type: Class
subclass of: Type
Example: nj|upgmp
has definition: A label (text token) describing the type of a phylogenetic tree.
Created in: beta12orEarlier
comment: For example 'nj', 'upgmp' etc.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Comparison matrix type
type: Class
subclass of: Sequence alignment parameter
subclass of: Type
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.
has exact synonym: Substitution matrix type
has definition: A label (text token) describing the type of a comparison matrix.
Created in: beta12orEarlier
Example: blosum|pam|gonnet|id
in subset: bioinformatics
in subset: data
in subset: edam

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
has definition: Unique name or identifier of a comparison matrix.
has exact synonym: Substitution matrix name
comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

PDB ID
type: Class
subclass of: Structure ID
Regular expression: [a-zA-Z_0-9]{4}
Created in: beta12orEarlier
has exact synonym: PDB identifier
has exact synonym: PDBID
has definition: An identifier of an entry from the PDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

Protein family name
type: Class
subclass of: Protein family identifier
subclass of: Name
has definition: Name of a protein family.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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
has definition: Name of an InterPro entry, usually indicating the type of protein matches for that entry.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

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

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

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

TIGRFam ID
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

GEO accession number
type: Class
subclass of: Gene expression report ID
Created in: beta12orEarlier
Regular expression: o^GDS[0-9]+
has definition: Accession number of an entry from the GEO database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

Disease ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
Created in: beta12orEarlier
has definition: Identifier of an entry from a database of disease.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

HIVDB identifier
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Identifier of an entry from the HIVDB database.
Created in: beta12orEarlier
deprecated: true
consider: Identifier
in subset: obsolete

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

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

Pathway ID (reactome)
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

Pathway ID (CPDB)
type: Class
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
comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

MIRIAM URI
type: Class
subclass of: URI
subclass of: Data resource definition accession
subclass of: Restriction
  on property: is identifier of
  some values from: MIRIAM datatype
Example: urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202
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.
has exact synonym: identifiers.org synonym
has definition: The URI (URL or URN) of a data entity from the MIRIAM database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Axiom
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'.
annotated source: MIRIAM data type primary name
annotated property: Example

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

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

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

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

PubChem CID
type: Class
subclass of: PubChem ID
subclass of: Compound accession
Created in: beta12orEarlier
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
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

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

NCBI taxonomy ID
type: Class
subclass of: Ontology concept ID
subclass of: Organism accession
Created in: beta12orEarlier
Example: 9662|3483|182682
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
Regular expression: [1-9][0-9]{0,8}
has exact synonym: NCBI taxonomy identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

FMA concept ID
type: Class
subclass of: Ontology concept ID
Created in: beta12orEarlier
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.
has definition: An identifier of a concept from Foundational Model of Anatomy.
Regular expression: FMA:[0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

myGrid concept ID
type: Class
subclass of: Ontology concept ID
has definition: An identifier of a concept from the myGrid ontology.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Tool name (signature)
type: Class
subclass of: Tool name
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.
has definition: The unique name of a signature (sequence classifier) method.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

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

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

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

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

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: bioinformatics
in subset: data
in subset: edam

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

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

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: bioinformatics
in subset: data
in subset: edam

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

Sequence cluster
type: Class
subclass of: Sequence set
subclass of: Restriction
  on property: has topic
  some values from: Protein families
subclass of: Restriction
  on property: has topic
  some values from: Sequence clustering
Created in: beta12orEarlier
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
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: bioinformatics
in subset: data
in subset: edam

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

HMMER synthetic sequences set
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Sequences generated by HMMER package in FASTA-style format.
consider: Sequence set
in subset: obsolete

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

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: bioinformatics
in subset: data
in subset: edam

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

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

Primer3 internal oligo mishybridizing library
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.
Created in: beta12orEarlier
deprecated: true
consider: Sequence set
in subset: obsolete

Primer3 mispriming library file
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
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.
deprecated: true
consider: Sequence set
in subset: obsolete

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

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

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

Sequence length
type: Class
subclass of: Sequence length specification
Created in: beta12orEarlier
has definition: The size (length) of a sequence, subsequence or region in a sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Word size
type: Class
subclass of: Sequence length
Created in: beta12orEarlier
has definition: Size of a sequence word.
has exact synonym: Word length
comment: Word size is used for example in word-based sequence database search methods.
in subset: bioinformatics
in subset: data
in subset: edam

Window size
type: Class
subclass of: Sequence length
has definition: Size of a sequence window.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence length range
type: Class
subclass of: Sequence length specification
has definition: Specification of range(s) of length of sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence information report
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.
consider: Sequence metadata
consider: Sequence record lite
in subset: obsolete

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

Feature record
type: Class
subclass of: Sequence report
has exact synonym: Sequence features
has exact synonym: Features
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: General sequence features
comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.
has related synonym: SO:0000110
Created in: beta12orEarlier
has exact synonym: Sequence features report
has related synonym: D058977
in subset: bioinformatics
in subset: data
in subset: edam

Sequence features (comparative)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
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.
Obsolete since: beta13
has definition: Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.
consider: Feature record
in subset: obsolete

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

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

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

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

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

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: bioinformatics
in subset: data
in subset: edam

Sequence composition (base position variability)
type: Class
subclass of: Nucleic acid sequence composition
has definition: Report on or plot of third base position variability in a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence composition table
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: A table of character or word composition / frequency of a molecular sequence.
consider: Sequence composition
in subset: obsolete

Sequence composition (base frequencies)
type: Class
subclass of: Nucleic acid sequence composition
has definition: A table of base frequencies of a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence composition (base words)
type: Class
subclass of: Nucleic acid sequence composition
has definition: A table of word composition of a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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

DAS sequence feature annotation
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Annotation of a molecular sequence in DAS format.
Obsolete since: beta12orEarlier
consider: DASGFF
in subset: obsolete

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

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

Nucleic acid features
type: Class
subclass of: Feature record
subclass of: Nucleic acid report
has exact synonym: Feature table (nucleic acid)
has exact synonym: Nucleic acid feature table
has definition: Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence).
comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein features
type: Class
subclass of: Protein report
subclass of: Feature record
has exact synonym: Protein feature table
comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.
has exact synonym: Feature table (protein)
has definition: Protein sequence-specific feature annotation (positional features of a protein sequence).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Genetic map
type: Class
subclass of: Map
has db xref: Moby:GeneticMap
has exact synonym: Linkage map
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.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence map
type: Class
subclass of: Physical map
has definition: A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

Physical map
type: Class
subclass of: Map
Created in: beta12orEarlier
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.
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: bioinformatics
in subset: data
in subset: edam

Sequence signature map
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Image of a sequence with matches to signatures, motifs or profiles.
deprecated: true
consider: Sequence features (motifs)
in subset: obsolete

Cytogenetic map
type: Class
subclass of: Physical map
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.
has exact synonym: Cytogenic map
has exact synonym: Chromosome map
has exact synonym: Cytologic map
has definition: A map showing banding patterns derived from direct observation of a stained chromosome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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: bioinformatics
in subset: data
in subset: edam

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

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

Restriction map
type: Class
subclass of: Sequence map
subclass of: Nucleic acid features (restriction sites)
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: bioinformatics
in subset: data
in subset: edam

InterPro compact match image
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
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.
has definition: Image showing matches between protein sequence(s) and InterPro Entries.
Obsolete since: beta12orEarlier
consider: Sequence features (motifs)
in subset: obsolete

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

InterPro architecture image
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Image showing the architecture of InterPro domains in a protein sequence.
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
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Sequence features (motifs)
in subset: obsolete

SMART protein schematic
type: Class
subclass of: Obsolete concept (EDAM)
has definition: SMART protein schematic in PNG format.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Sequence features (motifs)
in subset: obsolete

GlobPlot domain image
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Sequence features (motifs)
in subset: obsolete

Sequence features (motifs)
type: Class
subclass of: Feature record
has definition: Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.
Created in: beta12orEarlier
comment: Use this concept if another, more specific concept is not available.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence features (repeats)
type: Class
subclass of: Feature record
has definition: Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
comment: The report might include derived data map such as classification, annotation, organization, periodicity etc.
has exact synonym: Repeat sequence map
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (gene and transcript structure)
type: Class
subclass of: Gene annotation
subclass of: Nucleic acid features
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.
Created in: beta12orEarlier
has exact synonym: Gene annotation (structure)
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (mobile genetic elements)
type: Class
subclass of: Nucleic acid features
Created in: beta12orEarlier
has definition: A report on a region of a nucleic acid sequence containin mobile genetic elements.
has exact synonym: Nucleic acid features (transposons)
comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (PolyA signal or site)
type: Class
subclass of: Nucleic acid features (mRNA features)
Created in: beta12orEarlier
has definition: A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.
comment: 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.
has exact synonym: PolyA site
has exact synonym: PolyA signal
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (quadruplexes)
type: Class
subclass of: Nucleic acid features (structure)
Created in: beta12orEarlier
has definition: A report on quadruplex-forming motifs in a nucleotide sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (CpG island and isochore)
type: Class
subclass of: Nucleic acid features (transcriptional)
has definition: A report or plot of CpG rich regions (isochores) in a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (restriction sites)
type: Class
subclass of: Nucleic acid features (binding)
has definition: Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (nucleosome exclusion sequences)
type: Class
subclass of: Nucleic acid features (replication and recombination)
has definition: A report on nucleosome formation potential or exclusion sequence(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (splice sites)
type: Class
subclass of: Nucleic acid features (mRNA features)
has exact synonym: Nucleic acid report (RNA splicing)
has exact synonym: Nucleic acid report (RNA splice model)
Created in: beta12orEarlier
has definition: A report on splice sites in a nucleotide sequence or alternative RNA splicing events.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (matrix/scaffold attachment sites)
type: Class
subclass of: Nucleic acid features (transcriptional)
Created in: beta12orEarlier
has definition: A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Gene features (exonic splicing enhancer)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A report on exonic splicing enhancers (ESE) in an exon.
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
consider: Nucleic acid features (exon)
in subset: obsolete

Nucleic acid features (microRNA)
type: Class
subclass of: Nucleic acid features (non-coding RNA)
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
has definition: A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (operon)
type: Class
subclass of: Nucleic acid features (gene and transcript structure)
Created in: beta12orEarlier
has definition: A report on operons (operators, promoters and genes) from a bacterial genome.
comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.
has exact synonym: Gene features (operon)
in subset: bioinformatics
in subset: data
in subset: edam

Gene features (promoter)
type: Class
subclass of: Nucleic acid features (transcriptional)
Created in: beta12orEarlier
has definition: A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (coding sequence)
type: Class
subclass of: Nucleic acid features (mRNA features)
has exact synonym: Gene features (coding sequence)
has exact synonym: Gene annotation (translation)
Created in: beta12orEarlier
has exact synonym: Gene features (coding region)
has definition: A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.
in subset: bioinformatics
in subset: data
in subset: edam

Gene features (SECIS element)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
has definition: A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.
Created in: beta12orEarlier
consider: Nucleic acid features (gene and transcript structure)
in subset: obsolete

Gene features (TFBS)
type: Class
subclass of: Gene features (promoter)
subclass of: Nucleic acid features (binding)
subclass of: Restriction
  on property: has topic
  some values from: Transcription factors and regulatory sites
has definition: A report on the transcription factor binding sites (TFBS) in a DNA sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Protein features (signal peptides)
type: Class
subclass of: Protein features
Created in: beta12orEarlier
has definition: A report on the location of signal peptides or signal peptide cleavage sites in protein sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (cleavage sites)
type: Class
subclass of: Protein features
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
Created in: beta12orEarlier
has definition: A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (post-translation modifications)
type: Class
subclass of: Protein features
has exact synonym: Post-translation modification
Created in: beta12orEarlier
has definition: A report on post-translation modifications in a protein sequence, typically describing the specific sites involved.
has exact synonym: Protein features (post-translation modification sites)
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (active sites)
type: Class
subclass of: Protein features
Created in: beta12orEarlier
has exact synonym: Enzyme active site
has definition: A report on catalytic residues (active site) of an enzyme.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (binding sites)
type: Class
subclass of: Protein features
has definition: A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Protein features (nucleic acid binding sites)
type: Class
subclass of: Protein features
Created in: beta12orEarlier
has definition: A report on RNA and DNA-binding proteins and binding sites in protein sequences.
in subset: bioinformatics
in subset: data
in subset: edam

MHC Class I epitopes report
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: A report on epitopes that bind to MHC class I molecules.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Protein features (binding sites)
in subset: obsolete

MHC Class II epitopes report
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A report on predicted epitopes that bind to MHC class II molecules.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Protein features (binding sites)
in subset: obsolete

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

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

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

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

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

MEME background frequencies file
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: MEME background frequencies file.
consider: Biological model
in subset: obsolete

MEME motifs directive file
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: File of directives for ordering and spacing of MEME motifs.
deprecated: true
Obsolete since: beta12orEarlier
consider: Biological model
in subset: obsolete

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

HMM emission and transition counts
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.4
deprecated: true
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.
consider: Transition matrix
consider: Emission matrix
in subset: obsolete

Regular expression
type: Class
subclass of: Parameter
Created in: beta12orEarlier
has definition: Regular expression pattern.
in subset: bioinformatics
in subset: data
in subset: edam

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

Sequence profile
type: Class
subclass of: Core 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: bioinformatics
in subset: data
in subset: edam
has exact synonym: SIO_010531

Protein signature
type: Class
subclass of: Protein family
Created in: beta12orEarlier
has exact synonym: InterPro entry
has definition: An entry (sequence classifier and associated data) from the InterPro database.
in subset: bioinformatics
in subset: data
in subset: edam

Prosite nucleotide pattern
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: A nucleotide regular expression pattern from the Prosite database.
Created in: beta12orEarlier
consider: Sequence motif
in subset: obsolete

Prosite protein pattern
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: A protein regular expression pattern from the Prosite database.
consider: Sequence motif
in subset: obsolete

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

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

Information content matrix
type: Class
subclass of: Position-specific scoring matrix
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
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Hidden Markov model
type: Class
subclass of: Sequence profile
has definition: A hidden Markov model representation of a set or alignment of sequences.
Created in: beta12orEarlier
has exact synonym: HMM
in subset: bioinformatics
in subset: data
in subset: edam

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

Domainatrix signature
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: A protein signature of the type used in the EMBASSY Signature package.
consider: Sequence profile
in subset: obsolete

HMMER NULL hidden Markov model
type: Class
subclass of: Obsolete concept (EDAM)
has definition: NULL hidden Markov model representation used by the HMMER package.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Hidden Markov model
in subset: obsolete

Protein family signature
type: Class
subclass of: Protein signature
has definition: A protein family signature (sequence classifier) from the InterPro database.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

Protein domain signature
type: Class
subclass of: Protein signature
comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries.
has definition: A protein domain signature (sequence classifier) from the InterPro database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein region signature
type: Class
subclass of: Protein signature
comment: A protein region signature defines a region which cannot be described as a protein family or domain signature.
Created in: beta12orEarlier
has definition: A protein region signature (sequence classifier) from the InterPro database.
in subset: bioinformatics
in subset: data
in subset: edam

Protein repeat signature
type: Class
subclass of: Protein signature
has definition: A protein repeat signature (sequence classifier) from the InterPro database.
Created in: beta12orEarlier
comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
in subset: bioinformatics
in subset: data
in subset: edam

Protein site signature
type: Class
subclass of: Protein signature
has definition: A protein site signature (sequence classifier) from the InterPro database.
Created in: beta12orEarlier
comment: A protein site signature is a classifier for a specific site in a protein.
in subset: bioinformatics
in subset: data
in subset: edam

Protein conserved site signature
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: A protein conserved site signature (sequence classifier) from the InterPro database.
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
Obsolete since: 1.4
consider: Protein site signature
in subset: obsolete

Protein active site signature
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.4
deprecated: true
has definition: A protein active site signature (sequence classifier) from the InterPro database.
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.
consider: Protein site signature
in subset: obsolete

Protein binding site signature
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
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
has definition: A protein binding site signature (sequence classifier) from the InterPro database.
Obsolete since: 1.4
consider: Protein site signature
in subset: obsolete

Protein post-translational modification signature
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.4
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.
has definition: A protein post-translational modification signature (sequence classifier) from the InterPro database.
consider: Protein site signature
in subset: obsolete

Sequence alignment (pair)
type: Class
subclass of: Sequence alignment
has definition: Alignment of exactly two molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: SIO_010068

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

Sequence alignment (nucleic acid)
type: Class
subclass of: Sequence alignment
subclass of: Nucleic acid report
has definition: Alignment of multiple nucleotide sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence alignment (protein)
type: Class
subclass of: Sequence alignment
subclass of: Protein alignment
Created in: beta12orEarlier
has definition: Alignment of multiple protein sequences.
in subset: bioinformatics
in subset: data
in subset: edam

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

Sequence alignment (nucleic acid pair)
type: Class
subclass of: Sequence alignment (pair)
subclass of: Sequence alignment (nucleic acid)
has definition: Alignment of exactly two nucleotide sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence alignment (protein pair)
type: Class
subclass of: Sequence alignment (pair)
subclass of: Sequence alignment (protein)
Created in: beta12orEarlier
has definition: Alignment of exactly two protein sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Hybrid sequence alignment (pair)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Alignment of exactly two molecular sequences of different types.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Sequence alignment (hybrid)
in subset: obsolete

Multiple nucleotide sequence alignment
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Alignment of more than two nucleotide sequences.
Obsolete since: beta12orEarlier
consider: Sequence alignment
in subset: obsolete

Multiple protein sequence alignment
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Alignment of more than two protein sequences.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Sequence alignment
in subset: obsolete

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

Score end gaps control
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Whether end gaps are scored or not.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Parameter
in subset: obsolete

Aligned sequence order
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Controls the order of sequences in an output sequence alignment.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Results sort order
in subset: obsolete

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: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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

Terminal gap penalty
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
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.
Created in: beta12orEarlier
consider: Terminal gap opening penalty
consider: Terminal gap extension penalty
in subset: obsolete

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

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

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: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

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

Terminal gap opening penalty
type: Class
subclass of: Gap opening penalty
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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

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

Sequence alignment report (site conservation)
type: Class
subclass of: Obsolete concept (EDAM)
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
has definition: Data on character conservation in a molecular sequence alignment.
Obsolete since: 1.4
Created in: beta12orEarlier
consider: Sequence similarity report
in subset: obsolete

Sequence alignment report (site correlation)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
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.
Created in: beta12orEarlier
Obsolete since: 1.4
consider: Sequence alignment report
in subset: obsolete

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

Sequence-profile alignment (HMM)
type: Class
subclass of: Sequence-profile alignment
has definition: Alignment of molecular sequence(s) to a hidden Markov model(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence-profile alignment (fingerprint)
type: Class
subclass of: Sequence-profile alignment
Created in: beta12orEarlier
has definition: Alignment of molecular sequences to a protein fingerprint from the PRINTS database.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

Phylogenetic tree report
type: Class
subclass of: Report
has definition: A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.
Created in: beta12orEarlier
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.
has exact synonym: Phylogenetic tree-derived report
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

Phylogenetic character contrasts
type: Class
subclass of: Phylogenetic raw 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: bioinformatics
in subset: data
in subset: edam

Comparison matrix (integers)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Matrix of integer numbers for sequence comparison.
has exact synonym: Substitution matrix (integers)
Obsolete since: beta12orEarlier
consider: Comparison matrix
in subset: obsolete

Comparison matrix (floats)
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Substitution matrix (floats)
has definition: Matrix of floating point numbers for sequence comparison.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Comparison matrix
in subset: obsolete

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

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

Nucleotide comparison matrix (integers)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Matrix of integer numbers for nucleotide comparison.
Created in: beta12orEarlier
has exact synonym: Nucleotide substitution matrix (integers)
consider: Comparison matrix (nucleotide)
in subset: obsolete

Nucleotide comparison matrix (floats)
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Nucleotide substitution matrix (floats)
has definition: Matrix of floating point numbers for nucleotide comparison.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: Comparison matrix (nucleotide)
in subset: obsolete

Amino acid comparison matrix (integers)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has exact synonym: Amino acid substitution matrix (integers)
has definition: Matrix of integer numbers for amino acid comparison.
Created in: beta12orEarlier
consider: Comparison matrix (amino acid)
in subset: obsolete

Amino acid comparison matrix (floats)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Matrix of floating point numbers for amino acid comparison.
deprecated: true
Created in: beta12orEarlier
has exact synonym: Amino acid substitution matrix (floats)
Obsolete since: beta12orEarlier
consider: Comparison matrix (amino acid)
in subset: obsolete

Protein features (membrane regions)
type: Class
subclass of: Protein features
has definition: An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.
comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.
Created in: beta12orEarlier
has exact synonym: Intramembrane region report
has exact synonym: Transmembrane region report
has exact synonym: Protein report (membrane protein)
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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

Protein-ligand complex
type: Class
subclass of: Protein structure
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.
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: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

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

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

Protein structure (all atoms)
type: Class
subclass of: Protein structure
has definition: 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

Structure alignment (pair)
type: Class
subclass of: Structure alignment
Created in: beta12orEarlier
has definition: Alignment (superimposition) of exactly two molecular tertiary (3D) structures.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Structure alignment (nucleic acid)
type: Class
subclass of: Structure alignment
subclass of: Nucleic acid report
has definition: Alignment (superimposition) of nucleic acid tertiary (3D) structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Structure alignment (protein pair)
type: Class
subclass of: Structure alignment (pair)
subclass of: Structure alignment (protein)
has definition: Alignment (superimposition) of exactly two protein tertiary (3D) structures.
Created in: beta12orEarlier
has exact synonym: Pairwise protein structural alignment
in subset: bioinformatics
in subset: data
in subset: edam

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

Structure alignment (protein all atoms)
type: Class
subclass of: Structure alignment (protein)
Created in: beta12orEarlier
has definition: Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).
in subset: bioinformatics
in subset: data
in subset: edam

Structure alignment (protein C-alpha atoms)
type: Class
subclass of: Structure alignment (protein)
Created in: beta12orEarlier
has exact synonym: C-alpha trace
comment: C-beta atoms from amino acid side-chains may be considered.
has definition: Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

Structure alignment (nucleic acid pair)
type: Class
subclass of: Structure alignment (pair)
subclass of: Structure alignment (nucleic acid)
has definition: Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Structure alignment (RNA)
type: Class
subclass of: Structure alignment (nucleic acid)
Created in: beta12orEarlier
has definition: Alignment (superimposition) of RNA tertiary (3D) structures.
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

DaliLite hit table
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
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.
has definition: DaliLite hit table of protein chain tertiary structure alignment data.
consider: Structure alignment report
in subset: obsolete

Molecular similarity score
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: A score reflecting structural similarities of two molecules.
Created in: beta12orEarlier
consider: Structure similarity score
in subset: obsolete

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

Tanimoto similarity score
type: Class
subclass of: Structure similarity score
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.
has definition: A measure of the similarity between two ligand fingerprints.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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

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.
in subset: bioinformatics
in subset: data
in subset: edam

Amino acid pair-wise contact potentials
type: Class
subclass of: Amino acid property
Created in: beta12orEarlier
has definition: Statistical protein contact potentials.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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.
in subset: bioinformatics
in subset: data
in subset: edam

Enzyme property
type: Class
subclass of: Protein property
subclass of: Restriction
  on property: has topic
  some values from: Enzymes
has definition: An informative report on a specific enzyme.
has exact synonym: Enzyme report
Created in: beta12orEarlier
has exact synonym: Protein report (enzyme)
in subset: bioinformatics
in subset: data
in subset: edam

Restriction enzyme property
type: Class
subclass of: Enzyme property
has exact synonym: Restriction enzyme report
has exact synonym: Protein report (restriction enzyme)
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.
Created in: beta12orEarlier
has exact synonym: Restriction enzyme pattern data
has definition: An informative report on a specific restriction enzyme such as enzyme reference data.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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.
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
in subset: bioinformatics
in subset: data
in subset: edam

Protein charge plot
type: Class
subclass of: Protein property
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

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

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

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

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

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

Peptide immunogenicity data
type: Class
subclass of: Protein property
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.
has exact synonym: Peptide immunogenicity
Created in: beta12orEarlier
has exact synonym: Peptide immunogenicity report
has definition: An report on allergenicity / immunogenicity of peptides and proteins.
in subset: bioinformatics
in subset: data
in subset: edam

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

Protein structure report
type: Class
subclass of: Protein report
subclass of: Structure report
has exact synonym: Protein structure report (domain)
has exact synonym: Protein report (structure)
has definition: Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains.
Created in: beta12orEarlier
has exact synonym: Protein property (structural)
comment: This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).
has exact synonym: Protein structure-derived report
has exact synonym: Protein structural property
in subset: bioinformatics
in subset: data
in subset: edam

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

Protein residue interactions
type: Class
subclass of: Protein interaction
subclass of: Molecular interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
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.
has exact synonym: Atom interaction data
Created in: beta12orEarlier
has exact synonym: Residue interaction data
in subset: bioinformatics
in subset: data
in subset: edam

Protein flexibility or motion report
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Protein structure report (flexibility or motion)
Obsolete since: 1.4
deprecated: true
Created in: beta12orEarlier
has exact synonym: Protein flexibility or motion
has definition: Informative report on flexibility or motion of a protein structure.
has exact synonym: Protein property (flexibility or motion)
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.
consider: Protein structure report
in subset: obsolete

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

Protein surface report
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.
Obsolete since: 1.4
has exact synonym: Protein structure report (surface)
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.
consider: Protein structure report
in subset: obsolete

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

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: bioinformatics
in subset: data
in subset: edam

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

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

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

Protein hydrogen bonds
type: Class
subclass of: Protein residue interactions
Created in: beta12orEarlier
has definition: Patterns of hydrogen bonding in protein structures.
in subset: bioinformatics
in subset: data
in subset: edam

Protein non-canonical interactions
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.4
has definition: Non-canonical atomic interactions in protein structures.
deprecated: true
has exact synonym: Protein non-canonical interactions report
consider: Protein structure report
in subset: obsolete

CATH node
type: Class
subclass of: Protein domain classification node
has exact synonym: CATH classification node report
Created in: beta12orEarlier
has definition: Information on a node from the CATH database.
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.
in subset: bioinformatics
in subset: data
in subset: edam

SCOP node
type: Class
subclass of: Protein domain classification node
Created in: beta12orEarlier
has definition: Information on a node from the SCOP database.
has exact synonym: SCOP classification node
in subset: bioinformatics
in subset: data
in subset: edam

EMBASSY domain classification
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Protein domain classification
in subset: obsolete

CATH class
type: Class
subclass of: CATH node
has definition: Information on a protein 'class' node from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

CATH architecture
type: Class
subclass of: CATH node
has definition: Information on a protein 'architecture' node from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

CATH topology
type: Class
subclass of: CATH node
Created in: beta12orEarlier
has definition: Information on a protein 'topology' node from the CATH database.
in subset: bioinformatics
in subset: data
in subset: edam

CATH homologous superfamily
type: Class
subclass of: CATH node
has definition: Information on a protein 'homologous superfamily' node from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

CATH structurally similar group
type: Class
subclass of: CATH node
has definition: Information on a protein 'structurally similar group' node from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

CATH functional category
type: Class
subclass of: CATH node
Created in: beta12orEarlier
has definition: Information on a protein 'functional category' node from the CATH database.
in subset: bioinformatics
in subset: data
in subset: edam

Protein fold recognition report
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s).
Obsolete since: beta12orEarlier
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.
consider: Protein features (domains)
in subset: obsolete

Protein-protein interaction
type: Class
subclass of: Protein interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains).
has exact synonym: Protein structure report (protein complex)
Created in: beta12orEarlier
has definition: Data on protein-protein interaction(s).
in subset: bioinformatics
in subset: data
in subset: edam

Protein-ligand interaction
type: Class
subclass of: Protein interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Data on protein-ligand (small molecule) interaction(s).
in subset: bioinformatics
in subset: data
in subset: edam

Protein-nucleic acid interaction
type: Class
subclass of: Protein interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
has definition: Data on protein-DNA/RNA interaction(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid melting profile
type: Class
subclass of: Nucleic acid thermodynamic data
Created in: beta12orEarlier
has definition: Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.
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.
has exact synonym: Nucleic acid stability profile
in subset: bioinformatics
in subset: data
in subset: edam

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

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

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

Nucleic acid stitch profile
type: Class
subclass of: Nucleic acid melting profile
comment: 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.
has definition: Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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

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

Vienna RNA parameters
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: RNA parameters used by the Vienna package.
consider: Parameter
in subset: obsolete

Vienna RNA structure constraints
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Structure constraints used by the Vienna package.
deprecated: true
consider: Parameter
in subset: obsolete

Vienna RNA concentration data
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: RNA concentration data used by the Vienna package.
Obsolete since: beta12orEarlier
consider: Parameter
in subset: obsolete

Vienna RNA calculated energy
type: Class
subclass of: Obsolete concept (EDAM)
has definition: RNA calculated energy data generated by the Vienna package.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Nucleic acid enthalpy
in subset: obsolete

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

Nucleic acid folding report
type: Class
subclass of: Nucleic acid property
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.
has exact synonym: Nucleic acid report (folding model)
has definition: A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.
Created in: beta12orEarlier
has exact synonym: Nucleic acid report (folding)
in subset: bioinformatics
in subset: data
in subset: edam

Codon usage table
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
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.
has definition: Table of codon usage data calculated from one or more nucleic acid sequences.
in subset: bioinformatics
in subset: data
in subset: edam

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

Codon adaptation index
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has exact synonym: CAI
has definition: A simple measure of synonymous codon usage bias often used to predict gene expression levels.
deprecated: true
consider: Codon usage bias
in subset: obsolete

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

Nc statistic
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
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.
Created in: beta12orEarlier
deprecated: true
consider: Codon usage bias
in subset: obsolete

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

Pharmacogenomic annotation
type: Class
subclass of: Genotype/phenotype annotation
has definition: Data on the influence of genotype on drug response.
comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Disease report
type: Class
subclass of: Genotype/phenotype annotation
subclass of: Restriction
  on property: has topic
  some values from: Pathology
has exact synonym: Disease report
Created in: beta12orEarlier
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.
has definition: An informative report on a specific disease.
in subset: bioinformatics
in subset: data
in subset: edam

Gene annotation (linkage disequilibrium)
type: Class
subclass of: Gene annotation (linkage)
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam

Heat map
type: Class
subclass of: Microarray image
comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.
Created in: beta12orEarlier
has definition: A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.
in subset: bioinformatics
in subset: data
in subset: edam

Affymetrix probe sets library file
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has related synonym: CDF file
has definition: Affymetrix library file of information about which probes belong to which probe set.
deprecated: true
consider: Oligonucleotide probe sets annotation
in subset: obsolete

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

Molecular weights standard fingerprint
type: Class
subclass of: Peptide mass fingerprint
has definition: Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (metabolic)
type: Class
subclass of: Pathway or network
has definition: A report typically including a map (diagram) of a metabolic pathway.
Created in: beta12orEarlier
comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (genetic information processing)
type: Class
subclass of: Pathway or network
has definition: A report typically including a map (diagram) of a genetic information processing pathway.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (environmental information processing)
type: Class
subclass of: Pathway or network
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of an environmental information processing pathway.
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (signal transduction)
type: Class
subclass of: Pathway or network
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of a signal transduction pathway.
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (cellular process)
type: Class
subclass of: Pathway or network
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of a cellular process pathway.
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (disease)
type: Class
subclass of: Pathway or network
has definition: A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (drug structure relationship)
type: Class
subclass of: Pathway or network
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of drug structure relationships.
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (protein-protein interaction)
type: Class
subclass of: Pathway or network
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of a network of protein interactions.
in subset: bioinformatics
in subset: data
in subset: edam

MIRIAM datatype
type: Class
subclass of: Data resource definition
Created in: beta12orEarlier
has definition: An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.
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.
in subset: bioinformatics
in subset: data
in subset: edam

E-value
type: Class
subclass of: Statistical estimate score
has exact synonym: Expectation value
has definition: A simple floating point number defining the lower or upper limit of an expectation value (E-value).
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Database version information
type: Class
subclass of: Version information
subclass of: Database metadata
Created in: beta12orEarlier
has definition: Information on a database (or ontology) version, for example name, version number and release date.
has exact synonym: Ontology version information
in subset: bioinformatics
in subset: data
in subset: edam

Tool version information
type: Class
subclass of: Version information
subclass of: Tool metadata
Created in: beta12orEarlier
has definition: Information on an application version, for example name, version number and release date.
in subset: bioinformatics
in subset: data
in subset: edam

CATH version information
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Information on a version of the CATH database.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Database version information
in subset: obsolete

Swiss-Prot to PDB mapping
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: Cross-mapping of Swiss-Prot codes to PDB identifiers.
consider: Database cross-mapping
in subset: obsolete

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

Job status
type: Class
subclass of: Job metadata
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).
Created in: beta12orEarlier
has definition: Metadata on the status of a submitted job.
in subset: bioinformatics
in subset: data
in subset: edam

Job ID
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: The (typically numeric) unique identifier of a submitted job.
Obsolete since: 1.0
replaced by: Job identifier
in subset: obsolete

Job type
type: Class
subclass of: Type
has definition: A label (text token) describing the type of job, for example interactive or non-interactive.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Tool log
type: Class
subclass of: Job metadata
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam

DaliLite log file
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.
deprecated: true
Created in: beta12orEarlier
consider: Tool log
in subset: obsolete

STRIDE log file
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: STRIDE log file.
consider: Tool log
in subset: obsolete

NACCESS log file
type: Class
subclass of: Obsolete concept (EDAM)
has definition: NACCESS log file.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Tool log
in subset: obsolete

EMBOSS wordfinder log file
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: EMBOSS wordfinder log file.
consider: Tool log
in subset: obsolete

EMBOSS domainatrix log file
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: EMBOSS (EMBASSY) domainatrix application log file.
Created in: beta12orEarlier
consider: Tool log
in subset: obsolete

EMBOSS sites log file
type: Class
subclass of: Obsolete concept (EDAM)
has definition: EMBOSS (EMBASSY) sites application log file.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Tool log
in subset: obsolete

EMBOSS supermatcher error file
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: EMBOSS (EMBASSY) supermatcher error file.
consider: Tool log
in subset: obsolete

EMBOSS megamerger log file
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: EMBOSS megamerger log file.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Tool log
in subset: obsolete

EMBOSS whichdb log file
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: EMBOSS megamerger log file.
deprecated: true
Obsolete since: beta12orEarlier
consider: Tool log
in subset: obsolete

EMBOSS vectorstrip log file
type: Class
subclass of: Obsolete concept (EDAM)
has definition: EMBOSS vectorstrip log file.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Tool log
in subset: obsolete

Username
type: Class
subclass of: User ID
Created in: beta12orEarlier
has definition: A username on a computer system.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Password
type: Class
subclass of: User ID
has definition: A password on a computer system.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Email address
type: Class
subclass of: User ID
has db xref: Moby:EmailAddress
has definition: A valid email address of an end-user.
has db xref: Moby:Email
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Number of iterations
type: Class
subclass of: Search parameter
Created in: beta12orEarlier
has definition: Number of iterations of an algorithm.
in subset: bioinformatics
in subset: data
in subset: edam

Number of output entities
type: Class
subclass of: Search parameter
Created in: beta12orEarlier
has definition: Number of entities (for example database hits, sequences, alignments etc) to write to an output file.
in subset: bioinformatics
in subset: data
in subset: edam

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

Drug report
type: Class
subclass of: Small molecule report
subclass of: Restriction
  on property: has topic
  some values from: Drugs and target structures
has exact synonym: Drug annotation
Created in: beta12orEarlier
has definition: An informative report on a specific drug.
consider: Small molecule report
in subset: bioinformatics
in subset: data
in subset: edam

Phylogenetic tree image
type: Class
subclass of: Phylogenetic tree report
subclass of: Image
comment: See also 'Phylogenetic tree'
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: bioinformatics
in subset: data
in subset: edam

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

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

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

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

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

Fate map
type: Class
subclass of: Embryo report
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: bioinformatics
in subset: data
in subset: edam

Microarray spots image
type: Class
subclass of: Microarray image
subclass of: Experimental measurement
has definition: An image of spots from a microarray experiment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

BioPax
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: A term from the BioPax ontology.
Obsolete since: beta12orEarlier
consider: Ontology term
in subset: obsolete

GO
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: Moby:GOTerm
has db xref: Moby:GO_Term
Created in: beta12orEarlier
has definition: A term definition from The Gene Ontology (GO).
deprecated: true
has db xref: Moby:Annotated_GO_Term_With_Probability
has db xref: Moby:Annotated_GO_Term
has exact synonym: Gene Ontology term
Obsolete since: beta12orEarlier
consider: Ontology term
in subset: obsolete

MeSH
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: A term from the MeSH vocabulary.
deprecated: true
consider: Ontology term
in subset: obsolete

HGNC
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: A term from the HGNC controlled vocabulary.
deprecated: true
Created in: beta12orEarlier
consider: Ontology term
in subset: obsolete

NCBI taxonomy vocabulary
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A term from the NCBI taxonomy vocabulary.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Ontology term
in subset: obsolete

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

UMLS
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: A term from the UMLS vocabulary.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Ontology term
in subset: obsolete

FMA
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: A term from Foundational Model of Anatomy.
Created in: beta12orEarlier
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.
Obsolete since: beta12orEarlier
consider: Ontology term
in subset: obsolete

EMAP
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: A term from the EMAP mouse ontology.
consider: Ontology term
in subset: obsolete

ChEBI
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: A term from the ChEBI ontology.
consider: Ontology term
in subset: obsolete

MGED
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A term from the MGED ontology.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: Ontology term
in subset: obsolete

myGrid
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: A term from the myGrid ontology.
deprecated: true
Obsolete since: beta12orEarlier
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.
consider: Ontology term
in subset: obsolete

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

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

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

Ontology relation type
type: Class
subclass of: Ontology concept metadata
has definition: A relation type defined in an ontology.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Ontology concept comment
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A comment on a concept from an ontology.
deprecated: true
Obsolete since: 1.4
Created in: beta12orEarlier
consider: Ontology concept metadata
in subset: obsolete

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

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

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

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

Atomic x coordinate
type: Class
subclass of: Atomic coordinate
has definition: Cartesian x coordinate of an atom (in a molecular structure).
has db xref: PDBML:_atom_site.Cartn_x in PDBML
Created in: beta12orEarlier
has exact synonym: Cartesian x coordinate
has db xref: WHATIF: PDBx_Cartn_x
in subset: bioinformatics
in subset: data
in subset: edam

Atomic y coordinate
type: Class
subclass of: Atomic coordinate
has definition: Cartesian y coordinate of an atom (in a molecular structure).
has db xref: PDBML:_atom_site.Cartn_y in PDBML
Created in: beta12orEarlier
has exact synonym: Cartesian y coordinate
has db xref: WHATIF: PDBx_Cartn_y
in subset: bioinformatics
in subset: data
in subset: edam

Atomic z coordinate
type: Class
subclass of: Atomic coordinate
has exact synonym: Cartesian z coordinate
Created in: beta12orEarlier
has definition: Cartesian z coordinate of an atom (in a molecular structure).
has db xref: WHATIF: PDBx_Cartn_z
has db xref: PDBML:_atom_site.Cartn_z
in subset: bioinformatics
in subset: data
in subset: edam

PDB atom name
type: Class
subclass of: Atom name
has definition: Identifier (a string) of a specific atom from a PDB file for a molecular structure.
has db xref: WHATIF: atom_type
has db xref: PDBML:pdbx_PDB_atom_name
has db xref: WHATIF: alternate_atom
has db xref: WHATIF: PDBx_auth_atom_id
Created in: beta12orEarlier
has db xref: WHATIF: PDBx_type_symbol
in subset: bioinformatics
in subset: data
in subset: edam
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.
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.
has related synonym: CHEBI:33250
has exact synonym: Atom data
in subset: bioinformatics
in subset: data
in subset: edam

Protein residue
type: Class
subclass of: Protein structure
has exact synonym: Residue
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.
has definition: Data on a single amino acid residue position in a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

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

CATH domain report
type: Class
subclass of: Obsolete concept (EDAM)
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.
has definition: Summary of domain classification information for a CATH domain.
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
consider: Protein domain classification
in subset: obsolete

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

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

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

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

Sequence version information
type: Class
subclass of: Sequence metadata
subclass of: Version information
has definition: Information on an molecular sequence version.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Score or penalty
type: Class
subclass of: Parameter
has definition: A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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

Gene name (ASPGD)
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS
has definition: Name of a gene from Aspergillus Genome Database.
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.3
consider: Gene symbol
in subset: obsolete

Gene name (CGD)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS
deprecated: true
has definition: Name of a gene from Candida Genome Database.
consider: Gene symbol
in subset: obsolete

Gene name (dictyBase)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name of a gene from dictyBase database.
deprecated: true
Obsolete since: 1.3
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase
consider: Gene symbol
in subset: obsolete

Gene name (EcoGene primary)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.3
has exact synonym: EcoGene primary gene name
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G
has definition: Primary name of a gene from EcoGene Database.
consider: Gene symbol
in subset: obsolete

Gene name (MaizeGDB)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Name of a gene from MaizeGDB (maize genes) database.
Obsolete since: 1.3
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus
consider: Gene symbol
in subset: obsolete

Gene name (SGD)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name of a gene from Saccharomyces Genome Database.
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS
Created in: beta12orEarlier
Obsolete since: 1.3
deprecated: true
consider: Gene symbol
in subset: obsolete

Gene name (TGD)
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS
deprecated: true
has definition: Name of a gene from Tetrahymena Genome Database.
Obsolete since: 1.3
Created in: beta12orEarlier
consider: Gene symbol
in subset: obsolete

Gene name (CGSC)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Symbol of a gene from E.coli Genetic Stock Center.
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
deprecated: true
Obsolete since: 1.3
Created in: beta12orEarlier
consider: Gene symbol
in subset: obsolete

Gene name (HGNC)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Symbol of a gene approved by the HUGO Gene Nomenclature Committee.
has exact synonym: HGNC gene symbol
has exact synonym: Gene name (HUGO)
Regular expression: HGNC:[0-9]{1,5}
has exact synonym: HUGO gene symbol
has exact synonym: HGNC gene name
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
has exact synonym: HUGO gene name
has exact synonym: Official gene name
has exact synonym: HGNC symbol
deprecated: true
Obsolete since: 1.3
has exact synonym: HUGO symbol
Created in: beta12orEarlier
consider: Gene symbol
in subset: obsolete

Gene name (MGD)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.3
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD
has definition: Symbol of a gene from the Mouse Genome Database.
Regular expression: MGI:[0-9]+
consider: Gene symbol
in subset: obsolete

Gene name (Bacillus subtilis)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
Created in: beta12orEarlier
has definition: Symbol of a gene from Bacillus subtilis Genome Sequence Project.
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
consider: Gene symbol
in subset: obsolete

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

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

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

Gene ID (GeneDB Glossina morsitans)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Gene identifier from Glossina morsitans GeneDB database.
Obsolete since: beta13
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans
deprecated: true
consider: Gene ID (GeneDB)
in subset: obsolete

Gene ID (GeneDB Leishmania major)
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
has definition: Gene identifier from Leishmania major GeneDB database.
consider: Gene ID (GeneDB)
in subset: obsolete

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

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

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

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

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

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

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

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

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

Sequence assembly component
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: A component of a larger sequence assembly.
consider: Sequence assembly
in subset: obsolete

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

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

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

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

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: bioinformatics
in subset: data
in subset: edam

Deletion map
type: Class
subclass of: Cytogenetic map
has exact synonym: Deletion-based cytogenetic map
has definition: A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

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

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

Map set
type: Class
subclass of: Map attribute
has db xref: Moby:GCP_CorrelatedMapSet
has definition: Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.
has db xref: Moby:GCP_CorrelatedLinkageMapSet
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Map feature
type: Class
subclass of: Obsolete concept (EDAM)
comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
Created in: beta12orEarlier
has db xref: Moby:MapFeature
has definition: A feature which may mapped (positioned) on a genetic or other type of map.
deprecated: true
Obsolete since: beta12orEarlier
consider: Feature record
consider: Nucleic acid features
consider: Map attribute
in subset: obsolete

Map type
type: Class
subclass of: Map attribute
subclass of: Type
Created in: beta12orEarlier
comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
has definition: A designation of the type of map (genetic map, physical map, sequence map etc) or map set.
in subset: bioinformatics
in subset: data
in subset: edam

Protein fold name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a protein fold.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Taxon
type: Class
subclass of: Organism name
has db xref: Moby:BriefTaxonConcept
has definition: The name of a group of organisms belonging to the same taxonomic rank.
comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
has exact synonym: Taxonomic rank
has exact synonym: Taxonomy rank
Created in: beta12orEarlier
has db xref: Moby:PotentialTaxon
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Organism identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Organism report
has definition: A unique identifier of a (group of) organisms.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Genus name
type: Class
subclass of: Taxon
has definition: The name of a genus of organism.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Taxonomic classification
type: Class
subclass of: Organism name
has db xref: Moby:TaxonTCS
has db xref: Moby:TaxonScientificName
has exact synonym: Taxonomic information
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.
has exact synonym: Taxonomic name
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.
Created in: beta12orEarlier
has db xref: Moby:GCP_Taxon
has db xref: Moby:TaxonName
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

iHOP organism ID
type: Class
subclass of: Organism accession
has definition: A unique identifier for an organism used in the iHOP database.
has db xref: Moby_namespace:iHOPorganism
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Synonym
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An alternative for a word.
deprecated: true
Obsolete since: beta12orEarlier
has exact synonym: Alternative name
Created in: beta12orEarlier
consider: Keyword
in subset: obsolete

Misspelling
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: A common misspelling of a word.
consider: Keyword
in subset: obsolete

Acronym
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: An abbreviation of a phrase or word.
Obsolete since: beta12orEarlier
deprecated: true
consider: Keyword
in subset: obsolete

Misnomer
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: A term which is likely to be misleading of its meaning.
consider: Keyword
in subset: obsolete

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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Annotated URI
type: Class
subclass of: Data reference
subclass of: Metadata
has db xref: Moby:DescribedLink
has definition: A URI along with annotation describing the data found at the address.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

UniProt keywords
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: Ontology
in subset: obsolete

Gene ID (GeneFarm)
type: Class
subclass of: Gene ID
Created in: beta12orEarlier
has definition: Identifier of a gene from the GeneFarm database.
has db xref: Moby_namespace:GENEFARM_GeneID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Blattner number
type: Class
subclass of: Gene ID
has definition: The blattner identifier for a gene.
has db xref: Moby_namespace:Blattner_number
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (MIPS Maize)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
has db xref: Moby_namespace:MIPS_GE_Maize
Created in: beta12orEarlier
has definition: Identifier for genetic elements in MIPS Maize database.
has exact synonym: MIPS genetic element identifier (Maize)
consider: Gene ID (MIPS)
in subset: obsolete

Gene ID (MIPS Medicago)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Identifier for genetic elements in MIPS Medicago database.
has db xref: Moby_namespace:MIPS_GE_Medicago
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has exact synonym: MIPS genetic element identifier (Medicago)
consider: Gene ID (MIPS)
in subset: obsolete

Gene name (DragonDB)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has db xref: Moby_namespace:DragonDB_Gene
Created in: beta12orEarlier
has definition: The name of an Antirrhinum Gene from the DragonDB database.
deprecated: true
consider: Gene symbol
in subset: obsolete

Gene name (Arabidopsis)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
Created in: beta12orEarlier
has definition: A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.
deprecated: true
has db xref: Moby_namespace:ArabidopsisGeneSymbol
consider: Gene symbol
in subset: obsolete

iHOP symbol
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (GeneFarm)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: GeneFarm gene ID
has db xref: Moby_namespace:GENEFARM_GeneName
has definition: Name of a gene from the GeneFarm database.
Obsolete since: 1.3
deprecated: true
consider: Gene symbol
in subset: obsolete

Locus ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence coordinates
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (AGI)
type: Class
subclass of: Locus ID
has exact synonym: AGI identifier
Created in: beta12orEarlier
has exact synonym: AGI locus code
has exact synonym: Arabidopsis gene loci number
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
Regular expression: AT[1-5]G[0-9]{5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (ASPGD)
type: Class
subclass of: Locus ID
has definition: Identifier for loci from ASPGD (Aspergillus Genome Database).
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (MGG)
type: Class
subclass of: Locus ID
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
Created in: beta12orEarlier
has definition: Identifier for loci from Magnaporthe grisea Database at the Broad Institute.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (CGD)
type: Class
subclass of: Locus ID
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD
has exact synonym: CGDID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
has exact synonym: CGD locus identifier
has definition: Identifier for loci from CGD (Candida Genome Database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (CMR)
type: Class
subclass of: Locus ID
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
has definition: Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NCBI locus tag
type: Class
subclass of: Locus ID
has definition: Identifier for loci from NCBI database.
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
has exact synonym: Locus ID (NCBI)
has db xref: Moby_namespace:LocusID
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (SGD)
type: Class
subclass of: Locus ID
subclass of: SGD ID
has exact synonym: SGDID
has definition: Identifier for loci from SGD (Saccharomyces Genome Database).
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD
Created in: beta12orEarlier
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (MMP)
type: Class
subclass of: Locus ID
Created in: beta12orEarlier
has db xref: Moby_namespace:MMP_Locus
has definition: Identifier of loci from Maize Mapping Project.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (DictyBase)
type: Class
subclass of: Locus ID
has definition: Identifier of locus from DictyBase (Dictyostelium discoideum).
Created in: beta12orEarlier
has db xref: Moby_namespace:DDB_gene
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (EntrezGene)
type: Class
subclass of: Locus ID
has db xref: Moby_namespace:EntrezGene_EntrezGeneID
has db xref: Moby_namespace:EntrezGene_ID
Created in: beta12orEarlier
has definition: Identifier of a locus from EntrezGene database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (MaizeGDB)
type: Class
subclass of: Locus ID
Created in: beta12orEarlier
has db xref: Moby_namespace:MaizeGDB_Locus
has definition: Identifier of locus from MaizeGDB (Maize genome database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Quantitative trait locus
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: Moby:SO_QTL
deprecated: true
comment: A QTL sometimes but does not necessarily correspond to a gene.
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).
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has exact synonym: QTL
consider: Sequence coordinates
in subset: obsolete

Gene ID (KOME)
type: Class
subclass of: Gene ID
has db xref: Moby_namespace:GeneId
Created in: beta12orEarlier
has definition: Identifier of a gene from the KOME database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (Tropgene)
type: Class
subclass of: Locus ID
Created in: beta12orEarlier
has db xref: Moby:Tropgene_locus
has definition: Identifier of a locus from the Tropgene database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Alignment
type: Class
subclass of: Core data
Created in: beta12orEarlier
has definition: An alignment of molecular sequences, structures or profiles derived from them.
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

UniProt keyword
type: Class
subclass of: Keyword
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW
has db xref: Moby_namespace:SP_KW
has definition: A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Ordered locus name
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
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.
deprecated: true
Obsolete since: beta12orEarlier
consider: Locus ID
in subset: obsolete

Sequence coordinates
type: Class
subclass of: Sequence position
subclass of: Sequence range
subclass of: Map attribute
has db xref: PDBML:_atom_site.id
has db xref: Moby:GCP_MapPoint
has db xref: Moby:GCP_MapPosition
has db xref: Moby:GCP_MapInterval
Created in: beta12orEarlier
has db xref: Moby:Locus
has db xref: Moby:MapPosition
has db xref: Moby:HitPosition
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.
has db xref: Moby:GenePosition
has definition: A position in a map (for example a genetic map), either a single position (point) or a region / interval.
has exact synonym: Sequence co-ordinates
has exact synonym: Locus
has db xref: Moby:Position
has exact synonym: Map position
in subset: bioinformatics
in subset: data
in subset: edam

Amino acid property
type: Class
subclass of: Molecular property
has exact synonym: Amino acid data
Created in: beta12orEarlier
has definition: Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.
in subset: bioinformatics
in subset: data
in subset: edam

Annotation
type: Class
subclass of: Obsolete concept (EDAM)
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.
Obsolete since: beta13
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true
Created in: beta12orEarlier
consider: Report
in subset: obsolete

Map attribute
type: Class
subclass of: Metadata
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: An attribute of a molecular map (genetic or physical).
in subset: bioinformatics
in subset: data
in subset: edam

Vienna RNA structural data
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Data used by the Vienna RNA analysis package.
deprecated: true
consider: Parameter
in subset: obsolete

Sequence mask parameter
type: Class
subclass of: Sequence parameter
has definition: Data used to replace (mask) characters in a molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Enzyme kinetics data
type: Class
subclass of: Reaction data
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
has definition: Data concerning chemical reaction(s) catalysed by enzyme(s).
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Hanes Woolf plot
type: Class
subclass of: Enzyme kinetics data
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).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Experimental data
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Experimental measurement data
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Raw data from or annotation on laboratory experiments.
deprecated: true
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.
consider: Experiment annotation
consider: Experimental measurement
in subset: obsolete

Genome version information
type: Class
subclass of: Version information
subclass of: Genome metadata
has definition: Information on a genome version.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Evidence
type: Class
subclass of: Parameter
Created in: beta12orEarlier
has definition: Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record lite
type: Class
subclass of: Sequence record
has definition: A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
has definition: One or more molecular sequences, possibly with associated annotation.
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.
Created in: beta12orEarlier
has narrow synonym: D008969
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: BioMolecularSequenceInformation

Sequence record lite (nucleic acid)
type: Class
subclass of: Sequence record lite
subclass of: Sequence record (nucleic acid)
has definition: A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record lite (protein)
type: Class
subclass of: Sequence record lite
subclass of: Sequence record (protein)
has definition: A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Report
type: Class
subclass of: Data
Created in: beta12orEarlier
has exact synonym: document
comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing.
has exact synonym: Document
has definition: A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself.
has exact synonym: Text
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: SIO_000148

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: bioinformatics
in subset: data
in subset: edam

Structural data
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: Data concerning molecular structural data.
deprecated: true
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
consider: Structure
consider: Structure report
in subset: obsolete

Sequence motif (nucleic acid)
type: Class
subclass of: Sequence motif
Created in: beta12orEarlier
has definition: A nucleotide sequence motif.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence motif (protein)
type: Class
subclass of: Sequence motif
has definition: An amino acid sequence motif.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Search parameter
type: Class
subclass of: Parameter
has definition: Some simple value controlling a search operation, typically a search of a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Database hits
type: Class
subclass of: Data reference
has definition: A report of hits from searching a database of some type.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Secondary structure
type: Class
subclass of: Core data
has definition: The secondary structure assignment (predicted or real) of a nucleic acid or protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Matrix
type: Class
subclass of: Core data
has definition: An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences.
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Alignment report
type: Class
subclass of: Report
comment: This is a broad data type and is used a placeholder for other, more specific types.
has definition: An informative report about a molecular alignment of some type, including alignment-derived data or metadata.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid report
type: Class
subclass of: Molecule report
Created in: beta12orEarlier
has definition: An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.
in subset: bioinformatics
in subset: data
in subset: edam

Structure report
type: Class
subclass of: Report
has exact synonym: Structure-derived report
Created in: beta12orEarlier
has definition: An informative report on general information, properties or features of one or more molecular tertiary (3D) structures.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid structure report
type: Class
subclass of: Nucleic acid property
subclass of: 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).
Created in: beta12orEarlier
has exact synonym: Nucleic acid property (structural)
has exact synonym: Nucleic acid structural property
comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.
in subset: bioinformatics
in subset: data
in subset: edam

Molecular property
type: Class
subclass of: Core data
has exact synonym: Physicochemical property
has definition: A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.
has related synonym: SO:0000400
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

DNA base structural data
type: Class
subclass of: Nucleic acid property
subclass of: Nucleic acid structure report
Created in: beta12orEarlier
has definition: Structural data for DNA base pairs or runs of bases, such as energy or angle data.
in subset: bioinformatics
in subset: data
in subset: edam

Database entry version information
type: Class
subclass of: Version information
subclass of: Database entry 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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Accession
type: Class
subclass of: Identifier
has definition: A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers
has broad synonym: SIO_000675
has broad synonym: SIO_000731

Nucleic acid features (SNP)
type: Class
subclass of: Nucleic acid features (polymorphism annotation)
has exact synonym: SNP annotation
comment: An SNP is an individual point mutation or substitution of a single nucleotide.
has exact synonym: Single nucleotide polymorphism
has definition: Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Data reference
type: Class
subclass of: Core 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.
comment: A list of database accessions or identifiers are usually included.
in subset: bioinformatics
in subset: data
in subset: edam

Job identifier
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: An identifier of a submitted job.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers
has exact synonym: data_009

Name
type: Class
subclass of: Identifier
has exact synonym: Symbolic name
has definition: A name of a thing, which need not necessarily uniquely identify it.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers
has exact synonym: SIO_000116
has exact synonym: name
has broad synonym: label

Axiom
comment: Closely related, but focusing on labeling and human readability but not on identification.
annotated source: Name
annotated property: hasBroadSynonym
annotated target: label

Type
type: Class
subclass of: Parameter
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam
has exact synonym: type

User ID
type: Class
subclass of: Person identifier
Created in: beta12orEarlier
has definition: An identifier of a software end-user (typically a person).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

KEGG organism code
type: Class
subclass of: KEGG object identifier
subclass of: Organism name
has definition: A three-letter code used in the KEGG databases to uniquely identify organisms.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (KEGG GENES)
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: Moby_namespace:GeneId
has definition: Name of an entry (gene) from the KEGG GENES database.
Obsolete since: 1.3
deprecated: true
Regular expression: [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*
has exact synonym: KEGG GENES entry name
Created in: beta12orEarlier
consider: Gene symbol
in subset: obsolete

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Compound ID (BioCyc)
type: Class
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 identifier
has exact synonym: BioCyc compound ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Reaction ID (BioCyc)
type: Class
subclass of: BioCyc ID
subclass of: Reaction ID
subclass of: Restriction
  on property: has topic
  some values from: Peptides and amino acids
has definition: Identifier of a biological reaction from the BioCyc reactions database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Enzyme ID (BioCyc)
type: Class
subclass of: BioCyc ID
subclass of: Enzyme ID
has definition: Identifier of an enzyme from the BioCyc enzymes database.
Created in: beta12orEarlier
has exact synonym: BioCyc enzyme ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Reaction ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Reaction data
has definition: Identifier of a biological reaction from a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Identifier (hybrid)
type: Class
subclass of: Identifier
Created in: beta12orEarlier
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'.
has definition: An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Molecular property identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Molecular property
has definition: Identifier of a molecular property.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Codon usage table ID
type: Class
subclass of: Identifier (typed)
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
has exact synonym: Codon usage table identifier
Created in: beta12orEarlier
has definition: Identifier of a codon usage table, for example a genetic code.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

FlyBase primary identifier
type: Class
subclass of: FlyBase ID
has definition: Primary identifier of an object from the FlyBase database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

WormBase identifier
type: Class
subclass of: Identifier (hybrid)
has definition: Identifier of an object from the WormBase database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

WormBase wormpep ID
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Nucleic acid features (codon)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
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.
Obsolete since: beta12orEarlier
consider: Nucleic acid features
in subset: obsolete

Map identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Map
Created in: beta12orEarlier
has definition: An identifier of a map of a molecular sequence.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Person identifier
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: An identifier of a software end-user (typically a person).
in subset: bioinformatics
in subset: data
in subset: edam
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
has definition: Name or other identifier of a nucleic acid molecule.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Translation frame specification
type: Class
subclass of: Sequence parameter
has definition: Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Genetic code identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Genetic code
Created in: beta12orEarlier
has definition: An identifier of a genetic code.
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence profile type
type: Class
subclass of: Type
subclass of: Sequence parameter
Created in: beta12orEarlier
has definition: A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.
in subset: bioinformatics
in subset: data
in subset: edam

Operating system name
type: Class
subclass of: Name
has definition: Name of a computer operating system such as Linux, PC or Mac.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Mutation type
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A type of point or block mutation, including insertion, deletion, change, duplication and moves.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: Type
in subset: obsolete

Logical operator
type: Class
subclass of: Name
has definition: A logical operator such as OR, AND, XOR, and NOT.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Results sort order
type: Class
subclass of: Search parameter
has definition: A control of the order of data that is output, for example the order of sequences in an alignment.
Created in: beta12orEarlier
comment: Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.
in subset: bioinformatics
in subset: data
in subset: edam

Toggle
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: A simple parameter that is a toggle (boolean value), typically a control for a modal tool.
Created in: beta12orEarlier
consider: Parameter
in subset: obsolete

Sequence width
type: Class
subclass of: Obsolete concept (EDAM)
has definition: The width of an output sequence or alignment.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Sequence length
in subset: obsolete

Gap penalty
type: Class
subclass of: Alignment score or penalty
has definition: A penalty for introducing or extending a gap in an alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid melting temperature
type: Class
subclass of: Nucleic acid thermodynamic data
has exact synonym: Melting temperature
has definition: A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Concentration
type: Class
subclass of: Molecular property (general)
has definition: The concentration of a chemical compound.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Window step size
type: Class
subclass of: Sequence length
has definition: Size of the incremental 'step' a sequence window is moved over a sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

EMBOSS graph
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An image of a graph generated by the EMBOSS suite.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: Image
in subset: obsolete

EMBOSS report
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: An application report generated by the EMBOSS suite.
consider: Report
in subset: obsolete

Sequence offset
type: Class
subclass of: Sequence position
subclass of: Sequence features metadata
has definition: An offset for a single-point sequence position.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Threshold
type: Class
subclass of: Score or penalty
has definition: A value that serves as a threshold for a tool (usually to control scoring or output).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein report (transcription factor)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: Transcription factor binding site data
has definition: An informative report on a transcription factor protein.
comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
Obsolete since: beta13
deprecated: true
consider: Protein report
in subset: obsolete

Database category name
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: The name of a category of biological or bioinformatics database.
deprecated: true
consider: Database name
in subset: obsolete

Sequence profile name
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Name of a sequence profile.
Obsolete since: beta12orEarlier
consider: Sequence profile ID
in subset: obsolete

Color
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Specification of one or more colors.
consider: Rendering parameter
in subset: obsolete

Rendering parameter
type: Class
subclass of: Parameter
has exact synonym: Graphics parameter
has exact synonym: Graphical parameter
has definition: A parameter that is used to control rendering (drawing) to a device or image.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence name
type: Class
subclass of: Sequence identifier
subclass of: Name
has definition: Any arbitrary name of a molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Date
type: Class
subclass of: Geotemporal metadata
Created in: beta12orEarlier
has definition: A temporal date.
in subset: bioinformatics
in subset: data
in subset: edam

Word composition
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Word composition data for a molecular sequence.
Created in: beta12orEarlier
consider: Sequence composition (base words)
consider: Amino acid word frequencies
in subset: obsolete

Fickett testcode plot
type: Class
subclass of: Nucleic acid features (coding sequence)
Created in: beta12orEarlier
has definition: A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence similarity report
type: Class
subclass of: Sequence alignment report
has definition: A plot of sequence similarities identified from word-matching or character comparison.
has exact synonym: Sequence similarity plot
has exact synonym: Sequence conservation report
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Helical wheel
type: Class
subclass of: Protein secondary structure image
has definition: An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Helical net
type: Class
subclass of: Protein secondary structure image
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.
comment: Useful for highlighting amphipathicity and other properties.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein sequence properties plot
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A plot of general physicochemical properties of a protein sequence.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Protein property
in subset: obsolete

Protein ionization curve
type: Class
subclass of: Protein property
has definition: A plot of pK versus pH for a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence composition plot
type: Class
subclass of: Sequence composition
has definition: A plot of character or word composition / frequency of a molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid density plot
type: Class
subclass of: Nucleic acid property
has definition: Density plot (of base composition) for a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (siRNA)
type: Class
subclass of: Nucleic acid features (non-coding RNA)
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
has definition: A report on siRNA duplexes in mRNA.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence set (stream)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.
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
Created in: beta12orEarlier
consider: Sequence set
in subset: obsolete

FlyBase secondary identifier
type: Class
subclass of: FlyBase ID
Created in: beta12orEarlier
comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database.
has definition: Secondary identifier of an object from the FlyBase database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cardinality
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: The number of a certain thing.
in subset: obsolete

Exactly 1
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: A single thing.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
in subset: obsolete

1 or more
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: One or more things.
in subset: obsolete

Exactly 2
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Exactly two things.
in subset: obsolete

2 or more
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Two or more things.
in subset: obsolete

Sequence checksum
type: Class
subclass of: Sequence metadata
subclass of: Sequence parameter
has exact synonym: Hash
has exact synonym: Hash code
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 value
has exact synonym: Hash sum
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (chemical modification)
type: Class
subclass of: Protein features
has exact synonym: Protein modification annotation
has related synonym: GO:0006464
has related synonym: MOD:00000
Created in: beta12orEarlier
has definition: A report on a chemical modification of a protein.
in subset: bioinformatics
in subset: data
in subset: edam

Error
type: Class
subclass of: Job metadata
has definition: Data on an error generated by computer system or tool.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Database entry metadata
type: Class
subclass of: Database metadata
has definition: Basic information on any arbitrary database entry.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Gene cluster
type: Class
subclass of: Obsolete concept (EDAM)
has definition: A cluster of similar genes.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: Sequence cluster (nucleic acid)
in subset: obsolete

Sequence record full
type: Class
subclass of: Sequence record
has db xref: SO:2000061
has definition: A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
Created in: beta12orEarlier
has related synonym: D058977
in subset: bioinformatics
in subset: data
in subset: edam

Plasmid identifier
type: Class
subclass of: Nucleic acid identifier
Created in: beta12orEarlier
has definition: An identifier of a plasmid in a database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Mutation ID
type: Class
subclass of: Accession
subclass of: Mutation identifier
has definition: A unique identifier of a specific mutation catalogued in a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Mutation annotation (basic)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
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.
consider: Nucleic acid features (mutation)
in subset: obsolete

Mutation annotation (prevalence)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..
deprecated: true
Created in: beta12orEarlier
consider: Nucleic acid features (mutation)
in subset: obsolete

Mutation annotation (prognostic)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.
Created in: beta12orEarlier
consider: Nucleic acid features (mutation)
in subset: obsolete

Mutation annotation (functional)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
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.
consider: Nucleic acid features (mutation)
in subset: obsolete

Codon number
type: Class
subclass of: Sequence position
has definition: The number of a codon, for instance, at which a mutation is located.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Tumor annotation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
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.
Obsolete since: 1.4
deprecated: true
consider: Disease report
in subset: obsolete

Server metadata
type: Class
subclass of: System metadata
Created in: beta12orEarlier
has definition: Basic information about a server on the web, such as an SRS server.
in subset: bioinformatics
in subset: data
in subset: edam

Database field name
type: Class
subclass of: Name
Created in: beta12orEarlier
has definition: The name of a field in a database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (SYSTERS)
type: Class
subclass of: Sequence cluster ID
Created in: beta12orEarlier
has exact synonym: SYSTERS cluster ID
has definition: Unique identifier of a sequence cluster from the SYSTERS database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ontology metadata
type: Class
subclass of: Metadata
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
has definition: Data concerning a biological ontology.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Raw SCOP domain classification
type: Class
subclass of: Obsolete concept (EDAM)
comment: These are the parsable data files provided by SCOP.
Obsolete since: beta13
has definition: Raw SCOP domain classification data files.
Created in: beta12orEarlier
deprecated: true
consider: Protein domain classification
in subset: obsolete

Raw CATH domain classification
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
comment: These are the parsable data files provided by CATH.
has definition: Raw CATH domain classification data files.
consider: Protein domain classification
in subset: obsolete

Heterogen annotation
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files.
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.4
consider: Small molecule report
in subset: obsolete

Phylogenetic property values
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Phylogenetic property values data.
Created in: beta12orEarlier
consider: Phylogenetic character data
in subset: obsolete

Sequence set (bootstrapped)
type: Class
subclass of: Sequence set
has definition: A collection of sequences output from a bootstrapping (resampling) procedure.
comment: Bootstrapping is often performed in phylogenetic analysis.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Phylogenetic consensus tree
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: A consensus phylogenetic tree derived from comparison of multiple trees.
deprecated: true
consider: Phylogenetic tree
in subset: obsolete

Schema
type: Class
subclass of: Core data
has definition: A data schema for organising or transforming data of some type.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

DTD
type: Class
subclass of: Schema
Created in: beta12orEarlier
has definition: A DTD (document type definition).
in subset: bioinformatics
in subset: data
in subset: edam

XML Schema
type: Class
subclass of: Schema
has definition: An XML Schema.
has exact synonym: XSD
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Relax-NG schema
type: Class
subclass of: Schema
has definition: A relax-NG schema.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

XSLT stylesheet
type: Class
subclass of: Schema
has definition: An XSLT stylesheet.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Data resource definition name
type: Class
subclass of: Data resource definition ID
subclass of: Name
has definition: The name of a data type.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (MIPS)
type: Class
subclass of: Gene ID
has exact synonym: MIPS genetic element identifier
Created in: beta12orEarlier
has definition: Identifier for genetic elements in MIPS database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence identifier (protein)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: An identifier of protein sequence(s) or protein sequence database entries.
consider: Sequence accession (protein)
in subset: obsolete

Sequence identifier (nucleic acid)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: An identifier of nucleotide sequence(s) or nucleotide sequence database entries.
consider: Sequence accession (nucleic acid)
in subset: obsolete

EMBL accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
has exact synonym: EMBL identifier
has exact synonym: EMBL accession number
has definition: An accession number of an entry from the EMBL sequence database.
Created in: beta12orEarlier
has exact synonym: EMBL ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UniProt ID
type: Class
subclass of: Sequence name
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
has exact synonym: UniProt entry name
has exact synonym: UniProt identifier
Created in: beta12orEarlier
has exact synonym: UniProtKB entry name
has definition: An identifier of a polypeptide in the UniProt database.
has exact synonym: UniProtKB identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GenBank accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
has exact synonym: GenBank identifier
has exact synonym: GenBank ID
has exact synonym: GenBank accession number
Created in: beta12orEarlier
has definition: Accession number of an entry from the GenBank sequence database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gramene secondary identifier
type: Class
subclass of: Gramene identifier
has exact synonym: Gramene secondary ID
has definition: Secondary (internal) identifier of a Gramene database entry.
has exact synonym: Gramene internal ID
has exact synonym: Gramene internal identifier
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence variation ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of an entry from a database of molecular sequence variation.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID
type: Class
subclass of: Gene identifier
subclass of: Locus ID
Created in: beta12orEarlier
has exact synonym: Gene accession
has exact synonym: Gene code
has definition: A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (AceView)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Name of an entry (gene) from the AceView genes database.
deprecated: true
Obsolete since: 1.3
has exact synonym: AceView gene name
consider: Gene symbol
in subset: obsolete

Gene ID (ECK)
type: Class
subclass of: Gene ID (EcoGene)
has db xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK
has exact synonym: E. coli K-12 gene identifier
has definition: Identifier of an E. coli K-12 gene from EcoGene Database.
Created in: beta12orEarlier
has exact synonym: ECK accession
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (HGNC)
type: Class
subclass of: Gene ID
has definition: Identifier for a gene approved by the HUGO Gene Nomenclature Committee.
Created in: beta12orEarlier
has exact synonym: HGNC ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name
type: Class
subclass of: Gene identifier
subclass of: Name
Created in: beta12orEarlier
has narrow synonym: Allele name
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.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (NCBI)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Name of an entry (gene) from the NCBI genes database.
Obsolete since: 1.3
has exact synonym: NCBI gene name
Created in: beta12orEarlier
consider: Gene symbol
in subset: obsolete

SMILES string
type: Class
subclass of: Chemical formula
Created in: beta12orEarlier
has definition: A specification of a chemical structure in SMILES format.
in subset: bioinformatics
in subset: data
in subset: edam

STRING ID
type: Class
subclass of: Protein interaction ID
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the STRING database of protein-protein interactions.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Virus annotation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.4
deprecated: true
has definition: An informative report on a specific virus.
consider: Organism report
in subset: obsolete

Virus annotation (taxonomy)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.4
deprecated: true
Created in: beta12orEarlier
has definition: An informative report on the taxonomy of a specific virus.
consider: Organism report
in subset: obsolete

Reaction ID (SABIO-RK)
type: Class
subclass of: Reaction ID
Regular expression: [0-9]+
Created in: beta12orEarlier
has definition: Identifier of a biological reaction from the SABIO-RK reactions database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Carbohydrate structure report
type: Class
subclass of: Structure report
Created in: beta12orEarlier
has definition: Annotation on or information derived from one or more specific carbohydrate 3D structure(s).
in subset: bioinformatics
in subset: data
in subset: edam

GI number
type: Class
subclass of: Sequence accession (hybrid)
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.
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: gi number
has exact synonym: NCBI GI number
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NCBI version
type: Class
subclass of: Sequence accession (hybrid)
has exact synonym: accession.version
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.
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
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell line name
type: Class
subclass of: Strain name
has definition: The name of a cell line.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell line name (exact)
type: Class
subclass of: Cell line name
has definition: The name of a cell line.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell line name (truncated)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The name of a cell line.
in subset: bioinformatics
in subset: data
in subset: edam
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.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell line name (assonant)
type: Class
subclass of: Cell line name
Created in: beta12orEarlier
has definition: The name of a cell line.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Enzyme ID
type: Class
subclass of: Enzyme identifier
subclass of: Protein accession
has exact synonym: Enzyme accession
has definition: A unique, persistent identifier of an enzyme.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

REBASE enzyme number
type: Class
subclass of: Enzyme ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme from the REBASE enzymes database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

DrugBank ID
type: Class
subclass of: Drug accession
has definition: Unique identifier of a drug from the DrugBank database.
Regular expression: DB[0-9]{5}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GI number (protein)
type: Class
subclass of: GI number
has definition: A unique identifier assigned to NCBI protein sequence records.
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.
Created in: beta12orEarlier
has exact synonym: protein gi
has exact synonym: protein gi number
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Bit score
type: Class
subclass of: Sequence similarity
Created in: beta12orEarlier
comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.
has definition: A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system.
in subset: bioinformatics
in subset: data
in subset: edam

Translation phase specification
type: Class
subclass of: Sequence parameter
subclass of: Sequence features metadata
has exact synonym: Phase
has definition: Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Metadata
type: Class
subclass of: Report
Created in: beta12orEarlier
has exact synonym: Provenance metadata
comment: This is a broad data type and is used a placeholder for other, more specific types.
has definition: Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing.
in subset: bioinformatics
in subset: data
in subset: edam

Ontology identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Ontology
has definition: Any arbitrary identifier of an ontology.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Genome build identifier
type: Class
subclass of: Genome identifier
has definition: An identifier of a build of a particular genome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Pathway or network accession
Regular expression: [a-zA-Z_0-9]{2,3}[0-9]{5}
Created in: beta12orEarlier
has exact synonym: KEGG pathway ID
has definition: Identifier of a pathway from the KEGG pathway database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (NCI-Nature)
type: Class
subclass of: Pathway or network accession
has definition: Identifier of a pathway from the NCI-Nature pathway database.
Regular expression: [a-zA-Z_0-9]+
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (ConsensusPathDB)
type: Class
subclass of: Pathway or network accession
subclass of: ConsensusPathDB identifier
has definition: Identifier of a pathway from the ConsensusPathDB pathway database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (UniRef)
type: Class
subclass of: Sequence cluster ID
Created in: beta12orEarlier
has exact synonym: UniRef entry accession
has exact synonym: UniRef cluster id
has definition: Unique identifier of an entry from the UniRef database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (UniRef100)
type: Class
subclass of: Sequence cluster ID (UniRef)
has definition: Unique identifier of an entry from the UniRef100 database.
has exact synonym: UniRef100 entry accession
Created in: beta12orEarlier
has exact synonym: UniRef100 cluster id
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (UniRef90)
type: Class
subclass of: Sequence cluster ID (UniRef)
has definition: Unique identifier of an entry from the UniRef90 database.
has exact synonym: UniRef90 cluster id
Created in: beta12orEarlier
has exact synonym: UniRef90 entry accession
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (UniRef50)
type: Class
subclass of: Sequence cluster ID (UniRef)
has definition: Unique identifier of an entry from the UniRef50 database.
has exact synonym: UniRef50 cluster id
has exact synonym: UniRef50 entry accession
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ontological data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning an ontology.
deprecated: true
comment: This is a broad data type and is used a placeholder for other, more specific types.
Obsolete since: beta13
Created in: beta12orEarlier
consider: Ontology
consider: Ontology metadata
in subset: obsolete

RNA family annotation
type: Class
subclass of: Nucleic acid classification
has definition: An informative report on a specific RNA family or other group of classified RNA sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

RNA family identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: RNA family annotation
has definition: Identifier of an RNA family, typically an entry from a RNA sequence classification database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein signature type
type: Class
subclass of: Type
subclass of: Sequence parameter
has definition: A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Domain-nucleic acid interaction
type: Class
subclass of: Protein-nucleic acid interaction
Created in: beta12orEarlier
has definition: Data on protein domain-DNA/RNA interaction(s).
in subset: bioinformatics
in subset: data
in subset: edam

Domain-domain interaction
type: Class
subclass of: Protein-protein interaction
Created in: beta12orEarlier
has definition: Data on protein domain-protein domain interaction(s).
in subset: bioinformatics
in subset: data
in subset: edam

Domain-domain interaction (indirect)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data on indirect protein domain-protein domain interaction(s).
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Domain-domain interaction
in subset: obsolete

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
has definition: Accession number of a nucleotide or protein sequence database entry.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

2D PAGE data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning two-dimensional polygel electrophoresis.
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
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.
consider: 2D PAGE image
consider: Experiment annotation (2D PAGE)
in subset: obsolete

Experiment annotation (2D PAGE)
type: Class
subclass of: Experiment annotation
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
has definition: An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network accession
type: Class
subclass of: Pathway or network identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: A persistent, unique identifier of a biological pathway or network (typically a database entry).
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam

ASTD ID
type: Class
subclass of: Sequence accession (nucleic acid)
subclass of: Identifier (hybrid)
has definition: Identifier of an object from the ASTD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ASTD ID (exon)
type: Class
subclass of: ASTD ID
has definition: Identifier of an exon from the ASTD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ASTD ID (intron)
type: Class
subclass of: ASTD ID
has definition: Identifier of an intron from the ASTD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

2D PAGE spot (annotated)
type: Class
subclass of: 2D PAGE image (annotated)
has definition: An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.
Created in: beta12orEarlier
has exact synonym: 2D PAGE spot annotation
in subset: bioinformatics
in subset: data
in subset: edam

Spot ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has definition: Unique identifier of a spot from a two-dimensional (protein) gel.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Spot serial number
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Spot ID (HSC-2DPAGE)
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein-motif interaction
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.
deprecated: true
Obsolete since: beta13
consider: Protein-protein interaction
in subset: obsolete

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

Experiment annotation (genotype)
type: Class
subclass of: Experiment annotation
has definition: Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Genotype experiment ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Experiment annotation
has definition: Identifier of an entry from a database of genotype experiment metadata.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

EGA accession
type: Class
subclass of: Genotype experiment ID
has definition: Identifier of an entry from the EGA database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

IPI protein ID
type: Class
subclass of: Sequence accession (protein)
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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

EPD ID
type: Class
subclass of: Promoter ID
has exact synonym: EPD identifier
has definition: Identifier of an entry (promoter) from the EPD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TAIR accession
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
has definition: Identifier of an entry from the TAIR database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TAIR accession (At gene)
type: Class
subclass of: TAIR accession (gene)
has definition: Identifier of an Arabidopsis thaliana gene from the TAIR database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UniSTS accession
type: Class
subclass of: Sequence accession (nucleic acid)
has definition: Identifier of an entry from the UniSTS database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UNITE accession
type: Class
subclass of: Sequence accession (nucleic acid)
has definition: Identifier of an entry from the UNITE database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UTR accession
type: Class
subclass of: Sequence accession (nucleic acid)
has definition: Identifier of an entry from the UTR database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UniParc accession
type: Class
subclass of: Sequence accession (protein)
has exact synonym: UPI
has definition: Accession number of a UniParc (protein sequence) database entry.
has exact synonym: UniParc ID
Regular expression: UPI[A-F0-9]{10}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

mFLJ/mKIAA number
type: Class
subclass of: Gene ID
has definition: Identifier of an entry from the Rouge or HUGE databases.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Fungi annotation
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An informative report on a specific fungus.
Obsolete since: 1.4
Created in: beta12orEarlier
deprecated: true
consider: Organism report
in subset: obsolete

Fungi annotation (anamorph)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.4
has definition: An informative report on a specific fungus anamorph.
Created in: beta12orEarlier
consider: Organism report
in subset: obsolete

Nucleic acid features (exon)
type: Class
subclass of: Nucleic acid features (coding sequence)
has exact synonym: Gene features (exon)
Created in: beta12orEarlier
has definition: An informative report on an exon in a nucleotide sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Ensembl protein ID
type: Class
subclass of: Ensembl ID
subclass of: Protein accession
has definition: Unique identifier for a protein from the Ensembl database.
has exact synonym: Protein ID (Ensembl)
Created in: beta12orEarlier
has exact synonym: Ensembl ID (protein)
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene annotation (transcript)
type: Class
subclass of: Gene annotation
has definition: An informative report on a specific gene transcript, clone or EST.
has exact synonym: Gene annotation (clone or EST)
has exact synonym: Gene transcript annotation
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Toxin annotation
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.4
has definition: An informative report on a specific toxin.
Created in: beta12orEarlier
consider: Small molecule report
in subset: obsolete

Protein report (membrane protein)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: An informative report on a membrane protein.
deprecated: true
Created in: beta12orEarlier
consider: Protein features (membrane regions)
in subset: obsolete

Protein-drug interaction
type: Class
subclass of: Protein-ligand interaction
Created in: beta12orEarlier
has definition: Informative report on protein-drug interaction(s) including binding affinity data.
in subset: bioinformatics
in subset: data
in subset: edam

Map data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning a map of molecular sequence(s).
Obsolete since: beta13
deprecated: true
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
consider: Map
consider: Map attribute
in subset: obsolete

Phylogenetic raw data
type: Class
subclass of: Core data
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
has definition: Data concerning phylogeny, typically of molecular sequences.
has exact synonym: Phylogenetic data
in subset: bioinformatics
in subset: data
in subset: edam

Protein data
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Data concerning one or more protein molecules.
Obsolete since: beta13
comment: This is a broad data type and is used a placeholder for other, more specific types.
consider: Protein report
in subset: obsolete

Nucleic acid data
type: Class
subclass of: Obsolete concept (EDAM)
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
Obsolete since: beta13
has definition: Data concerning one or more nucleic acid molecules.
deprecated: true
consider: Nucleic acid report
in subset: obsolete

Article data
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
deprecated: true
has definition: Data concerning the scientific literature.
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.
Created in: beta12orEarlier
consider: Article
in subset: obsolete

Parameter
type: Class
subclass of: Data
disjoint with: Core data
has exact synonym: Parameter or primitive
has exact synonym: Tool parameter
has exact synonym: Tool-specific parameter
has definition: Typically a simple numerical or string value that controls the operation of a tool.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
has exact synonym: SIO_000144
has exact synonym: Parameter

Axiom
comment: Slightly narrower in the sense of changing the characteristics of a system/function.
annotated source: Parameter
annotated target: SIO_000144
annotated property: hasExactSynonym

Molecular data
type: Class
subclass of: Obsolete concept (EDAM)
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
Obsolete since: beta13
has definition: Data concerning a specific type of molecule.
deprecated: true
has exact synonym: Molecule-specific data
consider: Molecule report
in subset: obsolete

Molecule report
type: Class
subclass of: Report
has exact synonym: Molecular report
Created in: beta12orEarlier
has definition: An informative report on a specific molecule.
in subset: bioinformatics
in subset: data
in subset: edam

Organism report
type: Class
subclass of: Report
has exact synonym: Organism annotation
Created in: beta12orEarlier
has definition: An informative report on a specific organism.
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation
type: Class
subclass of: Report
has definition: Annotation on a wet lab experiment, such as experimental conditions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (mutation)
type: Class
subclass of: Nucleic acid features (variation)
has definition: Annotation on a mutation.
has exact synonym: Mutation annotation
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence parameter
type: Class
subclass of: Parameter
Created in: beta12orEarlier
has definition: A parameter concerning calculations on molecular sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence tag profile
type: Class
subclass of: Gene expression profile
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
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: data
in subset: edam

Mass spectrometry data
type: Class
subclass of: Experimental measurement
has definition: Data concerning a mass spectrometry measurement.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein structure raw data
type: Class
subclass of: Experimental measurement
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.
has definition: Raw data from experimental methods for determining protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Mutation identifier
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: An identifier of a mutation.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Alignment data
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Data concerning an alignment of two or more molecular sequences, structures or derived data.
Obsolete since: beta13
deprecated: true
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.
consider: Alignment
consider: Alignment report
in subset: obsolete

Data index data
type: Class
subclass of: Obsolete concept (EDAM)
comment: This is a broad data type and is used a placeholder for other, more specific types.
has exact synonym: Database index
Obsolete since: beta13
has definition: Data concerning an index of data.
Created in: beta12orEarlier
deprecated: true
consider: Data index
consider: Data index report
in subset: obsolete

Amino acid name (single letter)
type: Class
subclass of: Amino acid name
has definition: Single letter amino acid identifier, e.g. G.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Amino acid name (three letter)
type: Class
subclass of: Amino acid name
has definition: Three letter amino acid identifier, e.g. GLY.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Amino acid name (full name)
type: Class
subclass of: Amino acid name
has definition: Full name of an amino acid, e.g. Glycine.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Toxin identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Toxin structure
has definition: Identifier of a toxin.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ArachnoServer ID
type: Class
subclass of: Toxin accession
Created in: beta12orEarlier
has definition: Unique identifier of a toxin from the ArachnoServer database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Expressed gene list
type: Class
subclass of: ID list
has definition: A simple summary of expressed genes.
has exact synonym: Gene annotation (expressed gene list)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

BindingDB Monomer ID
type: Class
subclass of: Compound accession
has definition: Unique identifier of a monomer from the BindingDB database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GO concept name
type: Class
subclass of: Obsolete concept (EDAM)
has definition: The name of a concept from the GO ontology.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Ontology concept name
in subset: obsolete

GO concept ID (biological process)
type: Class
subclass of: GO concept ID
has definition: An identifier of a 'biological process' concept from the the Gene Ontology.
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GO concept ID (molecular function)
type: Class
subclass of: GO concept ID
has definition: An identifier of a 'molecular function' concept from the the Gene Ontology.
Regular expression: [0-9]{7}|GO:[0-9]{7}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GO concept name (cellular component)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: The name of a concept for a cellular component from the GO ontology.
consider: Ontology concept name
in subset: obsolete

Northern blot image
type: Class
subclass of: Experimental measurement
has definition: An image arising from a Northern Blot experiment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Blot ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
Created in: beta12orEarlier
has definition: Unique identifier of a blot from a Northern Blot.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

BlotBase blot ID
type: Class
subclass of: Blot ID
has definition: Unique identifier of a blot from a Northern Blot from the BlotBase database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Hierarchy
type: Class
subclass of: Classification
has exact synonym: Hierarchy annotation
has definition: A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Hierarchy identifier
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Identifier of an entry from a database of biological hierarchies.
Obsolete since: beta12orEarlier
consider: Biological model accession
in subset: obsolete

Brite hierarchy ID
type: Class
subclass of: Biological model accession
has definition: Identifier of an entry from the Brite database of biological hierarchies.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cancer type
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: A type (represented as a string) of cancer.
deprecated: true
consider: Type
in subset: obsolete

BRENDA organism ID
type: Class
subclass of: Organism accession
Created in: beta12orEarlier
has definition: A unique identifier for an organism used in the BRENDA database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UniGene taxon
type: Class
subclass of: Taxon
Created in: beta12orEarlier
has exact synonym: UniGene organism abbreviation
has definition: The name of a taxon using the controlled vocabulary of the UniGene database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UTRdb taxon
type: Class
subclass of: Taxon
has definition: The name of a taxon using the controlled vocabulary of the UTRdb database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Catalogue ID
type: Class
subclass of: Identifier (typed)
has exact synonym: Catalogue identifier
has definition: An identifier of a catalogue of biological resources.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Molecular interaction
type: Class
subclass of: Core data
has exact synonym: Molecular interaction data
Created in: beta12orEarlier
has definition: Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
has definition: Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).
Created in: beta12orEarlier
has exact synonym: Network
in subset: bioinformatics
in subset: data
in subset: edam

Small molecule data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning one or more small molecules.
Obsolete since: beta13
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true
consider: Small molecule report
in subset: obsolete

Genotype and phenotype data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning a particular genotype, phenotype or a genotype / phenotype relation.
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
consider: Genotype/phenotype annotation
in subset: obsolete

Microarray data
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
comment: This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931
has definition: Image or hybridisation data for a microarray, typically a study of gene expression.
Created in: beta12orEarlier
has exact synonym: Gene expression data
in subset: bioinformatics
in subset: data
in subset: edam

Compound ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Compound accession
has exact synonym: KEGG compound identifier
Created in: beta12orEarlier
has definition: Unique identifier of a chemical compound from the KEGG database.
Regular expression: C[0-9]+
has exact synonym: KEGG compound ID
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Drug ID (KEGG)
type: Class
subclass of: KEGG object identifier
subclass of: Drug accession
Regular expression: D[0-9]+
has definition: Unique identifier of a drug from the KEGG Drug database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ensembl ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.
Regular expression: ENS[A-Z]*[FPTG][0-9]{11}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ICD identifier
type: Class
subclass of: Disease ID
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
Regular expression: [A-Z][0-9]+(\.[-[0-9]+])?
Created in: beta12orEarlier
has definition: An identifier of a disease from the International Classification of Diseases (ICD) database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence cluster ID (CluSTr)
type: Class
subclass of: Sequence cluster ID
has exact synonym: CluSTr cluster ID
Created in: beta12orEarlier
Regular expression: [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?
has exact synonym: CluSTr ID
has definition: Unique identifier of a sequence cluster from the CluSTr database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

KEGG Glycan ID
type: Class
subclass of: KEGG object identifier
subclass of: Carbohydrate accession
Created in: beta12orEarlier
has definition: Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).
Regular expression: G[0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TCDB ID
type: Class
subclass of: Protein family accession
has definition: A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.
Regular expression: [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+
has exact synonym: TC number
comment: OBO file for regular expression.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

MINT ID
type: Class
subclass of: Protein interaction ID
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the MINT database of protein-protein interactions.
Regular expression: MINT\-[0-9]{1,5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

DIP ID
type: Class
subclass of: Protein interaction ID
Regular expression: DIP[\:\-][0-9]{3}[EN]
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the DIP database of protein-protein interactions.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Signaling Gateway protein ID
type: Class
subclass of: Protein accession
Regular expression: A[0-9]{6}
has definition: Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein modification ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has definition: Identifier of a protein modification catalogued in a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

RESID ID
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

RGD ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
has definition: Identifier of an entry from the RGD database.
Created in: beta12orEarlier
Regular expression: [0-9]{4,7}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TAIR accession (protein)
type: Class
subclass of: Sequence accession (protein)
subclass of: TAIR accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
Created in: beta12orEarlier
has definition: Identifier of a protein sequence from the TAIR database.
Regular expression: AASequence:[0-9]{10}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Compound ID (HMDB)
type: Class
subclass of: Compound accession
has definition: Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).
has exact synonym: HMDB ID
Created in: beta12orEarlier
Regular expression: HMDB[0-9]{5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

LIPID MAPS ID
type: Class
subclass of: Lipid accession
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
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

PeptideAtlas ID
type: Class
subclass of: Peptide ID
Regular expression: PAp[0-9]{8}
Created in: beta12orEarlier
has db xref: PDBML:pdbx_PDB_strand_id
has definition: Identifier of a peptide from the PeptideAtlas peptide databases.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Molecular interaction ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Molecular interaction
Created in: beta12orEarlier
has definition: Identifier of a report of molecular interactions from a database (typically).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

BioGRID interaction ID
type: Class
subclass of: Molecular interaction ID
has definition: A unique identifier of an interaction from the BioGRID database.
Created in: beta12orEarlier
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Enzyme ID (MEROPS)
type: Class
subclass of: Enzyme ID
Regular expression: S[0-9]{2}\.[0-9]{3}
has definition: Unique identifier of a peptidase enzyme from the MEROPS database.
Created in: beta12orEarlier
has exact synonym: MEROPS ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Mobile genetic element ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
Created in: beta12orEarlier
has definition: An identifier of a mobile genetic element.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ACLAME ID
type: Class
subclass of: Mobile genetic element ID
has definition: An identifier of a mobile genetic element from the Aclame database.
Regular expression: mge:[0-9]+
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

SGD ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
has definition: Identifier of an entry from the Saccharomyces genome database (SGD).
Created in: beta12orEarlier
Regular expression: PWY[a-zA-Z_0-9]{2}\-[0-9]{3}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Book ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has definition: Unique identifier of a book.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ISBN
type: Class
subclass of: Book ID
has definition: The International Standard Book Number (ISBN) is for identifying printed books.
Regular expression: (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Compound ID (3DMET)
type: Class
subclass of: Compound accession
has definition: Identifier of a metabolite from the 3DMET database.
Created in: beta12orEarlier
has exact synonym: 3DMET ID
Regular expression: B[0-9]{5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

MatrixDB interaction ID
type: Class
subclass of: Molecular interaction ID
Created in: beta12orEarlier
has definition: A unique identifier of an interaction from the MatrixDB database.
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_.*)
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

cPath ID
type: Class
subclass of: Identifier (hybrid)
subclass of: Pathway or network accession
has definition: A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.
Created in: beta12orEarlier
comment: These identifiers are unique within the cPath database, however, they are not stable between releases.
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

PubChem bioassay ID
type: Class
subclass of: Identifier (typed)
subclass of: PubChem ID
Created in: beta12orEarlier
Regular expression: [0-9]+
has definition: Identifier of an assay from the PubChem database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

PubChem ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
has definition: Identifier of an entry from the PubChem database.
Created in: beta12orEarlier
has exact synonym: PubChem identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Reaction ID (MACie)
type: Class
subclass of: Reaction ID
has definition: Identifier of an enzyme reaction mechanism from the MACie database.
has exact synonym: MACie entry number
Regular expression: M[0-9]{4}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (miRBase)
type: Class
subclass of: Gene ID
has exact synonym: miRNA name
Created in: beta12orEarlier
has exact synonym: miRNA identifier
Regular expression: MI[0-9]{7}
has definition: Identifier for a gene from the miRBase database.
has exact synonym: miRNA ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (ZFIN)
type: Class
subclass of: Gene ID
Regular expression: ZDB\-GENE\-[0-9]+\-[0-9]+
Created in: beta12orEarlier
has definition: Identifier for a gene from the Zebrafish information network genome (ZFIN) database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Reaction ID (Rhea)
type: Class
subclass of: Reaction ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme-catalysed reaction from the Rhea database.
Regular expression: [0-9]{5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Compound ID (ChEMBL)
type: Class
subclass of: Compound accession
Regular expression: [0-9]+
Created in: beta12orEarlier
has exact synonym: ChEMBL ID
has definition: Identifier of a small molecular from the ChEMBL database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

LGICdb identifier
type: Class
subclass of: Protein accession
Regular expression: [a-zA-Z_0-9]+
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

PharmGKB ID
type: Class
subclass of: Accession
subclass of: Identifier (hybrid)
Regular expression: PA[0-9]+
has definition: Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (PharmGKB)
type: Class
subclass of: Pathway or network accession
subclass of: PharmGKB ID
has definition: Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Created in: beta12orEarlier
Regular expression: PA[0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Disease ID (PharmGKB)
type: Class
subclass of: Disease ID
subclass of: PharmGKB ID
Regular expression: PA[0-9]+
Created in: beta12orEarlier
has definition: Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Drug ID (PharmGKB)
type: Class
subclass of: PharmGKB ID
subclass of: Drug accession
Regular expression: PA[0-9]+
Created in: beta12orEarlier
has definition: Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Drug ID (TTD)
type: Class
subclass of: Drug accession
Created in: beta12orEarlier
has definition: Identifier of a drug from the Therapeutic Target Database (TTD).
Regular expression: DAP[0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Target ID (TTD)
type: Class
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Identifier of a target protein from the Therapeutic Target Database (TTD).
Regular expression: TTDS[0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell type identifier
type: Class
subclass of: Identifier (typed)
has definition: A unique identifier of a type or group of cells.
has exact synonym: Cell type ID
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NeuronDB ID
type: Class
subclass of: Cell type accession
Created in: beta12orEarlier
has definition: A unique identifier of a neuron from the NeuronDB database.
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NeuroMorpho ID
type: Class
subclass of: Cell type accession
Regular expression: [a-zA-Z_0-9]+
has definition: A unique identifier of a neuron from the NeuroMorpho database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Compound ID (ChemIDplus)
type: Class
subclass of: Compound accession
Created in: beta12orEarlier
Regular expression: [0-9]+
has exact synonym: ChemIDplus ID
has definition: Identifier of a chemical from the ChemIDplus database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (SMPDB)
type: Class
subclass of: Pathway or network accession
Regular expression: SMP[0-9]{5}
has definition: Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

BioNumbers ID
type: Class
subclass of: Accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

T3DB ID
type: Class
subclass of: Toxin accession
has definition: Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.
Regular expression: T3D[0-9]+
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Carbohydrate identifier
type: Class
subclass of: Compound identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Carbohydrate structure report
subclass of: Restriction
  on property: is identifier of
  some values from: Carbohydrate structure
has definition: Identifier of a carbohydrate.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GlycomeDB ID
type: Class
subclass of: Carbohydrate accession
Regular expression: [0-9]+
Created in: beta12orEarlier
has definition: Identifier of an entry from the GlycomeDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

LipidBank ID
type: Class
subclass of: Lipid accession
has definition: Identifier of an entry from the LipidBank database.
Regular expression: [a-zA-Z_0-9]+[0-9]+
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CDD ID
type: Class
subclass of: Protein domain ID
has definition: Identifier of a conserved domain from the Conserved Domain Database.
Regular expression: cd[0-9]{5}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

MMDB ID
type: Class
subclass of: Structure ID
has definition: An identifier of an entry from the MMDB database.
has exact synonym: MMDB accession
Created in: beta12orEarlier
Regular expression: [0-9]{1,5}
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

iRefIndex ID
type: Class
subclass of: Protein interaction ID
Regular expression: [0-9]+
Created in: beta12orEarlier
has definition: Unique identifier of an entry from the iRefIndex database of protein-protein interactions.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ModelDB ID
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (DQCS)
type: Class
subclass of: Pathway or network accession
Created in: beta12orEarlier
has definition: Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ensembl ID (Homo sapiens)
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENS([EGTP])[0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division).
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Bos taurus')
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENSBTA([EGTP])[0-9]{11}
Obsolete since: beta12orEarlier
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division).
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Canis familiaris')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Regular expression: ENSCAF([EGTP])[0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division).
deprecated: true
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Cavia porcellus')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division).
deprecated: true
Regular expression: ENSCPO([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Ciona intestinalis')
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENSCIN([EGTP])[0-9]{11}
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division).
deprecated: true
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Ciona savignyi')
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Regular expression: ENSCSAV([EGTP])[0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Danio rerio')
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENSDAR([EGTP])[0-9]{11}
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division).
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Dasypus novemcinctus')
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Regular expression: ENSDNO([EGTP])[0-9]{11}
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division).
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Echinops telfairi')
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division).
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
Regular expression: ENSETE([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Erinaceus europaeus')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division).
Created in: beta12orEarlier
Regular expression: ENSEEU([EGTP])[0-9]{11}
deprecated: true
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Felis catus')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division).
Regular expression: ENSFCA([EGTP])[0-9]{11}
deprecated: true
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Gallus gallus')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division).
Regular expression: ENSGAL([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Gasterosteus aculeatus')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Regular expression: ENSGAC([EGTP])[0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division).
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Homo sapiens')
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division).
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
Regular expression: ENSHUM([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Loxodonta africana')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Regular expression: ENSLAF([EGTP])[0-9]{11}
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division).
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Macaca mulatta')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Regular expression: ENSMMU([EGTP])[0-9]{11}
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division).
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Monodelphis domestica')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Regular expression: ENSMOD([EGTP])[0-9]{11}
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division).
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Mus musculus')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division).
deprecated: true
Regular expression: ENSMUS([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Myotis lucifugus')
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division).
Obsolete since: beta12orEarlier
deprecated: true
Regular expression: ENSMLU([EGTP])[0-9]{11}
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ("Ornithorhynchus anatinus")
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Regular expression: ENSOAN([EGTP])[0-9]{11}
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division).
deprecated: true
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Oryctolagus cuniculus')
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division).
deprecated: true
Regular expression: ENSOCU([EGTP])[0-9]{11}
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Oryzias latipes')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division).
Created in: beta12orEarlier
deprecated: true
Regular expression: ENSORL([EGTP])[0-9]{11}
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Otolemur garnettii')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Regular expression: ENSSAR([EGTP])[0-9]{11}
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division).
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Pan troglodytes')
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division).
Regular expression: ENSPTR([EGTP])[0-9]{11}
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Rattus norvegicus')
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Regular expression: ENSRNO([EGTP])[0-9]{11}
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division).
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Spermophilus tridecemlineatus')
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division).
Obsolete since: beta12orEarlier
Regular expression: ENSSTO([EGTP])[0-9]{11}
Created in: beta12orEarlier
deprecated: true
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Takifugu rubripes')
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division).
Regular expression: ENSFRU([EGTP])[0-9]{11}
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Tupaia belangeri')
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENSTBE([EGTP])[0-9]{11}
deprecated: true
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division).
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

Ensembl ID ('Xenopus tropicalis')
type: Class
subclass of: Obsolete concept (EDAM)
Regular expression: ENSXET([EGTP])[0-9]{11}
deprecated: true
Created in: beta12orEarlier
has definition: Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division).
Obsolete since: beta12orEarlier
consider: Ensembl ID
in subset: obsolete

CATH identifier
type: Class
subclass of: Protein domain ID
subclass of: Restriction
  on property: is identifier of
  some values from: CATH node
has definition: Identifier of a protein domain (or other node) from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CATH node ID (family)
type: Class
subclass of: CATH node ID
subclass of: Restriction
  on property: is identifier of
  some values from: CATH node
Example: 2.10.10.10
has definition: A code number identifying a family from the CATH database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Enzyme ID (CAZy)
type: Class
subclass of: Enzyme ID
has exact synonym: CAZy ID
Created in: beta12orEarlier
has definition: Identifier of an enzyme from the CAZy enzymes database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Clone ID (IMAGE)
type: Class
subclass of: Clone ID
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: IMAGE cloneID
has exact synonym: I.M.A.G.E. cloneID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GO concept ID (cellular compartment)
type: Class
subclass of: GO concept ID
has exact synonym: GO concept identifier (cellular compartment)
Created in: beta12orEarlier
Regular expression: [0-9]{7}|GO:[0-9]{7}
has definition: An identifier of a 'cellular compartment' concept from the Gene Ontology.
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CleanEx entry name
type: Class
subclass of: Gene expression report ID
has definition: An identifier of a gene expression profile from the CleanEx database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CleanEx dataset code
type: Class
subclass of: Microarray experiment annotation ID
has definition: An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Genome metadata
type: Class
subclass of: Sequence metadata
Created in: beta12orEarlier
has definition: Provenance metadata or other general information concerning a genome as a whole.
in subset: bioinformatics
in subset: data
in subset: edam

Protein ID (CORUM)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a protein complex from the CORUM database.
has exact synonym: CORUM complex ID
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CDD PSSM-ID
type: Class
subclass of: Sequence profile ID
has definition: Unique identifier of a position-specific scoring matrix from the CDD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein ID (CuticleDB)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a protein from the CuticleDB database.
Created in: beta12orEarlier
has exact synonym: CuticleDB ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

DBD ID
type: Class
subclass of: Transcription factor accession
Created in: beta12orEarlier
has definition: Identifier of a predicted transcription factor from the DBD database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Oligonucleotide probe annotation
type: Class
subclass of: Microarray annotation
subclass of: Restriction
  on property: has topic
  some values from: Sequence design
has definition: General annotation on an oligonucleotide probe.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Oligonucleotide ID
type: Class
subclass of: Nucleic acid identifier
subclass of: Molecule accession
Created in: beta12orEarlier
has definition: Identifier of an oligonucleotide from a database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

dbProbe ID
type: Class
subclass of: Oligonucleotide ID
Created in: beta12orEarlier
has definition: Identifier of an oligonucleotide probe from the dbProbe database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Dinucleotide property
type: Class
subclass of: DNA base structural data
has definition: Physicochemical property data for one or more dinucleotides.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

DiProDB ID
type: Class
subclass of: Oligonucleotide ID
has definition: Identifier of an dinucleotide property from the DiProDB database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein features (disordered structure)
type: Class
subclass of: Protein features
subclass of: Protein structure report
has exact synonym: Protein structure report (disordered structure)
has definition: An informative report about disordered structure in a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein ID (DisProt)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a protein from the DisProt database.
Created in: beta12orEarlier
has exact synonym: DisProt ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Embryo report
type: Class
subclass of: Organism report
subclass of: Restriction
  on property: has topic
  some values from: Embryology
Created in: beta12orEarlier
has exact synonym: Embryo annotation
has definition: Annotation on an embryo or concerning embryological development.
in subset: bioinformatics
in subset: data
in subset: edam

Ensembl transcript ID
type: Class
subclass of: Ensembl ID
subclass of: Transcript ID
has definition: Unique identifier for a gene transcript from the Ensembl database.
has exact synonym: Transcript ID (Ensembl)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Inhibitor annotation
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: An informative report on one or more small molecules that are enzyme inhibitors.
Created in: beta12orEarlier
Obsolete since: 1.4
consider: Small molecule report
in subset: obsolete

Promoter ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has db xref: Moby:GeneAccessionList
has definition: An identifier of a promoter of a gene that is catalogued in a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

EST accession
type: Class
subclass of: Clone ID
Created in: beta12orEarlier
has definition: Identifier of an EST sequence.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

COGEME EST ID
type: Class
subclass of: EST accession
has definition: Identifier of an EST sequence from the COGEME database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

COGEME unisequence ID
type: Class
subclass of: EST accession
Created in: beta12orEarlier
comment: A unisequence is a single sequence assembled from ESTs.
has definition: Identifier of a unisequence from the COGEME database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

Family name
type: Class
subclass of: Taxon
has definition: The name of a family of organism.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Genus name (virus)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
has definition: The name of a genus of viruses.
consider: Genus name
in subset: obsolete

Family name (virus)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: The name of a family of viruses.
Obsolete since: beta13
consider: Family name
in subset: obsolete

Database name (SwissRegulon)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: The name of a SwissRegulon database.
Obsolete since: beta13
deprecated: true
consider: Database name
in subset: obsolete

Sequence feature ID (SwissRegulon)
type: Class
subclass of: Sequence feature ID
comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".
has definition: A feature identifier as used in the SwissRegulon database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

FIG ID
type: Class
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the NMPDR database.
comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (Xenbase)
type: Class
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene in the Xenbase database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (Genolist)
type: Class
subclass of: Gene ID
has definition: A unique identifier of gene in the Genolist database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (Genolist)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name of an entry (gene) from the Genolist genes database.
Obsolete since: 1.3
has exact synonym: Genolist gene name
Created in: beta12orEarlier
deprecated: true
consider: Gene symbol
in subset: obsolete

ABS ID
type: Class
subclass of: Promoter ID
has definition: Identifier of an entry (promoter) from the ABS database.
Created in: beta12orEarlier
has exact synonym: ABS identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

AraC-XylS ID
type: Class
subclass of: Transcription factor accession
Created in: beta12orEarlier
has definition: Identifier of a transcription factor from the AraC-XylS database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene name (HUGO)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Name of an entry (gene) from the HUGO database.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Gene name (HGNC)
in subset: obsolete

Locus ID (PseudoCAP)
type: Class
subclass of: Locus ID
has definition: Identifier of a locus from the PseudoCAP database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Locus ID (UTR)
type: Class
subclass of: Locus ID
has definition: Identifier of a locus from the UTR database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

MonosaccharideDB ID
type: Class
subclass of: Monosaccharide accession
Created in: beta12orEarlier
has definition: Unique identifier of a monosaccharide from the MonosaccharideDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Database name (CMD)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: The name of a subdivision of the Collagen Mutation Database (CMD) database.
deprecated: true
Created in: beta12orEarlier
consider: Database name
in subset: obsolete

Database name (Osteogenesis)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: The name of a subdivision of the Osteogenesis database.
Obsolete since: beta13
deprecated: true
Created in: beta12orEarlier
consider: Database name
in subset: obsolete

Genome identifier
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: An identifier of a particular genome.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GenomeReviews ID
type: Class
subclass of: Genome accession
has definition: An identifier of a particular genome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GlycoMap ID
type: Class
subclass of: Carbohydrate accession
has definition: Identifier of an entry from the GlycosciencesDB database.
Created in: beta12orEarlier
Regular expression: [0-9]+
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Carbohydrate conformational map
type: Class
subclass of: Carbohydrate structure report
has definition: A conformational energy map of the glycosidic linkages in a carbohydrate molecule.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (intron)
type: Class
subclass of: Nucleic acid features (mRNA features)
has exact synonym: Gene features (intron)
Created in: beta12orEarlier
has definition: An informative report on an intron in a nucleotide sequences.
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

TCID
type: Class
subclass of: Protein accession
Created in: beta12orEarlier
has definition: Identifier of a membrane transport proteins from the transport classification database (TCDB).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pfam domain name
type: Class
subclass of: Protein family name
Regular expression: PF[0-9]{5}
has definition: Name of a domain from the Pfam database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pfam clan ID
type: Class
subclass of: Protein family accession
has definition: Accession number of a Pfam clan.
Regular expression: CL[0-9]{4}
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (VectorBase)
type: Class
subclass of: Gene ID
has definition: Identifier for a gene from the VectorBase database.
Created in: beta12orEarlier
has exact synonym: VectorBase ID
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence motif metadata
type: Class
subclass of: Metadata
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.
in subset: bioinformatics
in subset: data
in subset: edam

Locus annotation
type: Class
subclass of: Obsolete concept (EDAM)
has definition: An informative report on a particular locus.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has exact synonym: Locus report
consider: Gene annotation
in subset: obsolete

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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Term ID list
type: Class
subclass of: ID list
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.
Created in: beta12orEarlier
has definition: One or more terms from one or more controlled vocabularies which are annotations on an entity.
in subset: bioinformatics
in subset: data
in subset: edam

HAMAP ID
type: Class
subclass of: Protein family accession
Created in: beta12orEarlier
has definition: Name of a protein family from the HAMAP database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Identifier with metadata
type: Class
subclass of: Identifier
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam

Gene symbol annotation
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Annotation about a gene symbol.
Created in: beta12orEarlier
deprecated: true
consider: Identifier with metadata
in subset: obsolete

Transcript ID
type: Class
subclass of: Nucleic acid identifier
subclass of: Molecule accession
subclass of: Restriction
  on property: is identifier of
  some values from: Gene annotation (transcript)
Created in: beta12orEarlier
has definition: Identifier of a RNA transcript.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

HIT ID
type: Class
subclass of: Transcript ID
Created in: beta12orEarlier
has definition: Identifier of an RNA transcript from the H-InvDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

HIX ID
type: Class
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene cluster in the H-InvDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

HPA antibody id
type: Class
subclass of: Protein accession
has definition: Identifier of a antibody from the HPA database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

IMGT/HLA ID
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (JCVI)
type: Class
subclass of: Gene ID
Created in: beta12orEarlier
has definition: A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Kinase name
type: Class
subclass of: Protein name
has definition: The name of a kinase protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ConsensusPathDB entity name
type: Class
subclass of: Name
subclass of: ConsensusPathDB identifier
has definition: Name of a physical entity from the ConsensusPathDB database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

CCAP strain number
type: Class
subclass of: Strain accession
Created in: beta12orEarlier
has definition: The number of a strain of algae and protozoa from the CCAP database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Stock number
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has definition: An identifier of stock from a catalogue of biological resources.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Stock number (TAIR)
type: Class
subclass of: Stock number
has definition: A stock number from The Arabidopsis information resource (TAIR).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

REDIdb ID
type: Class
subclass of: Sequence accession (nucleic acid)
has definition: Identifier of an entry from the RNA editing database (REDIdb).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

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

RNAVirusDB ID
type: Class
subclass of: Virus ID
has definition: A unique identifier for a virus from the RNAVirusDB database.
comment: Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Virus ID
type: Class
subclass of: Organism accession
subclass of: Virus identifier
has definition: An accession of annotation on a (group of) viruses (catalogued in a database).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NCBI Genome Project ID
type: Class
subclass of: Genome accession
Created in: beta12orEarlier
has definition: An identifier of a genome project assigned by NCBI.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NCBI genome accession
type: Class
subclass of: Genome accession
Created in: beta12orEarlier
has definition: A unique identifier of a whole genome assigned by the NCBI.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence profile metadata
type: Class
subclass of: Metadata
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on.
in subset: bioinformatics
in subset: data
in subset: edam

Protein ID (TopDB)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a membrane protein from the TopDB database.
has exact synonym: TopDB ID
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gel ID
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: Identifier of a two-dimensional (protein) gel.
has exact synonym: Gel identifier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Reference map name (SWISS-2DPAGE)
type: Class
subclass of: Name
subclass of: Gel ID
has definition: Name of a reference map gel from the SWISS-2DPAGE database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein ID (PeroxiBase)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a peroxidase protein from the PeroxiBase database.
Created in: beta12orEarlier
has exact synonym: PeroxiBase ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

SISYPHUS ID
type: Class
subclass of: Structure alignment ID
has definition: Identifier of an entry from the SISYPHUS database of tertiary structure alignments.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ORF ID
type: Class
subclass of: Locus ID
subclass of: ORF identifier
has definition: Accession of an open reading frame (catalogued in a database).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ORF identifier
type: Class
subclass of: Identifier (typed)
Created in: beta12orEarlier
has definition: An identifier of an open reading frame.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Linucs ID
type: Class
subclass of: Carbohydrate accession
Created in: beta12orEarlier
has definition: Identifier of an entry from the GlycosciencesDB database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein ID (LGICdb)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a ligand-gated ion channel protein from the LGICdb database.
has exact synonym: LGICdb ID
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

MaizeDB ID
type: Class
subclass of: EST accession
has definition: Identifier of an EST sequence from the MaizeDB database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene ID (MfunGD)
type: Class
subclass of: Gene ID
has definition: A unique identifier of gene in the MfunGD database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Orpha number
type: Class
subclass of: Disease ID
subclass of: Restriction
  on property: is identifier of
  some values from: Disease report
has definition: An identifier of a disease from the Orpha database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein ID (EcID)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a protein from the EcID database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein ID (ConoServer)
type: Class
subclass of: Protein accession
has definition: Unique identifier for a cone snail toxin protein from the ConoServer database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GeneSNP ID
type: Class
subclass of: Sequence variation ID
Created in: beta12orEarlier
has definition: Identifier of a GeneSNP database entry.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Lipid identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Lipid structure report
subclass of: Restriction
  on property: is identifier of
  some values from: Lipid structure
Created in: beta12orEarlier
has definition: Identifier of a lipid.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Databank
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: A flat-file (textual) data archive.
Obsolete since: beta12orEarlier
deprecated: true
in subset: obsolete

Web portal
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: A web site providing data (web pages) on a common theme to a HTTP client.
in subset: obsolete

Gene ID (VBASE2)
type: Class
subclass of: Gene ID
has exact synonym: VBASE2 ID
Created in: beta12orEarlier
has definition: Identifier for a gene from the VBASE2 database.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

DPVweb ID
type: Class
subclass of: Virus ID
has definition: A unique identifier for a virus from the DPVweb database.
Created in: beta12orEarlier
has exact synonym: DPVweb virus ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Pathway ID (BioSystems)
type: Class
subclass of: Pathway or network accession
Regular expression: [0-9]+
has definition: Identifier of a pathway from the BioSystems pathway database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Experimental data (proteomics)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Data concerning a proteomics experiment.
deprecated: true
consider: Experiment annotation (mass spectrometry)
in subset: obsolete

Abstract
type: Class
subclass of: Article metadata
has definition: An abstract of a scientific article.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Lipid structure
type: Class
subclass of: Structure
has definition: 3D coordinate and associated data for a lipid structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Drug structure
type: Class
subclass of: Small molecule structure
has definition: 3D coordinate and associated data for the (3D) structure of a drug.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Position-specific scoring matrix
type: Class
subclass of: Sequence profile
subclass of: Matrix
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Article metadata
type: Class
subclass of: Metadata
subclass of: Article report
subclass of: Restriction
  on property: has topic
  some values from: Literature and reference
has definition: Bibliographic data concerning scientific article(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Ontology concept
type: Class
subclass of: Core data
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
has definition: A concept from a biological ontology.
comment: This includes any fields from the concept definition such as concept name, definition, comments and so on.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Codon usage bias
type: Class
subclass of: Codon usage report
Created in: beta12orEarlier
has definition: A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation (Northern blot)
type: Class
subclass of: Experiment annotation
Created in: beta12orEarlier
has definition: General annotation on a Northern Blot experiment.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (VNTR)
type: Class
subclass of: Nucleic acid features (polymorphism annotation)
comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.
has exact synonym: Variable number of tandem repeat polymorphism
has exact synonym: VNTR annotation
Created in: beta12orEarlier
has definition: Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (microsatellite)
type: Class
subclass of: Nucleic acid features (polymorphism annotation)
Created in: beta12orEarlier
comment: 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.
has exact synonym: Microsatellite annotation
has definition: Annotation on a microsatellite polymorphism in a DNA sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (RFLP)
type: Class
subclass of: Nucleic acid features (polymorphism annotation)
has definition: Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence.
comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.
has exact synonym: RFLP annotation
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Radiation hybrid map
type: Class
subclass of: Physical map
Created in: beta12orEarlier
has exact synonym: RH map
has definition: A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.
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.
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Phylogenetic gene frequencies data
type: Class
subclass of: Phylogenetic continuous quantitative data
has definition: Gene frequencies data that may be read during phylogenetic tree calculation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence set (polymorphic)
type: Class
subclass of: Obsolete concept (EDAM)
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.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta13
consider: Sequence set (nucleic acid)
in subset: obsolete

DRCAT resource
type: Class
subclass of: Data resource definition
Created in: beta12orEarlier
has definition: An entry (resource) from the DRCAT bioinformatics resource catalogue.
in subset: bioinformatics
in subset: data
in subset: edam

Protein complex
type: Class
subclass of: Protein structure
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein structural motif
type: Class
subclass of: Protein structure
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Lipid structure report
type: Class
subclass of: Structure report
has definition: Annotation on or information derived from one or more specific lipid 3D structure(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Secondary structure image
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Image of one or more molecular secondary structures.
Obsolete since: 1.4
Created in: beta12orEarlier
consider: Secondary structure report
in subset: obsolete

Secondary structure report
type: Class
subclass of: Report
has definition: An informative report on general information, properties or features of one or more molecular secondary structures.
Created in: beta12orEarlier
has exact synonym: Secondary structure-derived report
in subset: bioinformatics
in subset: data
in subset: edam

DNA features
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: DNA sequence-specific feature annotation (not in a feature table).
Obsolete since: beta12orEarlier
consider: Nucleic acid features
in subset: obsolete

Nucleic acid features (RNA features)
type: Class
subclass of: Nucleic acid features (gene and transcript structure)
has exact synonym: RNA features
has definition: Features concerning RNA or regions of DNA that encode an RNA molecule.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Plot
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Biological data that is plotted as a graph of some type.
Obsolete since: beta12orEarlier
consider: Image
in subset: obsolete

Nucleic acid features (polymorphism annotation)
type: Class
subclass of: Nucleic acid features (variation)
Created in: beta12orEarlier
has definition: Annotation on a polymorphism.
has exact synonym: Polymorphism annotation
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record (protein)
type: Class
subclass of: Sequence record
subclass of: Protein sequence
has exact synonym: Protein sequence record
Created in: beta12orEarlier
has definition: A protein sequence and associated metadata.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record (nucleic acid)
type: Class
subclass of: Sequence record
subclass of: Nucleic acid sequence
Created in: beta12orEarlier
has exact synonym: Nucleic acid sequence record
has definition: A nucleic acid sequence and associated metadata.
has exact synonym: Nucleotide sequence record
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record full (protein)
type: Class
subclass of: Sequence record full
subclass of: Sequence record (protein)
Created in: beta12orEarlier
has definition: A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
has db xref: SO:2000061
in subset: bioinformatics
in subset: data
in subset: edam

Sequence record full (nucleic acid)
type: Class
subclass of: Sequence record full
subclass of: Sequence record (nucleic acid)
has db xref: SO:2000061
Created in: beta12orEarlier
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: bioinformatics
in subset: data
in subset: edam

Biological model accession
type: Class
subclass of: Biological model ID
subclass of: Accession
has definition: Accession of a mathematical model, typically an entry from a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Cell type accession
type: Class
subclass of: Accession
subclass of: Cell type identifier
has definition: Accession of a type or group of cells (catalogued in a database).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Compound accession
type: Class
subclass of: Compound identifier
subclass of: Molecule accession
has exact synonym: Chemical compound accession
Created in: beta12orEarlier
has definition: Accession of an entry from a database of chemicals.
has exact synonym: Small molecule accession
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Drug accession
type: Class
subclass of: Drug identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession of a drug.
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Toxin accession
type: Class
subclass of: Accession
subclass of: Toxin identifier
has definition: Accession of a toxin (catalogued in a database).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Monosaccharide accession
type: Class
subclass of: Monosaccharide identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession of a monosaccharide (catalogued in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Drug name
type: Class
subclass of: Compound name
subclass of: Drug identifier
has definition: Common name of a drug.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Carbohydrate accession
type: Class
subclass of: Carbohydrate identifier
subclass of: Molecule accession
Created in: beta12orEarlier
has definition: Accession of an entry from a database of carbohydrates.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Molecule accession
type: Class
subclass of: Molecule identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession of a specific molecule (catalogued in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Data resource definition accession
type: Class
subclass of: Data resource definition ID
subclass of: Accession
has definition: Accession of a data definition (catalogued in a database).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Genome accession
type: Class
subclass of: Accession
subclass of: Genome identifier
Created in: beta12orEarlier
has definition: An accession of a particular genome (in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Map accession
type: Class
subclass of: Accession
subclass of: Map identifier
Created in: beta12orEarlier
has definition: An accession of a map of a molecular sequence (deposited in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Lipid accession
type: Class
subclass of: Lipid identifier
subclass of: Molecule accession
has definition: Accession of an entry from a database of lipids.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Peptide ID
type: Class
subclass of: Peptide identifier
subclass of: Molecule accession
has definition: Accession of a peptide deposited in a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein accession
type: Class
subclass of: Protein identifier
subclass of: Molecule accession
has definition: Accession of a protein deposited in a database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Organism accession
type: Class
subclass of: Organism identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: An accession of annotation on a (group of) organisms (catalogued in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Organism name
type: Class
subclass of: Organism identifier
subclass of: Name
has definition: The name of an organism (or group of organisms).
has db xref: Moby:OrganismsLongName
Created in: beta12orEarlier
has db xref: Moby:InfraspecificEpithet
has db xref: Moby:FirstEpithet
has db xref: Moby:BriefOccurrenceRecord
has db xref: Moby:OccurrenceRecord
has db xref: Moby:OrganismsShortName
has db xref: Moby:Organism_Name
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein family accession
type: Class
subclass of: Protein family identifier
subclass of: Accession
Created in: beta12orEarlier
has definition: Accession of a protein family (that is deposited in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Transcription factor accession
type: Class
subclass of: Transcription factor identifier
subclass of: Accession
subclass of: Protein accession
has definition: Accession of an entry from a database of transcription factors or binding sites.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
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
has definition: Identifier of a strain of an organism variant, typically a plant, virus or bacterium.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Virus identifier
type: Class
subclass of: Organism identifier
Created in: beta12orEarlier
has definition: An accession of annotation on a (group of) viruses (catalogued in a database).
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence features metadata
type: Class
subclass of: Sequence metadata
has definition: Metadata on sequence features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Gramene identifier
type: Class
subclass of: Sequence accession (protein)
has definition: Identifier of a Gramene database entry.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

DDBJ accession
type: Class
subclass of: EMBL/GenBank/DDBJ ID
has definition: An identifier of an entry from the DDBJ sequence database.
has exact synonym: DDBJ identifier
has exact synonym: DDBJ ID
Created in: beta12orEarlier
has exact synonym: DDBJ accession number
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ConsensusPathDB identifier
type: Class
subclass of: Identifier (hybrid)
has definition: An identifier of an entity from the ConsensusPathDB database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning molecular sequence(s).
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
consider: Sequence
consider: Sequence report
in subset: obsolete

Codon usage data
type: Class
subclass of: Obsolete concept (EDAM)
comment: This is a broad data type and is used a placeholder for other, more specific types.
has definition: Data concerning codon usage.
Obsolete since: beta13
deprecated: true
Created in: beta12orEarlier
consider: Codon usage report
consider: Codon usage table
in subset: obsolete

Article report
type: Class
subclass of: Report
has definition: Data concerning or derived from the analysis of a scientific article.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Sequence report
type: Class
subclass of: Report
has definition: An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata).
has exact synonym: Sequence-derived report
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein secondary structure report
type: Class
subclass of: Secondary structure report
Created in: beta12orEarlier
has definition: An informative report about the properties or features of one or more protein secondary structures.
in subset: bioinformatics
in subset: data
in subset: edam

Hopp and Woods plot
type: Class
subclass of: Peptide immunogenicity data
Created in: beta12orEarlier
has definition: A Hopp and Woods plot of predicted antigenicity of a peptide or protein.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid melting curve
type: Class
subclass of: Nucleic acid melting profile
Created in: beta12orEarlier
has definition: A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
comment: Shows the proportion of nucleic acid which are double-stranded versus temperature.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid probability profile
type: Class
subclass of: Nucleic acid melting profile
comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature
has definition: A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid temperature profile
type: Class
subclass of: Nucleic acid melting profile
has exact synonym: Melting map
Created in: beta12orEarlier
comment: Plots melting temperature versus base position.
has definition: A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
in subset: bioinformatics
in subset: data
in subset: edam

Pathway or network (gene regulation)
type: Class
subclass of: Pathway or network
subclass of: Restriction
  on property: has topic
  some values from: Gene regulatory networks
Created in: beta12orEarlier
has definition: A report typically including a map (diagram) of a gene regulatory network.
in subset: bioinformatics
in subset: data
in subset: edam

2D PAGE image (annotated)
type: Class
subclass of: 2D PAGE image
has exact synonym: 2D PAGE image annotation
Created in: beta12orEarlier
has definition: An informative report on a two-dimensional (2D PAGE) gel.
in subset: bioinformatics
in subset: data
in subset: edam

Oligonucleotide probe sets annotation
type: Class
subclass of: Oligonucleotide probe annotation
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Microarray image
type: Class
subclass of: Microarray data
subclass of: Image
has definition: An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.
has exact synonym: Gene expression image
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Image
type: Class
subclass of: Core data
has definition: Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type.
Created in: beta12orEarlier
has exact synonym: Image data
in subset: bioinformatics
in subset: data
in subset: edam
has broad synonym: SIO_000079
has narrow synonym: SIO_000081

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: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Workflow data
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Data concerning a computational workflow.
Obsolete since: beta13
Created in: beta12orEarlier
consider: Workflow metadata
consider: Workflow
in subset: obsolete

Workflow
type: Class
subclass of: Core data
has definition: A computational workflow.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Secondary structure data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning molecular secondary structure data.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: Secondary structure
consider: Secondary structure report
in subset: obsolete

Raw sequence (protein)
type: Class
subclass of: Raw sequence
subclass of: Protein sequence
has definition: A raw protein sequence (string of characters).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Raw sequence (nucleic acid)
type: Class
subclass of: Raw sequence
subclass of: Nucleic acid sequence
has definition: A raw nucleic acid sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein sequence
type: Class
subclass of: Sequence
Created in: beta12orEarlier
has definition: One or more protein sequences, possibly with associated annotation.
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: AminoAcidSequenceInformation

Nucleic acid sequence
type: Class
subclass of: Sequence
has exact synonym: Nucleic acid sequences
has definition: One or more nucleic acid sequences, possibly with associated annotation.
has exact synonym: Nucleotide sequences
has exact synonym: Nucleotide sequence
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam
has related synonym: NucleotideSequenceInformation

Reaction data
type: Class
subclass of: Core data
has definition: Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.
has exact synonym: Reaction annotation
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
has exact synonym: Enzyme kinetics annotation
in subset: bioinformatics
in subset: data
in subset: edam

Peptide property
type: Class
subclass of: Molecular property
has definition: Data concerning small peptides.
has exact synonym: Peptide data
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Protein classification
type: Class
subclass of: Protein report
subclass of: Classification
subclass of: Restriction
  on property: has topic
  some values from: Protein families
Created in: beta12orEarlier
has definition: Data concerning the classification of protein sequences or structures.
has exact synonym: Protein classification data
comment: This is a broad data type and is used a placeholder for other, more specific types.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence motif data
type: Class
subclass of: Obsolete concept (EDAM)
comment: This is a broad data type and is used a placeholder for other, more specific types.
Created in: beta12orEarlier
has definition: Data concerning specific or conserved pattern in molecular sequences.
Obsolete since: beta13
deprecated: true
consider: Sequence motif
in subset: obsolete

Sequence profile data
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data concerning models representing a (typically multiple) sequence alignment.
Obsolete since: beta13
comment: This is a broad data type and is used a placeholder for other, more specific types.
deprecated: true
Created in: beta12orEarlier
consider: Sequence profile
in subset: obsolete

Pathway or network data
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
has definition: Data concerning a specific biological pathway or network.
consider: Pathway or network
consider: Pathway or network report
in subset: obsolete

Pathway or network report
type: Class
subclass of: Report
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
has definition: An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid thermodynamic data
type: Class
subclass of: Nucleic acid property
Created in: beta12orEarlier
has exact synonym: Nucleic acid thermodynamic property
has definition: A thermodynamic or kinetic property of a nucleic acid molecule.
has exact synonym: Nucleic acid property (thermodynamic or kinetic)
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid classification
type: Class
subclass of: Nucleic acid report
subclass of: Classification
subclass of: Restriction
  on property: has topic
  some values from: Gene families
comment: This is a broad data type and is used a placeholder for other, more specific types.
has exact synonym: Nucleic acid classification data
has definition: Data concerning the classification of nucleic acid sequences or structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

Classification
type: Class
subclass of: Core data
has exact synonym: Classification data
has definition: Data concerning a classification of molecular sequences, structures or other entities.
Created in: beta12orEarlier
comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (key folding sites)
type: Class
subclass of: Protein features
Created in: beta12orEarlier
has definition: A report on key residues involved in protein folding.
in subset: bioinformatics
in subset: data
in subset: edam

Protein torsion angle data
type: Class
subclass of: Protein property
Created in: beta12orEarlier
has definition: Torsion angle data for a protein structure.
has exact synonym: Torsion angle data
in subset: bioinformatics
in subset: data
in subset: edam

Protein structure image
type: Class
subclass of: Structure image
subclass of: Protein image
has exact synonym: Structure image (protein)
Created in: beta12orEarlier
has definition: An image of protein structure.
in subset: bioinformatics
in subset: data
in subset: edam

Phylogenetic character weights
type: Class
subclass of: Phylogenetic raw data
Created in: beta12orEarlier
has definition: Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence annotation track
type: Class
subclass of: Feature record
has exact synonym: Genome track
has exact synonym: Genome-browser track
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: Annotation track
has exact synonym: Genomic track
has exact synonym: Genome annotation track
Created in: beta12orEarlier
in subset: bioinformatics
in subset: data
in subset: edam

UniProt accession
type: Class
subclass of: Sequence accession (protein)
subclass of: Restriction
  on property: is identifier of
  some values from: Sequence record
has exact synonym: UniProt accession number
has exact synonym: UniProtKB accession
has definition: Accession number of a UniProt (protein sequence) database entry.
has narrow synonym: TrEMBL entry accession
has narrow synonym: Swiss-Prot entry accession
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 exact synonym: UniProt entry accession
Example: P43353|Q7M1G0|Q9C199|A5A6J6
Created in: beta12orEarlier
has exact synonym: UniProtKB accession number
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

NCBI genetic code ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
has definition: Identifier of a genetic code in the NCBI list of genetic codes.
Created in: beta12orEarlier
Example: 16
Regular expression: [1-9][0-9]?
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Ontology concept identifier
type: Class
subclass of: Identifier (typed)
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

GO concept name (biological process)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: The name of a concept for a biological process from the GO ontology.
deprecated: true
consider: Ontology concept name
in subset: obsolete

GO concept name (molecular function)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: The name of a concept for a molecular function from the GO ontology.
deprecated: true
Created in: beta12orEarlier
consider: Ontology concept name
in subset: obsolete

Taxonomy
type: Class
subclass of: Classification
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
has exact synonym: Taxonomic data
has definition: Data concerning the classification, identification and naming of organisms.
Created in: beta12orEarlier
comment: This is a broad data type and is used a placeholder for other, more specific types.
in subset: bioinformatics
in subset: data
in subset: edam

Protein ID (EMBL/GenBank/DDBJ)
type: Class
subclass of: Protein accession
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.
has definition: EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Core data
type: Class
subclass of: Data
Created in: beta13
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.
comment: Core data entities typically have a format and may be identified by an accession number.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence feature identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Feature record
has definition: Name or other identifier of molecular sequence feature(s).
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Structure identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Structure
has definition: An identifier of a molecular tertiary structure, typically an entry from a structure database.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Matrix identifier
type: Class
subclass of: Identifier (typed)
subclass of: Restriction
  on property: is identifier of
  some values from: Matrix
Created in: beta13
has definition: An identifier of an array of numerical values, such as a comparison matrix.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Protein sequence composition
type: Class
subclass of: Sequence composition
has exact synonym: Sequence property (protein composition)
has definition: A report (typically a table) on character or word composition / frequency of protein sequence(s).
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid sequence composition
type: Class
subclass of: Nucleic acid property
subclass of: Sequence composition
Created in: beta13
has definition: A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).
has exact synonym: Sequence property (nucleic acid composition)
in subset: bioinformatics
in subset: data
in subset: edam

Protein domain classification node
type: Class
subclass of: Protein domain classification
has definition: A node from a classification of protein structural domain(s).
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

CAS number
type: Class
subclass of: Drug accession
has definition: Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
has exact synonym: CAS registry number
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

ATC code
type: Class
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

UNII
type: Class
subclass of: Compound identifier
has exact synonym: Unique Ingredient Identifier
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).
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Geotemporal metadata
type: Class
subclass of: Metadata
has definition: Basic information concerning geographical location or time.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

System metadata
type: Class
subclass of: Metadata
Created in: beta13
has definition: Metadata concerning the software, hardware or other aspects of a computer system.
in subset: bioinformatics
in subset: data
in subset: edam

Sequence feature name
type: Class
subclass of: Name
subclass of: Sequence feature identifier
Created in: beta13
has definition: A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Experimental measurement
type: Class
subclass of: Core data
has narrow synonym: Raw experimental data
has exact synonym: Measurement data
has narrow synonym: Measurement metadata
has exact synonym: Experimentally measured data
has exact synonym: Measured 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.
has exact synonym: Measurement
has exact synonym: Experimental measurement data
has definition: Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Raw microarray data
type: Class
subclass of: Experimental measurement
subclass of: Microarray hybridisation data
comment: Such data as found in Affymetrix CEL or GPR files.
has definition: Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Processed microarray data
type: Class
subclass of: Gene expression profile
subclass of: Microarray hybridisation data
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.
has exact synonym: Gene expression report
has exact synonym: Microarray probe set data
Created in: beta13
has exact synonym: Gene annotation (expression)
has definition: Data generated from processing and analysis of probe set data from a microarray experiment.
in subset: bioinformatics
in subset: data
in subset: edam

Normalised microarray data
type: Class
subclass of: Microarray hybridisation data
has exact synonym: Gene expression data matrix
has definition: The final processed (normalised) data for a set of hybridisations in a microarray experiment.
comment: This combines data from all hybridisations.
Created in: beta13
has exact synonym: Gene expression matrix
in subset: bioinformatics
in subset: data
in subset: edam

Sample annotation
type: Class
subclass of: Experiment annotation (microarray)
Created in: beta13
comment: This might include compound and dose in a dose response experiment.
has definition: Annotation on a biological sample, for example experimental factors and their values.
in subset: bioinformatics
in subset: data
in subset: edam

Microarray annotation
type: Class
subclass of: Experiment annotation (microarray)
Created in: beta13
has definition: Annotation on the array itself used in a microarray experiment.
comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.
in subset: bioinformatics
in subset: data
in subset: edam

Microarray protocol annotation
type: Class
subclass of: Experiment annotation (microarray)
has definition: Annotation on laboratory and/or data processing protocols used in an microarray experiment.
Created in: beta13
comment: This might describe e.g. the normalisation methods used to process the raw data.
in subset: bioinformatics
in subset: data
in subset: edam

Microarray hybridisation data
type: Class
subclass of: Microarray data
Created in: beta13
has definition: Data concerning the hybridisations measured during a microarray experiment.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (topological domains)
type: Class
subclass of: Protein features
subclass of: Restriction
  on property: has topic
  some values from: Protein domains and folds
has definition: Summary of topological domains such as cytoplasmic regions in a protein.
Created in: beta13
has exact synonym: Protein topological domains
in subset: bioinformatics
in subset: data
in subset: edam

Sequence features (compositionally-biased regions)
type: Class
subclass of: Sequence composition
has definition: A report of regions in a molecular sequence that are biased to certain characters.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (sequence variants)
type: Class
subclass of: Protein features
has definition: A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (difference and change)
type: Class
subclass of: Nucleic acid features
has definition: A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (expression signal)
type: Class
subclass of: Nucleic acid features
has definition: A report on regions within a nucleic acid sequence containing a signal that alters a biological function.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (binding)
type: Class
subclass of: Nucleic acid features
has definition: A report on regions of a nucleic acid sequence that bind some other molecule.
comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (repeats)
type: Class
subclass of: Nucleic acid features
subclass of: Sequence features (repeats)
Created in: beta13
has definition: A report on repetitive elements within a nucleic acid sequence.
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.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (replication and recombination)
type: Class
subclass of: Nucleic acid features
comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.
has definition: A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (structure)
type: Class
subclass of: Nucleic acid features
Created in: beta13
has definition: A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (repeats)
type: Class
subclass of: Protein features
subclass of: Sequence features (repeats)
Created in: beta13
has definition: Location of short repetitive subsequences (repeat sequences) in a protein sequence.
in subset: bioinformatics
in subset: data
in subset: edam

Protein features (motifs)
type: Class
subclass of: Protein features
subclass of: Sequence features (motifs)
comment: Use this concept if another, more specific concept is not available.
Created in: beta13
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: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (motifs)
type: Class
subclass of: Nucleic acid features
subclass of: Sequence features (motifs)
Created in: beta13
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.
comment: Use this concept if another, more specific concept is not available.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (d-loop)
type: Class
subclass of: Nucleic acid features (structure)
comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
has definition: A report on displacement loops in a mitochondrial DNA sequence.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (stem loop)
type: Class
subclass of: Nucleic acid features (structure)
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.
has definition: A report on stem loops in a DNA sequence.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (mRNA features)
type: Class
subclass of: Nucleic acid features (RNA features)
Created in: beta13
has definition: Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.
comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
has exact synonym: mRNA features
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (signal or transit peptide)
type: Class
subclass of: Nucleic acid features (mRNA features)
Created in: beta13
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.
has definition: A report on a coding sequence for a signal or transit peptide.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (non-coding RNA)
type: Class
subclass of: Nucleic acid features (RNA features)
has exact synonym: Non-coding RNA features
Created in: beta13
has definition: Features concerning non-coding or functional RNA molecules, including tRNA and rRNA.
has exact synonym: ncRNA features
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (transcriptional)
type: Class
subclass of: Nucleic acid features (RNA features)
Created in: beta13
has definition: Features concerning transcription of DNA into RNA including the regulation of transcription.
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.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (STS)
type: Class
subclass of: Nucleic acid features
Created in: beta13
has definition: A report on sequence tagged sites (STS) in nucleic acid sequences.
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.
in subset: bioinformatics
in subset: data
in subset: edam

Nucleic acid features (immunoglobulin gene structure)
type: Class
subclass of: Nucleic acid features (gene and transcript structure)
has definition: A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

SCOP class
type: Class
subclass of: SCOP node
has definition: Information on a 'class' node from the SCOP database.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

SCOP fold
type: Class
subclass of: SCOP node
has definition: Information on a 'fold' node from the SCOP database.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

SCOP superfamily
type: Class
subclass of: SCOP node
has definition: Information on a 'superfamily' node from the SCOP database.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

SCOP family
type: Class
subclass of: SCOP node
Created in: beta13
has definition: Information on a 'family' node from the SCOP database.
in subset: bioinformatics
in subset: data
in subset: edam

SCOP protein
type: Class
subclass of: SCOP node
Created in: beta13
has definition: Information on a 'protein' node from the SCOP database.
in subset: bioinformatics
in subset: data
in subset: edam

SCOP species
type: Class
subclass of: SCOP node
has definition: Information on a 'species' node from the SCOP database.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation (mass spectrometry)
type: Class
subclass of: Experiment annotation
has definition: General annotation on a mass spectrometry experiment.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Gene family annotation
type: Class
subclass of: Gene annotation
subclass of: Nucleic acid classification
has definition: An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Protein image
type: Class
subclass of: Protein report
has definition: An image of a protein.
Created in: beta13
in subset: bioinformatics
in subset: data
in subset: edam

Protein alignment
type: Class
subclass of: Protein report
subclass of: Alignment
Created in: beta13
has definition: An alignment of protein sequences and/or structures.
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation (sequencing)
type: Class
subclass of: Experiment annotation
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
has definition: Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.
Created in: 1.0
in subset: bioinformatics
in subset: data
in subset: edam

Sequence assembly report
type: Class
subclass of: Sequence alignment report
subclass of: Sequence report
has exact synonym: Assembly report
comment: This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.
Created in: 1.1
has definition: An informative report about a DNA sequence assembly.
in subset: bioinformatics
in subset: data
in subset: edam

Genome index
type: Class
subclass of: Data index
has definition: An index of a genome sequence.
comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
Created in: 1.1
in subset: bioinformatics
in subset: data
in subset: edam

Experiment annotation (GWAS)
type: Class
subclass of: Experiment annotation
has exact synonym: Experiment annotation (genome-wide association study)
has definition: Metadata on a genome-wide association study (GWAS).
Created in: 1.1
in subset: bioinformatics
in subset: data
in subset: edam

Cytoband position
type: Class
subclass of: Sequence coordinates
comment: Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.
has definition: The position of a cytogenetic band in a genome.
Created in: 1.2
in subset: bioinformatics
in subset: data
in subset: edam

Cell type ontology ID
type: Class
subclass of: Ontology concept ID
subclass of: Cell type accession
Created in: beta12orEarlier
Regular expression: CL_[0-9]{7}
Created in: 1.2
has definition: Cell type ontology concept ID.
has exact synonym: CL ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Kinetic model
type: Class
subclass of: Pathway or network
has definition: Mathematical model of a network, that contains biochemical kinetics.
Created in: 1.2
in subset: bioinformatics
in subset: data
in subset: edam

COSMIC ID
type: Class
subclass of: Sequence variation ID
Created in: 1.3
has exact synonym: cosmic identifier
has exact synonym: COSMIC identifier
has exact synonym: cosmic id
has definition: Identifier of a COSMIC database entry.
has exact synonym: cosmic ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

HGMD ID
type: Class
subclass of: Sequence variation ID
has exact synonym: hgmd identifier
has definition: Identifier of a HGMD database entry.
has exact synonym: hgmd id
has exact synonym: HGMD identifier
Created in: beta12orEarlier
has exact synonym: hgmd ID
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence assembly ID
type: Class
subclass of: Sequence set ID
Created in: 1.3
has definition: Unique identifier of sequence assembly.
has narrow synonym: Sequence assembly version
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Sequence feature type
type: Class
subclass of: Type
Created in: 1.3
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: bioinformatics
in subset: data
in subset: edam

Gene annotation (homology)
type: Class
subclass of: Gene annotation
comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
has definition: An informative report on gene homologues between species.
has exact synonym: Homology information
Created in: beta12orEarlier
has exact synonym: Gene annotation (homology information)
in subset: bioinformatics
in subset: data
in subset: edam

Ensembl gene tree ID
type: Class
subclass of: Phylogenetic tree ID
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Gene tree
type: Class
subclass of: Phylogenetic tree
has definition: A phylogenetic tree that is an estimate of the character's phylogeny.
Created in: 1.3
in subset: bioinformatics
in subset: data
in subset: edam

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: bioinformatics
in subset: data
in subset: edam

Sample ID
type: Class
subclass of: Identifier (typed)
subclass of: Accession
subclass of: Restriction
  on property: is identifier of
  some values from: Sample annotation
has definition: Name or other identifier of an entry from a biosample database.
has exact synonym: Sample accession
Created in: 1.3
in subset: bioinformatics
in subset: data
in subset: edam
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: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Phenotype name
type: Class
subclass of: Identifier (typed)
subclass of: Name
has exact synonym: Phenotype
Created in: 1.3
has exact synonym: Phenotypes
has definition: Name of a phenotype.
in subset: bioinformatics
in subset: data
in subset: edam
in subset: identifiers

Transition matrix
type: Class
subclass of: Matrix
Created in: 1.4
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.
has definition: A HMM transition matrix contains the probabilities of switching from one HMM state to another.
in subset: data

Emission matrix
type: Class
subclass of: Matrix
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.
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.
in subset: data

Hidden Markov model
type: Class
subclass of: Biological model
has definition: A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.
Created in: 1.4
in subset: data

Format identifier
type: Class
subclass of: Identifier (typed)
Created in: 1.4
has definition: An identifier of a data format.
in subset: data

SMILES
type: Class
subclass of: Chemical formula format
subclass of: Textual format
has definition: Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.
Created in: beta12orEarlier
has db xref: Simplified molecular input line entry specification
Documentation: Simplified molecular input line entry specification
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: theory.smiles.html
Documentation: theory.smiles.html

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: bioinformatics
in subset: edam
in subset: formats

mf
type: Class
subclass of: Chemical formula format
subclass of: Textual format
comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range.
Created in: beta12orEarlier
has definition: Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.
in subset: bioinformatics
in subset: edam
in subset: formats

inchikey
type: Class
subclass of: Chemical formula format
subclass of: Textual format
comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.
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: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
in subset: formats

unambiguous pure
type: Class
subclass of: pure
subclass of: unambiguous sequence
has definition: Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

nucleotide
type: Class
subclass of: Textual format
subclass of: Raw sequence format
has definition: Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.
Created in: beta12orEarlier
comment: Non-sequence characters may be used for example for gaps.
has related synonym: Nucleotide sequence
in subset: bioinformatics
in subset: edam
in subset: formats

protein
type: Class
subclass of: Textual format
subclass of: Raw sequence format
comment: Non-sequence characters may be used for gaps and translation stop.
Created in: beta12orEarlier
has definition: Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.
has related synonym: Amino acid sequence
in subset: bioinformatics
in subset: edam
in subset: formats

consensus
type: Class
subclass of: unpure
subclass of: ambiguous
has definition: Alphabet for the consensus of two or more molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

pure nucleotide
type: Class
subclass of: nucleotide
subclass of: pure
has definition: Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

unambiguous pure nucleotide
type: Class
subclass of: unambiguous pure
subclass of: nucleotide
has definition: Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

dna
type: Class
subclass of: nucleotide
has definition: Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.
Created in: beta12orEarlier
has related synonym: DNA sequence
in subset: bioinformatics
in subset: edam
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.
has related synonym: RNA sequence
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

unambiguous pure protein
type: Class
subclass of: unambiguous pure
subclass of: protein
has definition: Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

pure protein
type: Class
subclass of: protein
subclass of: pure
has definition: Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

UniGene entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
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.
has definition: Format of an entry from UniGene.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

COG sequence cluster format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of an entry from the COG database of clusters of (related) protein sequences.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

EMBL feature location
type: Class
subclass of: Sequence range format
subclass of: Textual format
has definition: Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.
has exact synonym: Feature location
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Sanger inverted repeats
type: Class
subclass of: Sequence features (repeats) format
subclass of: Textual format
has definition: Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

est2genome format
type: Class
subclass of: Gene features (coding region) format
subclass of: Textual format
has definition: Format of a report on exon-intron structure generated by EMBOSS est2genome.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

restover format
type: Class
subclass of: Nucleic acid features (restriction sites) format
subclass of: Textual format
has definition: Report format for restriction enzyme recognition sites used by EMBOSS restover program.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

REBASE restriction sites
type: Class
subclass of: Nucleic acid features (restriction sites) format
subclass of: Textual format
has definition: Report format for restriction enzyme recognition sites used by REBASE database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

FASTA search results format
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using FASTA.
in subset: bioinformatics
in subset: edam
in subset: formats

BLAST results
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
comment: This includes score data, alignment data and summary table.
Created in: beta12orEarlier
has definition: Format of results of a sequence database search using some variant of BLAST.
in subset: bioinformatics
in subset: edam
in subset: formats

mspcrunch
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
has definition: Format of results of a sequence database search using some variant of MSPCrunch.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Smith-Waterman format
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
has definition: Format of results of a sequence database search using some variant of Smith Waterman.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

dhf
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
has definition: Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.
comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

lhf
type: Class
subclass of: Database hits (sequence) format
subclass of: Textual format
comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database.
has definition: Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
in subset: formats

InterPro protein view report format
type: Class
subclass of: InterPro hits format
Created in: beta12orEarlier
comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.
has definition: Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.
in subset: bioinformatics
in subset: edam
in subset: formats

InterPro match table format
type: Class
subclass of: InterPro hits format
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.
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: bioinformatics
in subset: edam
in subset: formats

HMMER Dirichlet prior
type: Class
subclass of: Dirichlet distribution format
subclass of: Textual format
has definition: Dirichlet distribution HMMER format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

MEME Dirichlet prior
type: Class
subclass of: Dirichlet distribution format
subclass of: Textual format
has definition: Dirichlet distribution MEME format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

JASPAR format
type: Class
subclass of: Sequence profile format
subclass of: Textual format
has definition: A profile (sequence classifier) in the format used in the JASPAR database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

HMMER-aln
type: Class
subclass of: FASTA-like (text)
subclass of: Textual format
subclass of: Alignment format (text)
has definition: FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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.
comment: The format is clustal-like and includes annotation of domain family classification information.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence-MEME profile alignment
type: Class
subclass of: Sequence-profile alignment format
subclass of: Textual format
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylip distance matrix
type: Class
subclass of: Sequence distance matrix format
subclass of: Textual format
has definition: Format of PHYLIP phylogenetic distance matrix data.
Created in: beta12orEarlier
comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).
in subset: bioinformatics
in subset: edam
in subset: formats

ClustalW dendrogram
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
has definition: Dendrogram (tree file) format generated by ClustalW.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylip continuous quantitative characters
type: Class
subclass of: Phylogenetic continuous quantitative character format
subclass of: Textual format
has definition: PHYLIP file format for continuous quantitative character data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Phylogenetic property values format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Format of phylogenetic property data.
consider: Phylogenetic character data format
in subset: obsolete

Phylip character frequencies format
type: Class
subclass of: Phylogenetic continuous quantitative character format
subclass of: Textual format
has definition: PHYLIP file format for phylogenetics character frequency data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylip cliques format
type: Class
subclass of: Phylogenetic tree report (cliques) format
subclass of: Textual format
has definition: Format of PHYLIP cliques data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

TreeBASE format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
has definition: The format of an entry from the TreeBASE database of phylogenetic data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

TreeFam format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
has definition: The format of an entry from the TreeFam database of phylogenetic data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

dssp
type: Class
subclass of: Protein secondary structure format
subclass of: Textual format
has definition: Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
in subset: formats

Dot-bracket format
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
has exact synonym: Vienna RNA secondary structure format
has exact synonym: Vienna RNA format
has definition: Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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
has definition: Format of an entry (or part of an entry) from the PDB database.
Created in: beta12orEarlier
has exact synonym: PDB entry format
in subset: bioinformatics
in subset: edam
in subset: formats

PDB format
type: Class
subclass of: PDB database entry format
subclass of: Textual format
has definition: Entry format of PDB database in PDB format.
Created in: beta12orEarlier
has exact synonym: PDB
in subset: bioinformatics
in subset: edam
in subset: formats

mmCIF
type: Class
subclass of: PDB database entry format
subclass of: Textual format
has exact synonym: mmcif
Created in: beta12orEarlier
has definition: Entry format of PDB database in mmCIF format.
has exact synonym: Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Domainatrix 3D-1D scoring matrix format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
in subset: obsolete

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: bioinformatics
in subset: edam
in subset: formats

IntEnz enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
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.
has definition: Format of an entry from IntEnz (The Integrated Relational Enzyme Database).
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

BRENDA enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Format of an entry from the BRENDA enzyme database.
deprecated: true
consider: HTML
in subset: obsolete

KEGG REACTION enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Format of an entry from the KEGG REACTION database of biochemical reactions.
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

KEGG ENZYME enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Format of an entry from the KEGG ENZYME database.
deprecated: true
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

REBASE proto enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: Format of an entry from the proto section of the REBASE enzyme database.
consider: HTML
in subset: obsolete

REBASE withrefm enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of an entry from the withrefm section of the REBASE enzyme database.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

Pcons report format
type: Class
subclass of: Protein structure report (quality evaluation) format
subclass of: Textual format
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.
Created in: beta12orEarlier
has definition: Format of output of the Pcons Model Quality Assessment Program (MQAP).
in subset: bioinformatics
in subset: edam
in subset: formats

ProQ report format
type: Class
subclass of: Protein structure report (quality evaluation) format
subclass of: Textual format
has definition: Format of output of the ProQ protein model quality predictor.
comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

SMART domain assignment report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
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.
has definition: Format of SMART domain assignment data.
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

BIND entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Entry format for the BIND database of protein interaction.
consider: HTML
in subset: obsolete

IntAct entry format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format for the IntAct database of protein interaction.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

InterPro entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
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.
has definition: Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.
deprecated: true
consider: HTML
in subset: obsolete

InterPro entry abstract format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.
Obsolete since: beta12orEarlier
comment: References are included and a functional inference is made where possible.
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

Gene3D entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: Entry format for the Gene3D protein secondary database.
consider: HTML
in subset: obsolete

PIRSF entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: Entry format for the PIRSF protein secondary database.
consider: HTML
in subset: obsolete

PRINTS entry format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format for the PRINTS protein secondary database.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

Panther Families and HMMs entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Entry format for the Panther library of protein families and subfamilies.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

Pfam entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Entry format for the Pfam protein secondary database.
consider: HTML
in subset: obsolete

SMART entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Entry format for the SMART protein secondary database.
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

Superfamily entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Entry format for the Superfamily protein secondary database.
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

TIGRFam entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Entry format for the TIGRFam protein secondary database.
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

ProDom entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Entry format for the ProDom protein domain classification database.
consider: HTML
in subset: obsolete

FSSP entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Entry format for the FSSP database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

findkm
type: Class
subclass of: Enzyme kinetics report format
subclass of: Textual format
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).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Ensembl gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: Entry format of Ensembl genome database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

DictyBase gene report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format of DictyBase genome database.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

CGD gene report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format of Candida Genome database.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

DragonDB gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Entry format of DragonDB genome database.
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

EcoCyc gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Entry format of EcoCyc genome database.
consider: HTML
in subset: obsolete

FlyBase gene report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format of FlyBase genome database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

Gramene gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Entry format of Gramene genome database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG GENES gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Entry format of KEGG GENES genome database.
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

MaizeGDB gene report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format of the Maize genetics and genomics database (MaizeGDB).
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

MGD gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Entry format of the Mouse Genome Database (MGD).
consider: HTML
in subset: obsolete

RGD gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Entry format of the Rat Genome Database (RGD).
Obsolete since: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

SGD gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Entry format of the Saccharomyces Genome Database (SGD).
Obsolete since: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

GeneDB gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Entry format of the Sanger GeneDB genome database.
consider: HTML
in subset: obsolete

TAIR gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Entry format of The Arabidopsis Information Resource (TAIR) genome database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

WormBase gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Entry format of the WormBase genomes database.
consider: HTML
in subset: obsolete

ZFIN gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Entry format of the Zebrafish Information Network (ZFIN) genome database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

TIGR gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Entry format of the TIGR genome database.
deprecated: true
consider: HTML
in subset: obsolete

dbSNP polymorphism report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Entry format for the dbSNP database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

OMIM entry format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of an entry from the OMIM database of genotypes and phenotypes.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

HGVbase entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Format of a record from the HGVbase database of genotypes and phenotypes.
deprecated: true
consider: HTML
in subset: obsolete

HIVDB entry format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of a record from the HIVDB database of genotypes and phenotypes.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG DISEASE entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Format of an entry from the KEGG DISEASE database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

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 hybridization oligos as generated by Whitehead primer3 program.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

CAF
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: beta12orEarlier
has definition: Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: caf
Documentation: caf

exp
type: Class
subclass of: Textual format
subclass of: Sequence assembly format (text)
Created in: beta12orEarlier
has definition: Sequence assembly project file EXP format.
in subset: bioinformatics
in subset: edam
in subset: formats

SCF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
has definition: Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: formats unix 2.html
Documentation: formats unix 2.html

PHD
type: Class
subclass of: Sequence trace format
subclass of: Textual format
has definition: PHD sequence trace format to store serialised chromatogram data (reads).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: PHD sequence format
Documentation: PHD sequence format

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
has exact synonym: Affymetrix image data file format
has definition: Format of Affymetrix data file of raw image data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
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
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

ArrayExpress entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Entry format for the ArrayExpress microarrays database.
deprecated: true
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

affymetrix-exp
type: Class
subclass of: Microarray experiment data format
subclass of: Textual format
Created in: beta12orEarlier
has exact synonym: Affymetrix experimental conditions data file format
has definition: Affymetrix data file format for information about experimental conditions and protocols.
in subset: bioinformatics
in subset: edam
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
has definition: Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.
Created in: beta12orEarlier
has exact synonym: Affymetrix probe normalised data format
in subset: bioinformatics
in subset: edam
in subset: formats

EMDB entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: Format of an entry from the Electron Microscopy DataBase (EMDB).
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG PATHWAY entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

MetaCyc entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: The format of an entry from the MetaCyc metabolic pathways database.
Obsolete since: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

HumanCyc entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: The format of a report from the HumanCyc metabolic pathways database.
consider: HTML
in subset: obsolete

INOH entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: The format of an entry from the INOH signal transduction pathways database.
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

PATIKA entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: The format of an entry from the PATIKA biological pathways database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

Reactome entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: The format of an entry from the reactome biological pathways database.
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

aMAZE entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: The format of an entry from the aMAZE biological pathways and molecular interactions database.
deprecated: true
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

CPDB entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: The format of an entry from the CPDB database.
consider: HTML
in subset: obsolete

Panther Pathways entry format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: The format of an entry from the Panther Pathways database.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

Taverna workflow format
type: Class
subclass of: Workflow format
subclass of: XML
Created in: beta12orEarlier
has definition: Format of Taverna workflows.
in subset: bioinformatics
in subset: edam
in subset: formats

BioModel mathematical model format
type: Class
subclass of: Obsolete concept (EDAM)
comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
deprecated: true
has definition: Format of mathematical models from the BioModel database.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG LIGAND entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: The format of an entry from the KEGG LIGAND chemical database.
consider: HTML
in subset: obsolete

KEGG COMPOUND entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
has definition: The format of an entry from the KEGG COMPOUND database.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG PLANT entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: The format of an entry from the KEGG PLANT database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

KEGG GLYCAN entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: The format of an entry from the KEGG GLYCAN database.
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

PubChem entry format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: The format of an entry from PubChem.
consider: HTML
in subset: obsolete

ChemSpider entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: The format of an entry from a database of chemical structures and property predictions.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

ChEBI entry format
type: Class
subclass of: Obsolete concept (EDAM)
comment: ChEBI includes an ontological classification defining relations between entities or classes of entities.
deprecated: true
has definition: The format of an entry from Chemical Entities of Biological Interest (ChEBI).
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

MSDchem ligand dictionary entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: The format of an entry from the MSDchem ligand dictionary.
consider: HTML
in subset: obsolete

HET group dictionary entry format
type: Class
subclass of: Small molecule report 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: bioinformatics
in subset: edam
in subset: formats

KEGG DRUG entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: The format of an entry from the KEGG DRUG database.
consider: HTML
in subset: obsolete

PubMed citation
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
has definition: Format of bibliographic reference as used by the PubMed database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Medline Display Format
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
comment: Bibliographic reference information including citation information is included
has definition: Format for abstracts of scientific articles from the Medline database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

CiteXplore-core
type: Class
subclass of: Textual format
subclass of: Bibliographic reference format
has definition: CiteXplore 'core' citation format including title, journal, authors and abstract.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

pmc
type: Class
subclass of: Article format
subclass of: Textual format
has definition: Article format of the PubMed Central database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

iHOP text mining abstract format
type: Class
subclass of: Text mining report format
subclass of: Textual format
has definition: iHOP abstract format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Oscar3
type: Class
subclass of: Text mining report format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Text mining abstract format from the Oscar 3 application.
comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.
in subset: bioinformatics
in subset: edam
in subset: formats

PDB atom record format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of an ATOM record (describing data for an individual atom) from a PDB file.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: PDB format
in subset: obsolete

CATH chain report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: Format of CATH domain classification information for a polypeptide chain.
Created in: beta12orEarlier
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.
consider: HTML
in subset: obsolete

CATH PDB report format
type: Class
subclass of: Obsolete concept (EDAM)
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
has definition: Format of CATH domain classification information for a protein PDB file.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

NCBI gene report format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Entry (gene) format of the NCBI database.
deprecated: true
consider: HTML
in subset: obsolete

GeneIlluminator gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has db xref: Moby:GI_Gene
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
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.
has definition: Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.
consider: HTML
in subset: obsolete

BacMap gene card format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has db xref: Moby:BacMapGeneCard
Created in: beta12orEarlier
deprecated: true
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.
consider: HTML
in subset: obsolete

ColiCard report format
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: Moby:ColiCard
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).
consider: HTML
in subset: obsolete

PlasMapper TextMap
type: Class
subclass of: Map format
subclass of: Textual format
has definition: Map of a plasmid (circular DNA) in PlasMapper TextMap format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

newick
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
has definition: Phylogenetic tree Newick (text) format.
Created in: beta12orEarlier
has exact synonym: nh
in subset: bioinformatics
in subset: edam
in subset: formats

TreeCon format
type: Class
subclass of: Textual format
subclass of: Phylogenetic tree format (text)
has definition: Phylogenetic tree TreeCon (text) format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Format
type: Class
disjoint with: Operation
disjoint with: Topic
disjoint with: DeprecatedClass
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.
has exact synonym: Data format
has definition: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
Created in: beta12orEarlier
has exact synonym: Exchange format
has broad synonym: Data model
has narrow synonym: File format
has related synonym: File format
has related synonym: List of file formats
has related synonym: IAO_0000098
in subset: bioinformatics
in subset: edam
in subset: formats
has related synonym: MachineLanguage
has broad synonym: Quality
has broad synonym: format
has related synonym: SIO_000612
has related synonym: SIO_000618
has related synonym: compression_004
has broad synonym: Continuant
has related synonym: Quality
has related synonym: quality
has related synonym: Perpetuant
has related synonym: Symbol structure

Axiom
comment: BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format.
annotated source: Format
annotated property: hasRelatedSynonym
annotated target: Quality

Axiom
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.
annotated source: Format
annotated property: hasNarrowSynonym

Axiom
comment: Closely related concept focusing on the specification of a data format.
annotated source: Format
annotated target: IAO_0000098
annotated property: hasRelatedSynonym

Axiom
comment: GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials.
annotated source: Format
annotated property: hasRelatedSynonym
annotated target: Perpetuant

Axiom
comment: Format can be a quality of a data record.
annotated source: Format
annotated property: hasRelatedSynonym
annotated target: quality

Axiom
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'.)
annotated target: Data model
annotated source: Format
annotated property: hasBroadSynonym

Axiom
comment: Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format.
annotated source: Format
annotated target: compression_004
annotated property: hasRelatedSynonym

Atomic data format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Data format for an individual atom.
Obsolete since: beta13
Created in: beta12orEarlier
consider: PDB database entry format
in subset: obsolete

Sequence record format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence record
Created in: beta12orEarlier
has definition: Data format for a molecular sequence record.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence feature annotation format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Feature record
has definition: Data format for molecular sequence feature information.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Alignment format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
Created in: beta12orEarlier
has definition: Data format for molecular sequence alignment information.
in subset: bioinformatics
in subset: edam
in subset: formats

acedb
type: Class
subclass of: Sequence record format (text)
has definition: ACEDB sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

clustal sequence format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Clustalw output format.
Created in: beta12orEarlier
deprecated: true
consider: ClustalW format
in subset: obsolete

codata
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Codata entry format.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

EMBL format
type: Class
subclass of: EMBL-like (text)
subclass of: Sequence feature table format (text)
Created in: beta12orEarlier
has exact synonym: EMBL
has exact synonym: EMBL sequence format
has definition: EMBL entry format.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

FASTA
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
has definition: FASTA format including NCBI-style IDs.
has exact synonym: FASTA sequence format
has exact synonym: FASTA format
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

FASTQ
type: Class
subclass of: FASTQ-like format (text)
Created in: beta12orEarlier
has definition: FASTQ short read format ignoring quality scores.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

gcg
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: GCG sequence format.
in subset: bioinformatics
in subset: edam
in subset: formats

GenBank format
type: Class
subclass of: GenBank-like format (text)
subclass of: Sequence feature table format (text)
has definition: Genbank entry format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

genpept
type: Class
subclass of: GenBank-like format (text)
has definition: Genpept protein entry format.
comment: Currently identical to refseqp format
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

hennig86
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: Hennig86 output sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

mase format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: Mase program sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

mega-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: Mega interleaved and non-interleaved sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

msf
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
has definition: GCG MSF (multiple sequence file) file format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

nbrf
type: Class
subclass of: Sequence record full format
subclass of: Textual format
Created in: beta12orEarlier
has definition: NBRF/PIR entry sequence format.
in subset: bioinformatics
in subset: edam
in subset: formats

nexus-seq
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
has definition: Nexus/paup interleaved sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

pdbatom
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: PDB sequence format (ATOM lines).
Created in: beta12orEarlier
comment: pdb format in EMBOSS.
in subset: bioinformatics
in subset: edam
in subset: formats

pdbatomnuc
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: PDB nucleotide sequence format (ATOM lines).
comment: pdbnuc format in EMBOSS.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

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).
comment: pdbnucseq format in EMBOSS.
in subset: bioinformatics
in subset: edam
in subset: formats

pdbseqres
type: Class
subclass of: PDB database entry format
subclass of: Textual format
subclass of: Sequence record format (text)
comment: pdbseq format in EMBOSS.
Created in: beta12orEarlier
has definition: PDB sequence format (SEQRES lines).
in subset: bioinformatics
in subset: edam
in subset: formats

Pearson format
type: Class
subclass of: FASTA-like (text)
has definition: Plain old FASTA sequence format (unspecified format for IDs).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

phylip sequence format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: Phylip interleaved sequence format.
consider: Phylip format
in subset: obsolete

phylipnon sequence format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Phylip non-interleaved sequence format.
deprecated: true
consider: Phylipnon
in subset: obsolete

raw
type: Class
subclass of: Textual format
subclass of: Raw sequence format
has definition: Raw sequence format with no non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

refseqp
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
comment: Currently identical to genpept format
has definition: Refseq protein entry sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

selex sequence format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Selex sequence format.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: selex
in subset: obsolete

Staden format
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Staden suite sequence format.
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: 003063.html
Documentation: 003063.html
has db xref: staden
Documentation: staden

Stockholm format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: Stockholm multiple sequence alignment format (used by Pfam and Rfam).
has db xref: Stockholm format
Documentation: Stockholm format
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

UniProtKB format
type: Class
subclass of: UniProt-like (text)
Created in: beta12orEarlier
has definition: UniProtKB entry sequence format.
in subset: bioinformatics
in subset: edam
in subset: formats

plain text format (unformatted)
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: Plain text sequence format (essentially unformatted).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

treecon sequence format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Treecon output sequence format.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: TreeCon-seq
in subset: obsolete

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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

dasdna
type: Class
subclass of: XML
subclass of: Sequence record format (XML)
comment: The use of this format is deprecated.
has definition: DAS sequence (XML) format (nucleotide-only).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
in subset: formats

jackknifernon
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
has definition: Jackknifer output sequence non-interleaved format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

meganon sequence format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Mega non-interleaved output sequence format.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: meganon
in subset: obsolete

NCBI format
type: Class
subclass of: FASTA-like (text)
Created in: beta12orEarlier
comment: There are several variants of this.
has definition: NCBI FASTA sequence format with NCBI-style IDs.
in subset: bioinformatics
in subset: edam
in subset: formats

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: bioinformatics
in subset: edam
in subset: formats

GFF2
type: Class
subclass of: GFF
has definition: General Feature Format (GFF) of sequence features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: spec.html
Documentation: spec.html

GFF3
type: Class
subclass of: GFF
has definition: Generic Feature Format version 3 (GFF3) of sequence features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: gff3.html
Documentation: gff3.html

pir
type: Class
subclass of: Sequence feature table format (text)
subclass of: Textual format
Created in: beta12orEarlier
has definition: PIR feature format.
in subset: bioinformatics
in subset: edam
in subset: formats

swiss feature
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Swiss-Prot feature format.
deprecated: true
consider: UniProtKB format
in subset: obsolete

DASGFF
type: Class
subclass of: XML
subclass of: Sequence feature table format (XML)
Created in: beta12orEarlier
has exact synonym: DASGFF feature
has definition: DAS GFF (XML) feature format.
has exact synonym: das feature
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

EMBL feature
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: EMBL feature format.
consider: EMBL format
in subset: obsolete

GenBank feature
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Genbank feature format.
Obsolete since: beta12orEarlier
consider: GenBank format
in subset: obsolete

ClustalW format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
has definition: ClustalW format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

FASTA-aln
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
has definition: Fasta format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

markx0
type: Class
subclass of: markx0 variant
has definition: Pearson MARKX0 alignment format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

markx1
type: Class
subclass of: markx0 variant
Created in: beta12orEarlier
has definition: Pearson MARKX1 alignment format.
in subset: bioinformatics
in subset: edam
in subset: formats

markx10
type: Class
subclass of: markx0 variant
has definition: Pearson MARKX10 alignment format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

markx2
type: Class
subclass of: markx0 variant
has definition: Pearson MARKX2 alignment format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

markx3
type: Class
subclass of: markx0 variant
has definition: Pearson MARKX3 alignment format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

mega
type: Class
subclass of: mega variant
Created in: beta12orEarlier
has definition: Mega format for (typically aligned) sequences.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

msf alignment format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: MSF format for (aligned) sequences.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: msf
in subset: obsolete

nexus alignment format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Nexus/paup format for (aligned) sequences.
consider: nexus-seq
in subset: obsolete

nexusnon alignment format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Nexus/paup non-interleaved format for (aligned) sequences.
deprecated: true
Created in: beta12orEarlier
consider: nexusnon
in subset: obsolete

pair
type: Class
subclass of: Alignment format (text)
Created in: beta12orEarlier
has definition: EMBOSS simple sequence pair alignment format.
in subset: bioinformatics
in subset: edam
in subset: formats

Phylip format
type: Class
subclass of: Phylip format variant
has definition: Phylip format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Phylipnon
type: Class
subclass of: Phylip format variant
has definition: Phylip non-interleaved format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

scores format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
has definition: Alignment format for score values for pairs of sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

selex
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
has definition: SELEX format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

srs format
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
has definition: Simple multiple sequence (alignment) format for SRS.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

srspair
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
has definition: Simple sequence pair (alignment) format for SRS.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylogenetic tree format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic tree
Created in: beta12orEarlier
has definition: Data format for a phylogenetic tree.
in subset: bioinformatics
in subset: edam
in subset: formats

Biological pathway or network format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Pathway or network
has definition: Data format for a biological pathway or network.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence-profile alignment format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence-profile alignment
has definition: Data format for a sequence-profile alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence-profile alignment (HMM) format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Data format for a sequence-HMM profile alignment.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Sequence-profile alignment format
in subset: obsolete

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: bioinformatics
in subset: edam
in subset: formats

Article format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Article
has definition: Data format for a full-text scientific article.
has exact synonym: Literature format
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Text mining report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Text mining report
has definition: Data format for an abstract (report) from text mining.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Enzyme kinetics report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Enzyme kinetics data
Created in: beta12orEarlier
has definition: Data format for reports on enzyme kinetics.
in subset: bioinformatics
in subset: edam
in subset: formats

Small molecule report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Small molecule report
has definition: Format of a report on a chemical compound.
has exact synonym: Chemical compound annotation format
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Gene annotation format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Gene annotation
Created in: beta12orEarlier
has definition: Format of a report on a particular locus, gene, gene system or groups of genes.
in subset: bioinformatics
in subset: edam
in subset: formats

Workflow format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Workflow
has definition: Format of a workflow.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Tertiary structure format
type: Class
subclass of: Format (typed)
has definition: Data format for a molecular tertiary structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Biological model format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.2
Created in: beta12orEarlier
has definition: Data format for a biological model.
consider: Biological pathway or network format
in subset: obsolete

Chemical formula format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Chemical formula
has definition: Text format of a chemical formula.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Phylogenetic character data format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic character data
has definition: Format of raw (unplotted) phylogenetic data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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
has definition: Format of phylogenetic invariants data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Electron microscopy model format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Annotation format for electron microscopy models.
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: Format (typed)
in subset: obsolete

Phylogenetic tree report (tree distances) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Phylogenetic tree distances
Created in: beta12orEarlier
has definition: Format for phylogenetic tree distance data.
in subset: bioinformatics
in subset: edam
in subset: formats

Polymorphism report format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.0
has definition: Format for sequence polymorphism data.
deprecated: true
Created in: beta12orEarlier
in subset: obsolete

Protein family report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Protein family
Created in: beta12orEarlier
has definition: Format for reports on a protein family.
in subset: bioinformatics
in subset: edam
in subset: formats

Molecular interaction format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Molecular interaction
has definition: Format for molecular interaction data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence assembly format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence assembly
has definition: Format for sequence assembly data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Microarray experiment data format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Experiment annotation (microarray)
has definition: Format for microarray experimental data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Gene expression report format
type: Class
subclass of: Gene annotation format
subclass of: Restriction
  on property: is format of
  some values from: Processed microarray data
Created in: beta12orEarlier
has definition: Format for a report on gene expression.
in subset: bioinformatics
in subset: edam
in subset: formats

Genotype and phenotype annotation format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Format of a report on genotype / phenotype information.
deprecated: true
Created in: beta12orEarlier
consider: Format (typed)
in subset: obsolete

Map format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Map
Created in: beta12orEarlier
has definition: Format of a map of (typically one) molecular sequence annotated with features.
in subset: bioinformatics
in subset: edam
in subset: formats

Nucleic acid features (primers) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Nucleic acid features (primers)
has definition: Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Protein report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Protein report
Created in: beta12orEarlier
has definition: Format of a report of general information about a specific protein.
in subset: bioinformatics
in subset: edam
in subset: formats

Protein report (enzyme) format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Format of a report of general information about a specific enzyme.
consider: Format (typed)
in subset: obsolete

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
has definition: Format of a matrix of 3D-1D scores (amino acid environment probabilities).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Protein structure report (quality evaluation) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Protein structural quality report
Created in: beta12orEarlier
has definition: Format of a report on the quality of a protein three-dimensional model.
in subset: bioinformatics
in subset: edam
in subset: formats

Database hits (sequence) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Database hits (sequence)
Created in: beta12orEarlier
has definition: Format of a report on sequence hits and associated data from searching a sequence database.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence distance matrix format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence distance matrix
has definition: Format of a matrix of genetic distances between molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence motif format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence motif
Created in: beta12orEarlier
has definition: Format of a sequence motif.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence profile format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence profile
Created in: beta12orEarlier
has definition: Format of a sequence profile.
in subset: bioinformatics
in subset: edam
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
has definition: Format of a hidden Markov model.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Dirichlet distribution format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Dirichlet distribution
Created in: beta12orEarlier
has definition: Data format of a dirichlet distribution.
in subset: bioinformatics
in subset: edam
in subset: formats

HMM emission and transition counts format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: HMM emission and transition counts
Created in: beta12orEarlier
has definition: Data format for the emission and transition counts of a hidden Markov model.
in subset: bioinformatics
in subset: edam
in subset: formats

RNA secondary structure format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: RNA secondary structure record
has definition: Format for secondary structure (predicted or real) of an RNA molecule.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Protein secondary structure format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Protein features (secondary structure)
Created in: beta12orEarlier
has definition: Format for secondary structure (predicted or real) of a protein molecule.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence range format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence range
has definition: Format used to specify range(s) of sequence positions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

ambiguous
type: Class
subclass of: Textual format
subclass of: Raw sequence format
has definition: Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence features (repeats) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence features (repeats)
has definition: Format used for map of repeats in molecular (typically nucleotide) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Nucleic acid features (restriction sites) format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Nucleic acid features (restriction sites)
has definition: Format used for report on restriction enzyme recognition sites in nucleotide sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Gene features (coding region) format
type: Class
subclass of: Gene annotation format
subclass of: Restriction
  on property: is format of
  some values from: Nucleic acid features (coding sequence)
has definition: Format used for report on coding regions in nucleotide sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence cluster format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Sequence cluster
has definition: Format used for clusters of molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Gene cluster format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format used for clusters of genes.
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
consider: Sequence cluster format (nucleic acid)
in subset: obsolete

EMBL-like (text)
type: Class
subclass of: Textual format
subclass of: EMBL-like format
has definition: A text format resembling EMBL entry format.
Created in: beta12orEarlier
comment: This concept may be used for the many non-standard EMBL-like text formats.
in subset: bioinformatics
in subset: edam
in subset: formats

FASTQ-like format (text)
type: Class
subclass of: Textual format
subclass of: FASTQ-like format
Created in: beta12orEarlier
comment: This concept may be used for non-standard FASTQ short read-like formats.
has definition: A text format resembling FASTQ short read format.
in subset: bioinformatics
in subset: edam
in subset: formats

EMBLXML
type: Class
subclass of: EMBL format (XML)
Created in: beta12orEarlier
has definition: XML format for EMBL entries.
in subset: bioinformatics
in subset: edam
in subset: formats

cdsxml
type: Class
subclass of: EMBL format (XML)
Created in: beta12orEarlier
has definition: XML format for EMBL entries.
in subset: bioinformatics
in subset: edam
in subset: formats

insdxml
type: Class
subclass of: EMBL format (XML)
has definition: XML format for EMBL entries.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

geneseq
type: Class
subclass of: EMBL-like (text)
Created in: beta12orEarlier
has definition: Geneseq sequence format.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

UniProt format
type: Class
subclass of: UniProt-like (text)
has definition: UniProt entry sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

ipi
type: Class
subclass of: UniProt-like (text)
has definition: ipi sequence format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

medline
type: Class
subclass of: Article format
subclass of: Textual format
Created in: beta12orEarlier
has definition: Abstract format used by MedLine database.
in subset: bioinformatics
in subset: edam
in subset: formats

Ontology format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Ontology
Created in: beta12orEarlier
has definition: Format used for ontologies.
in subset: bioinformatics
in subset: edam
in subset: formats

OBO format
type: Class
subclass of: Ontology format
has definition: A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

OWL format
type: Class
subclass of: Ontology format
subclass of: XML
Created in: beta12orEarlier
has definition: A serialisation format conforming to the Web Ontology Language (OWL) model.
in subset: bioinformatics
in subset: edam
in subset: formats

FASTA-like (text)
type: Class
subclass of: Textual format
subclass of: FASTA-like
has definition: A text format resembling FASTA format.
Created in: beta12orEarlier
comment: This concept may also be used for the many non-standard FASTA-like formats.
has narrow synonym: FASTA
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence record full format
type: Class
subclass of: Sequence record format
subclass of: Restriction
  on property: is format of
  some values from: Sequence record full
has definition: Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence record lite format
type: Class
subclass of: Sequence record format
subclass of: Restriction
  on property: is format of
  some values from: Sequence record lite
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

EMBL format (XML)
type: Class
subclass of: EMBL-like (XML)
comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation.
has definition: An XML format for EMBL entries.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

GenBank-like format (text)
type: Class
subclass of: Textual format
subclass of: GenBank-like format
Created in: beta12orEarlier
comment: This concept may be used for the non-standard GenBank-like text formats.
has definition: A text format resembling GenBank entry (plain text) format.
in subset: bioinformatics
in subset: edam
in subset: 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: bioinformatics
in subset: edam
in subset: formats

Strain data format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.0
Created in: beta12orEarlier
has definition: Format of a report on organism strain data / cell line.
in subset: obsolete

CIP strain data format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Format for a report of strain data as used for CIP database entries.
consider: HTML
in subset: obsolete

phylip property values
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: PHYLIP file format for phylogenetic property data.
deprecated: true
consider: Phylogenetic character data format
in subset: obsolete

STRING entry format (HTML)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Entry format (HTML) for the STRING database of protein interaction.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: HTML
in subset: obsolete

STRING entry format (XML)
type: Class
subclass of: Molecular interaction format
subclass of: XML
Created in: beta12orEarlier
has definition: Entry format (XML) for the STRING database of protein interaction.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

GTF
type: Class
subclass of: GFF
Created in: beta12orEarlier
has definition: Gene Transfer Format (GTF), a restricted version of GFF.
has db xref: format4
Documentation: GTF22.html
has db xref: GTF22.html
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

BioCyc enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of an entry from the BioCyc enzyme database.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

ENZYME enzyme report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Format of an entry from the Enzyme nomenclature database (ENZYME).
consider: HTML
in subset: obsolete

PseudoCAP gene report format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of a report on a gene from the PseudoCAP database.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: HTML
in subset: obsolete

GeneCards gene report format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Format of a report on a gene from the GeneCards database.
consider: HTML
in subset: obsolete

Textual format
type: Class
subclass of: Format
Created in: beta12orEarlier
has narrow synonym: Plain text
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).
has definition: Textual format.
has narrow synonym: Tabular format
has narrow synonym: CSV
has narrow synonym: TSV
has narrow synonym: TXT
in subset: bioinformatics
in subset: edam
in subset: formats
has exact synonym: text
has narrow synonym: http://www.iana.org/assignments/media-types/text/csv
has narrow synonym: plain

Axiom
comment: fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats.
annotated source: Textual format
annotated target: TXT
annotated property: hasNarrowSynonym

Axiom
annotated target: Tabular format
comment: Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format.
annotated source: Textual format
annotated property: hasNarrowSynonym

Axiom
comment: fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats.
annotated source: Textual format
annotated target: TSV
annotated property: hasNarrowSynonym

HTML
type: Class
subclass of: Format
subclass of: Restriction
  on property: is format of
  some values from: Report
has exact synonym: Hypertext Markup Language
Created in: beta12orEarlier
has definition: HTML format.
has exact synonym: HTML
in subset: bioinformatics
in subset: edam
in subset: formats

Axiom
comment: fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats.
annotated source: HTML
annotated target: HTML
annotated property: hasExactSynonym

XML
type: Class
subclass of: Format
has exact synonym: Extensible Markup Language
has definition: eXtensible Markup Language (XML) format.
Created in: beta12orEarlier
comment: Data in XML format can be serialised into text, or binary format.
has exact synonym: XML
in subset: bioinformatics
in subset: edam
in subset: formats

Axiom
comment: fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats.
annotated source: XML
annotated target: XML
annotated property: hasExactSynonym

Binary format
type: Class
subclass of: Format
has definition: Binary format.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: edam
in subset: formats

URI format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Typical textual representation of a URI.
deprecated: true
Obsolete since: beta13
consider: URI
in subset: obsolete

NCI-Nature pathway entry format
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: The format of an entry from the NCI-Nature pathways database.
deprecated: true
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

Format (typed)
type: Class
subclass of: Format
has definition: A broad class of format distinguished by the scientific nature of the data that is identified.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: edam
in subset: formats

BioXSD
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
subclass of: Restriction
  on property: is format of
  some values from: Feature record
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment
has definition: BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).
Created in: beta12orEarlier
has exact synonym: BioXSD XML format
has db xref: bioxsd.org
Documentation: bioxsd.org
in subset: bioinformatics
in subset: edam
in subset: formats

RDF format
type: Class
subclass of: Ontology format
subclass of: XML
has definition: A serialisation format conforming to the Resource Description Framework (RDF) model.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

GenBank-HTML
type: Class
subclass of: HTML
subclass of: GenBank-like format
has definition: Genbank entry format wrapped in HTML elements.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Protein features (domains) format
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Format of a report on protein features (domain composition).
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
consider: Format (typed)
in subset: obsolete

EMBL-like format
type: Class
subclass of: Sequence record full format
comment: This concept may be used for the many non-standard EMBL-like formats.
has definition: A format resembling EMBL entry (plain text) format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

FASTQ-like format
type: Class
subclass of: Sequence trace format
Created in: beta12orEarlier
comment: This concept may be used for non-standard FASTQ short read-like formats.
has definition: A format resembling FASTQ short read format.
in subset: bioinformatics
in subset: edam
in subset: formats

FASTA-like
type: Class
subclass of: Sequence record lite format
has definition: A format resembling FASTA format.
Created in: beta12orEarlier
comment: This concept may be used for the many non-standard FASTA-like formats.
in subset: bioinformatics
in subset: edam
in subset: formats

uniprotkb-like format
type: Class
subclass of: Sequence record full format
subclass of: Sequence feature table format (text)
has definition: A sequence format resembling uniprotkb entry format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: Feature record
Created in: beta12orEarlier
has definition: Format for a sequence feature table.
in subset: bioinformatics
in subset: edam
in subset: formats

OBO
type: Class
subclass of: OBO format
subclass of: Textual format
has definition: OBO ontology text format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

OBO-XML
type: Class
subclass of: OBO format
subclass of: XML
has definition: OBO ontology XML format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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.
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence record format (XML)
type: Class
subclass of: Sequence record format
has definition: Data format for a molecular sequence record.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylogenetic tree format (text)
type: Class
subclass of: Phylogenetic tree format
has definition: Text format for a phylogenetic tree.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Phylogenetic tree format (XML)
type: Class
subclass of: Phylogenetic tree format
has definition: XML format for a phylogenetic tree.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

EMBL-like (XML)
type: Class
subclass of: XML
subclass of: EMBL-like format
Created in: beta12orEarlier
comment: This concept may be used for the any non-standard EMBL-like XML formats.
has definition: An XML format resembling EMBL entry format.
in subset: bioinformatics
in subset: edam
in subset: formats

GenBank-like format
type: Class
subclass of: Sequence record full format
comment: This concept may be used for the non-standard GenBank-like formats.
Created in: beta12orEarlier
has definition: A format resembling GenBank entry (plain text) format.
in subset: bioinformatics
in subset: edam
in subset: formats

STRING entry format
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: Entry format for the STRING database of protein interaction.
Created in: beta12orEarlier
consider: HTML
in subset: obsolete

Sequence assembly format (text)
type: Class
subclass of: Sequence assembly format
has definition: Text format for sequence assembly data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Amino acid identifier format
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Text format (representation) of amino acid residues.
Obsolete since: beta13
consider: Amino acid identifier
in subset: obsolete

completely unambiguous
type: Class
subclass of: Textual format
subclass of: Raw sequence format
has definition: Alphabet for a molecular sequence without any unknown positions or ambiguity characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

completely unambiguous pure
type: Class
subclass of: pure
subclass of: completely unambiguous
has definition: Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

completely unambiguous pure dna
type: Class
subclass of: dna
subclass of: completely unambiguous pure
has definition: Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Raw sequence format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Raw sequence
has definition: Format of a raw molecular sequence (i.e. the alphabet used).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has related synonym: Symbol sequence

BAM
type: Class
subclass of: Sequence trace format
subclass of: Binary format
subclass of: Alignment format (pair only)
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: SAM-1.3.pdf
Documentation: SAM-1.3.pdf

SAM
type: Class
subclass of: Sequence trace format
subclass of: Textual format
subclass of: Alignment format (pair only)
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.
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: SAM-1.3.pdf
has db xref: SAM-1.3.pdf

SBML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: beta12orEarlier
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.
Documentation: sbml.org
has db xref: sbml.org
in subset: bioinformatics
in subset: edam
in subset: formats

completely unambiguous pure protein
type: Class
subclass of: protein
subclass of: completely unambiguous pure
has definition: Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Bibliographic reference format
type: Class
subclass of: Format (typed)
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
has definition: Format of a bibliographic reference.
in subset: bioinformatics
in subset: edam
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: Sequence annotation track
Created in: beta12orEarlier
has definition: Format of a sequence annotation track.
in subset: bioinformatics
in subset: edam
in subset: formats

Alignment format (pair only)
type: Class
subclass of: Alignment format
subclass of: Restriction
  on property: is format of
  some values from: Sequence alignment (pair)
has definition: Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

Sequence variation annotation format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Nucleic acid features (variation)
Created in: beta12orEarlier
has definition: Format of sequence variation annotation.
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Phylip format variant
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
subclass of: Alignment format (text)
has definition: Some variant of Phylip format for (aligned) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

AB1
type: Class
subclass of: Sequence trace format
subclass of: Binary format
comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats

ACE
type: Class
subclass of: Sequence assembly format
subclass of: Textual format
Created in: beta12orEarlier
has definition: ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).
has db xref: README.14.0.txt
Documentation: README.14.0.txt
in subset: bioinformatics
in subset: edam
in subset: formats

BED
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
has definition: Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.
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).
Created in: beta12orEarlier
has db xref: format1
Documentation: format1
in subset: bioinformatics
in subset: edam
in subset: formats

bigBed
type: Class
subclass of: Binary format
subclass of: Sequence annotation track format
has definition: bigBed format for large sequence annotation tracks, similar to textual BED format.
Created in: beta12orEarlier
has db xref: format1.5
Documentation: format1.5
in subset: bioinformatics
in subset: edam
in subset: formats

WIG
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
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.
has db xref: wiggle.html
Documentation: wiggle.html
in subset: bioinformatics
in subset: edam
in subset: formats

bigWig
type: Class
subclass of: Binary format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
has definition: bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.
Documentation: format6.1
has db xref: format6.1
in subset: bioinformatics
in subset: edam
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
has definition: PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.
Documentation: format2
has db xref: format2
in subset: bioinformatics
in subset: edam
in subset: formats

MAF
type: Class
subclass of: Textual format
subclass of: Alignment format (text)
subclass of: Sequence annotation track format
Created in: beta12orEarlier
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.
has definition: Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.
Documentation: format5
has db xref: format5
in subset: bioinformatics
in subset: edam
in subset: formats

2bit
type: Class
subclass of: Binary format
subclass of: Raw sequence format
has definition: 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'.
Created in: beta12orEarlier
has db xref: http://genome-source.cse.ucsc.edu/gitweb/
Documentation: 2bitformat.html
has db xref: 2bitformat.html
in subset: bioinformatics
in subset: edam
in subset: formats

.nib
type: Class
subclass of: Binary format
subclass of: Raw sequence format
has definition: .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'.
Created in: beta12orEarlier
Documentation: format8
has db xref: format8
in subset: bioinformatics
in subset: edam
in subset: formats

genePred
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
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.
has definition: genePred table format for gene prediction tracks.
Documentation: format9
has db xref: format9
in subset: bioinformatics
in subset: edam
in subset: formats

pgSnp
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
Created in: beta12orEarlier
has definition: Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.
has db xref: format10
Documentation: format10
in subset: bioinformatics
in subset: edam
in subset: formats

axt
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
Created in: beta12orEarlier
has definition: axt format of alignments, typically produced from BLASTZ.
Documentation: axt.html
has db xref: axt.html
in subset: bioinformatics
in subset: edam
in subset: formats

LAV
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
has definition: LAV format of alignments generated by BLASTZ and LASTZ.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: lav format.html
Documentation: lav format.html

Pileup
type: Class
subclass of: Textual format
subclass of: Alignment format (pair only)
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).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: pileup.shtml
has db xref: pileup.shtml

VCF
type: Class
subclass of: Textual format
subclass of: Sequence variation annotation format
has definition: Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: specs.html
has db xref: specs.html

SRF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
has definition: Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: srf.sourceforge.net
Documentation: srf.sourceforge.net

ZTR
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: beta12orEarlier
has definition: ZTR format for storing chromatogram data from DNA sequencing instruments.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: formats unix 12.html
has db xref: formats unix 12.html

GVF
type: Class
subclass of: GFF3
subclass of: Sequence variation annotation format
Created in: beta12orEarlier
has definition: Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: gvf.html
has db xref: gvf.html

BCF
type: Class
subclass of: Binary format
subclass of: Sequence variation annotation format
has definition: BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: mpileup.shtml

Matrix format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Matrix
Created in: beta13
has definition: Format of a matrix (array) of numerical values.
in subset: bioinformatics
in subset: edam
in subset: formats

Protein domain classification format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Protein domain classification
Created in: beta13
has definition: Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).
in subset: bioinformatics
in subset: edam
in subset: formats

Raw SCOP domain classification format
type: Class
subclass of: Protein domain classification format
comment: These are the parsable data files provided by SCOP.
Created in: beta13
has definition: Format of raw SCOP domain classification data files.
in subset: bioinformatics
in subset: edam
in subset: formats

Raw CATH domain classification format
type: Class
subclass of: Protein domain classification format
has definition: Format of raw CATH domain classification data files.
Created in: beta13
comment: These are the parsable data files provided by CATH.
in subset: bioinformatics
in subset: edam
in subset: formats

CATH domain report format
type: Class
subclass of: Protein domain classification format
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.
Created in: beta13
has definition: Format of summary of domain classification information for a CATH domain.
in subset: bioinformatics
in subset: edam
in subset: formats

SBRML
type: Class
subclass of: XML
subclass of: Biological pathway or network report format
has definition: Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.
Created in: 1.0
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: http://www.comp-sys-bio.org/tiki-index.php
Documentation: http://www.comp-sys-bio.org/tiki-index.php

BioPAX
type: Class
subclass of: Biological pathway or network format
Created in: 1.0
has definition: BioPAX is an exchange format for pathway data, with its data model defined in OWL.
Documentation: www.biopax.org
has db xref: www.biopax.org
in subset: bioinformatics
in subset: edam
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
has definition: EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: ApplicationResult.xsd
has db xref: ApplicationResult.xsd

PSI MI XML (MIF)
type: Class
subclass of: Molecular interaction format
subclass of: XML
has exact synonym: MIF
has definition: XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.
Created in: 1.0
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: mif
has db xref: mif

phyloXML
type: Class
subclass of: XML
subclass of: Phylogenetic tree format (XML)
Created in: 1.0
has definition: phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.
Documentation: www.phyloxml.org
has db xref: www.phyloxml.org
in subset: bioinformatics
in subset: edam
in subset: formats

NeXML
type: Class
subclass of: XML
subclass of: Phylogenetic tree format (XML)
has definition: NeXML is a standardised XML format for rich phyloinformatic data.
Created in: 1.0
has db xref: www.nexml.org
Documentation: www.nexml.org
in subset: bioinformatics
in subset: edam
in subset: formats

MAGE-ML
type: Class
subclass of: Microarray experiment data format
subclass of: Gene expression report format
subclass of: XML
Created in: 1.0
has definition: MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: mage-ml.html
has db xref: mage-ml.html

MAGE-TAB
type: Class
subclass of: Microarray experiment data format
subclass of: Gene expression report format
subclass of: Textual format
has definition: MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).
Created in: 1.0
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: mage-tab
Documentation: mage-tab

GCDML
type: Class
subclass of: XML
subclass of: Experiment annotation format
subclass of: Restriction
  on property: is format of
  some values from: Experiment annotation (sequencing)
has definition: GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).
Created in: 1.0
has db xref: gcdml.gensc.org
Documentation: gcdml.gensc.org
in subset: bioinformatics
in subset: edam
in subset: formats

GTrack
type: Class
subclass of: Textual format
subclass of: Sequence annotation track format
has definition: GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG).
Created in: 1.0
has db xref: www.gtrack.no
Documentation: www.gtrack.no
in subset: bioinformatics
in subset: edam
in subset: formats

Biological pathway or network report format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Pathway or network report
Created in: beta12orEarlier
has definition: Data format for a report of information derived from a biological pathway or network.
in subset: bioinformatics
in subset: edam
in subset: formats

Experiment annotation format
type: Class
subclass of: Format (typed)
has definition: Data format for annotation on a laboratory experiment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
comment: Reflects a UCSC Browser DB table.
has definition: Cytoband format for chromosome cytobands.
in subset: bioinformatics
in subset: edam
in subset: formats
has db xref: Cytoband
Documentation: Cytoband

CopasiML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
subclass of: Biological pathway or network report format
has definition: CopasiML, the native format of COPASI.
Created in: 1.2
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: http://www.copasi.org/tiki-index.php
has db xref: http://www.copasi.org/tiki-index.php

CellML
type: Class
subclass of: Biological pathway or network format
subclass of: XML
Created in: 1.2
has definition: CellML, the format for mathematical models of biological and other networks.
has db xref: www.cellml.org
Documentation: www.cellml.org
in subset: bioinformatics
in subset: edam
in subset: formats

PSI MI TAB (MITAB)
type: Class
subclass of: Molecular interaction format
subclass of: Textual format
has definition: Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.
Created in: 1.2
Documentation: README
has db xref: README
in subset: bioinformatics
in subset: edam
in subset: formats

PSI-PAR
type: Class
subclass of: PSI MI XML (MIF)
Created in: 1.2
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: bioinformatics
in subset: edam
in subset: formats
Documentation: psi-par
has db xref: psi-par

mzML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
has definition: mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.
comment: mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.
Documentation: mzml
has db xref: mzml
in subset: bioinformatics
in subset: edam
in subset: formats

Mass spectrometry data format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Mass spectrometry data
has definition: Format for mass spectrometry data.
Created in: 1.2
in subset: bioinformatics
in subset: edam
in subset: formats

TraML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
has definition: TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.
has db xref: traml
Documentation: traml
in subset: bioinformatics
in subset: edam
in subset: formats

mzIdentML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
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.
Documentation: mzidentml
has db xref: mzidentml
in subset: bioinformatics
in subset: edam
in subset: formats

mzQuantML
type: Class
subclass of: XML
subclass of: Mass spectrometry data format
Created in: 1.2
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.
has db xref: mzquantml
Documentation: mzquantml
in subset: bioinformatics
in subset: edam
in subset: formats

GelML
type: Class
subclass of: XML
subclass of: Experiment annotation format
subclass of: Restriction
  on property: is format of
  some values from: Experiment annotation (mass spectrometry)
Created in: 1.2
has definition: GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.
Documentation: gelml
has db xref: gelml
in subset: bioinformatics
in subset: edam
in subset: formats

spML
type: Class
subclass of: XML
subclass of: Experiment annotation format
subclass of: Restriction
  on property: is format of
  some values from: Experiment annotation (mass spectrometry)
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.
Created in: 1.2
Documentation: psidev.info
has db xref: psidev.info
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: formats

Manchester OWL Syntax
type: Class
subclass of: OWL format
subclass of: Textual format
comment: This format was influenced by the OWL Abstract Syntax and the DL style syntax.
Created in: 1.2
has definition: A syntax for writing OWL class expressions.
in subset: bioinformatics
in subset: edam
in subset: formats

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".
comment: This format is used in Protege 4.
in subset: bioinformatics
in subset: edam
in subset: formats

Turtle
type: Class
subclass of: Textual format
subclass of: RDF format
has definition: The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs.
Created in: 1.2
comment: The SPARQL Query Language incorporates a very similar syntax.
in subset: bioinformatics
in subset: edam
in subset: formats

N-Triples
type: Class
subclass of: Textual format
subclass of: RDF format
Created in: 1.2
has definition: A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.
comment: N-Triples should not be confused with Notation 3 which is a superset of Turtle.
in subset: bioinformatics
in subset: edam
in subset: formats

Notation3
type: Class
subclass of: Textual format
subclass of: RDF format
has definition: A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind.
has exact synonym: N3
in subset: bioinformatics
in subset: edam
in subset: formats

RDF/XML
type: Class
subclass of: OWL format
subclass of: XML
subclass of: RDF format
comment: RDF/XML is a serialization syntax for OWL DL, but not for OWL Full.
Created in: 1.2
has narrow synonym: RDF
has definition: Resource Description Framework (RDF) XML format.
in subset: bioinformatics
in subset: edam
in subset: formats
has exact synonym: SWO_3000006

OWL/XML
type: Class
subclass of: OWL format
subclass of: XML
has narrow synonym: OWL
Created in: 1.2
has definition: OWL ontology XML serialisation format.
in subset: bioinformatics
in subset: edam
in subset: formats

A2M
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: 1.3
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.
Documentation: a2m-desc.html
has db xref: a2m-desc.html
in subset: bioinformatics
in subset: edam
in subset: formats

SFF
type: Class
subclass of: Sequence trace format
subclass of: Binary format
Created in: 1.3
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: bioinformatics
in subset: edam
in subset: formats
Documentation: sff
has db xref: sff

MAP
type: Class
subclass of: PED/MAP
has exact synonym: Plink MAP
Created in: 1.3
has definition: The MAP file describes SNPs and is used by the Plink package.
Documentation: ped
in subset: bioinformatics
in subset: edam
in subset: formats

PED
type: Class
subclass of: PED/MAP
has definition: The PED file describes individuals and genetic data and is used by the Plink package.
Created in: 1.3
has exact synonym: Plink PED
Documentation: ped
in subset: bioinformatics
in subset: edam
in subset: formats

Individual genetic data format
type: Class
subclass of: Format (typed)
Created in: 1.3
has definition: Data format for a metadata on an individual and their genetic data.
in subset: bioinformatics
in subset: edam
in subset: formats

PED/MAP
type: Class
subclass of: Textual format
subclass of: Individual genetic data format
Created in: 1.3
has exact synonym: Plink PED/MAP
has definition: The PED/MAP file describes data used by the Plink package.
Documentation: ped
in subset: bioinformatics
in subset: edam
in subset: formats

CT
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
has exact synonym: Connectivity Table file format
has exact synonym: Connect format
has definition: File format of a CT (Connectivity Table) file from the RNAstructure package.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: File Formats.html
Documentation: data formats.html

SS
type: Class
subclass of: RNA secondary structure format
subclass of: Textual format
has definition: XRNA old input style format.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: xrna faq.html

RNAML
type: Class
subclass of: Alignment format
subclass of: RNA secondary structure format
subclass of: XML
Created in: beta12orEarlier
has definition: RNA Markup Language.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: rnaml

GDE
type: Class
subclass of: Textual format
subclass of: Sequence record format (text)
Created in: beta12orEarlier
has definition: Format for the Genetic Data Environment (GDE).
Documentation: GDE2.2 manual.pdf
in subset: bioinformatics
in subset: edam
in subset: formats

BLC
type: Class
subclass of: Alignment format (text)
has exact synonym: Block file format
has definition: A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: SECTION00018250000000000000

Data index format
type: Class
subclass of: Format (typed)
subclass of: Restriction
  on property: is format of
  some values from: Data index
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: formats

BAI
type: Class
subclass of: Data index format
subclass of: Restriction
  on property: is format of
  some values from: Data index
has definition: BAM indexing format
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: SAMv1.pdf

HMMER2
type: Class
subclass of: HMMER format
Created in: 1.3
has definition: HMMER profile HMM file for HMMER versions 2.x
Documentation: Userguide.pdf
in subset: bioinformatics
in subset: edam
in subset: formats

HMMER3
type: Class
subclass of: HMMER format
has definition: HMMER profile HMM file for HMMER versions 3.x
Created in: 1.3
Documentation: Userguide.pdf
in subset: bioinformatics
in subset: edam
in subset: formats

PO
type: Class
subclass of: Alignment format (text)
Created in: 1.3
has definition: EMBOSS simple sequence pair alignment format.
in subset: bioinformatics
in subset: edam
in subset: formats
Documentation: http://sourceforge.net/projects/poamsa/files/latest/download

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: bioinformatics
in subset: edam
in subset: formats

Operation
type: Class
disjoint with: Topic
disjoint with: DeprecatedClass
has narrow synonym: Function (programming)
has narrow synonym: Lambda abstraction
has narrow synonym: Mathematical function
has narrow synonym: Computational procedure
has narrow synonym: Computational subroutine
has narrow synonym: Computational operation
has related synonym: Process
Created in: beta12orEarlier
has related synonym: sumo:Function
has narrow synonym: Mathematical operation
has narrow synonym: Computational method
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). 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.
has related synonym: Computational tool
has narrow synonym: Function (computer science)
has narrow synonym: Function (mathematics)
has narrow synonym: Subroutine
has related synonym: Method
in subset: bioinformatics
in subset: edam
in subset: operations
has broad synonym: SIO_000017
has related synonym: SIO_000649
has exact synonym: operation_001
has related synonym: SWO_0000003
has broad synonym: Continuant
has related synonym: Function
has related synonym: Quality
has related synonym: process
has related synonym: quality
has related synonym: Perpetuant

Axiom
comment: Operation is a function that is computational. It typically has input(s) and output(s), which are always data.
annotated target: Function
annotated source: Operation
annotated property: hasBroadSynonym

Axiom
comment: Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Process

Axiom
comment: Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: process

Axiom
comment: However, operation is not a GFO 'Concept' present only in someone's mind.
annotated source: Operation
annotated property: hasBroadSynonym
annotated target: Function

Axiom
comment: Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'.
annotated source: Operation
annotated target: Function
annotated property: hasBroadSynonym

Axiom
comment: Method may in addition focus on how to achieve the result, not just on what to achieve as with operation.
annotated source: Operation
annotated target: Method
annotated property: hasRelatedSynonym

Axiom
comment: However, one may think that an operation is not a process and not a physical entity.
annotated source: Operation
annotated target: SIO_000649
annotated property: hasRelatedSynonym

Axiom
comment: Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.
annotated target: Process
annotated source: Operation
annotated property: hasRelatedSynonym

Axiom
comment: BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s).
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Function

Axiom
annotated target: Computational tool
comment: Computational tool provides one or more operations.
annotated source: Operation
annotated property: hasRelatedSynonym

Axiom
comment: Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Process

Axiom
comment: However, one may think that an operation is not a process.
annotated source: Operation
annotated target: SWO_0000003
annotated property: hasRelatedSynonym

Axiom
comment: Function, including an operation, can be a quality/property of e.g. a computational tool.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: quality

Axiom
comment: GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Perpetuant

Axiom
comment: Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool.
annotated source: Operation
annotated property: hasRelatedSynonym
annotated target: Quality

Search and retrieval
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Data search, query and retrieval
subclass of: Restriction
  on property: has output
  some values from: Data
has exact synonym: Database retrieval
has definition: Search or query a data resource and retrieve entries and / or annotation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (database cross-reference)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
deprecated: true
has definition: Search database to retrieve all relevant references to a particular entity or entry.
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Annotation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Ontology and terminology
subclass of: Restriction
  on property: has input
  some values from: Ontology
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
Created in: beta12orEarlier
has definition: Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.
in subset: bioinformatics
in subset: edam
in subset: operations

Data indexing
type: Class
subclass of: Data index processing
subclass of: Restriction
  on property: has output
  some values from: Data index
has exact synonym: Database indexing
has definition: Generate an index of (typically a file of) biological data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data index analysis
type: Class
subclass of: Data index processing
subclass of: Restriction
  on property: has input
  some values from: Data index
subclass of: Restriction
  on property: has output
  some values from: Data index report
Created in: beta12orEarlier
has definition: Analyse an index of biological data.
has exact synonym: Database index analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Annotation retrieval (sequence)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Retrieve basic information about a molecular sequence.
Obsolete since: beta12orEarlier
deprecated: true
consider: Sequence retrieval
in subset: obsolete

Sequence generation
type: Class
subclass of: Sequence file processing
has definition: Generate a molecular sequence by some means.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence editing
type: Class
subclass of: Sequence file processing
subclass of: Editing
Created in: beta12orEarlier
has definition: Edit or change a molecular sequence, either randomly or specifically.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence merging
type: Class
subclass of: Sequence editing
has exact synonym: Sequence splicing
has definition: Merge two or more (typically overlapping) molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence conversion
type: Class
subclass of: Sequence editing
Created in: beta12orEarlier
has definition: Convert a molecular sequence from one type to another.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence complexity calculation
type: Class
subclass of: Sequence composition calculation
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
subclass of: Restriction
  on property: has output
  some values from: Sequence complexity
has definition: Calculate sequence complexity, for example to find low-complexity regions in sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence ambiguity calculation
type: Class
subclass of: Sequence composition calculation
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
subclass of: Restriction
  on property: has output
  some values from: Sequence ambiguity
Created in: beta12orEarlier
has definition: Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence composition calculation
type: Class
subclass of: Sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
subclass of: Restriction
  on property: has output
  some values from: Sequence composition
has definition: Calculate character or word composition or frequency of a molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
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.
Created in: beta12orEarlier
has definition: Find and/or analyse repeat sequences in (typically nucleotide) sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence motif discovery
type: Class
subclass of: Feature prediction
subclass of: Sequence motif processing
subclass of: Restriction
  on property: has output
  some values from: Sequence features (motifs)
Created in: beta12orEarlier
has exact synonym: Motif discovery
has definition: Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).
comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency).
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence motif recognition
type: Class
subclass of: Feature prediction
subclass of: Sequence motif processing
subclass of: Restriction
  on property: has output
  some values from: Sequence features (motifs)
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
has exact synonym: Sequence motif detection
has definition: Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).
Created in: beta12orEarlier
has exact synonym: Motif detection
has exact synonym: Motif recognition
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence motif comparison
type: Class
subclass of: Sequence motif processing
subclass of: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence features (motifs)
has definition: Find motifs shared by molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Transcription regulatory sequence analysis
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.
Obsolete since: beta13
comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
Created in: beta12orEarlier
consider: Transcription regulatory element prediction
in subset: obsolete

Conserved transcription regulatory sequence identification
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Transcription regulatory element prediction
subclass of: Restriction
  on property: has output
  some values from: Gene features (TFBS)
has definition: Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).
Created in: beta12orEarlier
comment: 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.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein property calculation (from structure)
type: Class
subclass of: Protein property calculation
subclass of: Protein structure analysis
subclass of: Restriction
  on property: has output
  some values from: Protein property
subclass of: Restriction
  on property: has topic
  some values from: Protein structure analysis
comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
has exact synonym: Protein structural property calculation
Created in: beta12orEarlier
has definition: Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein flexibility and motion analysis
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Molecular dynamics simulation
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.
has definition: Analyse flexibility and motion in protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structural motif recognition
type: Class
subclass of: Protein feature prediction (from structure)
subclass of: Restriction
  on property: has topic
  some values from: Protein structural motifs and surfaces
subclass of: Restriction
  on property: has output
  some values from: Protein features (3D motif)
has exact synonym: Protein structural feature identification
Created in: beta12orEarlier
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.
has definition: Identify or screen for 3D structural motifs in protein structure(s).
in subset: bioinformatics
in subset: edam
in subset: operations

Protein domain recognition
type: Class
subclass of: Protein feature prediction (from structure)
subclass of: Restriction
  on property: has output
  some values from: Protein features (domains)
subclass of: Restriction
  on property: has topic
  some values from: Protein domains and folds
has definition: Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein architecture analysis
type: Class
subclass of: Protein structure analysis
has definition: Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Residue interaction calculation
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Restriction
  on property: has output
  some values from: Protein residue interactions
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
has db xref: WHATIF: SymShellOneXML
has db xref: WHATIF: SymShellFiveXML
has definition: Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).
has db xref: WHATIF:ListContactsNormal
Created in: beta12orEarlier
has db xref: WHATIF:ListSideChainContactsNormal
has db xref: WHATIF:ListSideChainContactsRelaxed
has db xref: WHATIF: SymShellTwoXML
has db xref: WHATIF:ListContactsRelaxed
has db xref: WHATIF: SymShellTenXML
in subset: bioinformatics
in subset: edam
in subset: operations

Torsion angle calculation
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Restriction
  on property: has output
  some values from: Protein torsion angle data
has definition: Calculate, visualise or analyse phi/psi angles of a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein property calculation
type: Class
subclass of: Protein data processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has input
  some values from: Protein property
subclass of: Restriction
  on property: has output
  some values from: Protein property
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
has exact synonym: Protein property rendering
Created in: beta12orEarlier
comment: This includes methods to render and visualise the properties of a protein sequence.
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: bioinformatics
in subset: edam
in subset: operations

Peptide immunogenicity prediction
type: Class
subclass of: Protein interaction prediction
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Peptide immunogenicity data
subclass of: Restriction
  on property: has topic
  some values from: Immunology
has definition: Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Feature prediction
type: Class
subclass of: Sequence analysis
subclass of: Prediction, detection and recognition
subclass of: Restriction
  on property: has output
  some values from: Feature record
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
has related synonym: SO:0000110
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 detection
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (feature table)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Extract a sequence feature table from a sequence database entry.
Obsolete since: beta13
consider: Data retrieval
in subset: obsolete

Feature table query
type: Class
subclass of: Feature table processing
subclass of: Restriction
  on property: has input
  some values from: Sequence feature table
subclass of: Restriction
  on property: has output
  some values from: Feature record
subclass of: Restriction
  on property: has input
  some values from: Sequence record full
has definition: Query the features (in a feature table) of molecular sequence(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Feature comparison
type: Class
subclass of: Comparison
subclass of: Feature table processing
subclass of: Restriction
  on property: has input
  some values from: Sequence record full
subclass of: Restriction
  on property: has input
  some values from: Sequence feature table
has exact synonym: Feature table comparison
has definition: Compare the feature tables of two or more molecular sequences.
has exact synonym: Sequence feature comparison
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (sequence alignment)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Display basic information about a sequence alignment.
Obsolete since: beta13
deprecated: true
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Sequence alignment analysis
type: Class
subclass of: Sequence alignment processing
subclass of: Alignment analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment report
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
Created in: beta12orEarlier
has definition: Analyse a molecular sequence alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment comparison
type: Class
subclass of: Sequence alignment analysis
subclass of: Comparison
comment: See also 'Sequence profile alignment'.
Created in: beta12orEarlier
has definition: Compare (typically by aligning) two molecular sequence alignments.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment conversion
type: Class
subclass of: Sequence alignment editing
has definition: Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid property processing
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: Process (read and / or write) physicochemical property data of nucleic acids.
deprecated: true
Created in: beta12orEarlier
consider: Nucleic acid property calculation
in subset: obsolete

Nucleic acid property calculation
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid property
has definition: Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Splice transcript prediction
type: Class
subclass of: Splicing analysis
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
has definition: Predict splicing alternatives or transcript isoforms from analysis of sequence data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Frameshift error detection
type: Class
subclass of: Sequencing error detection
subclass of: Mutation detection
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
Created in: beta12orEarlier
has definition: Detect frameshift errors in DNA sequences (from sequencing projects).
in subset: bioinformatics
in subset: edam
in subset: operations

Vector sequence detection
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Nucleic acid sequence comparison
has definition: Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure prediction
type: Class
subclass of: Protein feature prediction (from sequence)
subclass of: Protein secondary structure processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Protein structure prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein secondary structure
subclass of: Restriction
  on property: has output
  some values from: Protein features (secondary structure)
Created in: beta12orEarlier
has definition: Predict secondary structure of protein sequences.
has exact synonym: Secondary structure prediction (protein)
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.
in subset: bioinformatics
in subset: edam
in subset: operations

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 (super-secondary)
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
has definition: Predict super-secondary structure of protein sequence(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Transmembrane protein prediction
type: Class
subclass of: Protein secondary structure prediction
subclass of: Transmembrane protein analysis
subclass of: Restriction
  on property: has output
  some values from: Protein features (membrane regions)
Created in: beta12orEarlier
has definition: Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Transmembrane protein analysis
type: Class
subclass of: Protein data processing
subclass of: Restriction
  on property: has output
  some values from: Protein features (membrane regions)
subclass of: Restriction
  on property: has topic
  some values from: Membrane and lipoproteins
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).
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structure prediction
type: Class
subclass of: Prediction, detection and recognition
subclass of: Structure processing
subclass of: Restriction
  on property: has topic
  some values from: Structure prediction
subclass of: Restriction
  on property: has output
  some values from: Structure
Created in: beta12orEarlier
has definition: Predict tertiary structure of a molecular (biopolymer) sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Residue interaction prediction
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Sequence alignment analysis (protein)
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.
comment: Methods usually involve multiple sequence alignment analysis.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction raw data analysis
type: Class
subclass of: Protein interaction analysis
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
subclass of: Restriction
  on property: has input
  some values from: Protein interaction raw data
Created in: beta12orEarlier
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: bioinformatics
in subset: edam
in subset: operations

Protein-protein interaction prediction (from protein sequence)
type: Class
subclass of: Protein-protein interaction prediction
subclass of: Protein function prediction (from sequence)
has definition: Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein-protein interaction prediction (from protein structure)
type: Class
subclass of: Protein-protein interaction prediction
subclass of: Protein feature prediction (from structure)
has definition: Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction network analysis
type: Class
subclass of: Protein interaction network processing
subclass of: Pathway or network analysis
subclass of: Protein interaction analysis
subclass of: Restriction
  on property: has input
  some values from: Pathway or network (protein-protein interaction)
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
Created in: beta12orEarlier
has definition: Analyse a network of protein interactions.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction network comparison
type: Class
subclass of: Protein interaction network analysis
subclass of: Protein function comparison
subclass of: Restriction
  on property: has input
  some values from: Pathway or network (protein-protein interaction)
has definition: Compare two or more networks of protein interactions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

RNA secondary structure prediction
type: Class
subclass of: Nucleic acid feature prediction
subclass of: RNA secondary structure processing
subclass of: Restriction
  on property: has output
  some values from: RNA secondary structure record
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
Created in: beta12orEarlier
has definition: Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).
comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid folding analysis
type: Class
subclass of: Modelling and simulation
subclass of: Nucleic acid data processing
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid folding report
has exact synonym: Nucleic acid folding
has exact synonym: Nucleic acid folding modelling
has definition: Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (restriction enzyme annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Retrieve information on restriction enzymes or restriction enzyme sites.
deprecated: true
has exact synonym: Restriction enzyme information retrieval
Obsolete since: beta13
consider: Data retrieval
in subset: obsolete

Genetic marker identification
type: Class
subclass of: Obsolete concept (EDAM)
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.
has definition: Identify genetic markers in DNA sequences.
Obsolete since: beta13
Created in: beta12orEarlier
deprecated: true
consider: Nucleic acid feature prediction
in subset: obsolete

Genetic mapping
type: Class
subclass of: DNA mapping
subclass of: Restriction
  on property: has output
  some values from: Genetic map
has exact synonym: Functional mapping
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.
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.
has exact synonym: Genetic map generation
has exact synonym: Linkage mapping
comment: This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Linkage analysis
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Mapping
subclass of: Restriction
  on property: has output
  some values from: Gene annotation (linkage)
has definition: Analyse genetic linkage.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage table generation
type: Class
subclass of: Codon usage table processing
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage table comparison
type: Class
subclass of: Codon usage table processing
subclass of: Nucleic acid comparison
has definition: Compare two or more codon usage tables.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage analysis
type: Class
subclass of: Nucleic acid data processing
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
subclass of: Restriction
  on property: has input
  some values from: Codon usage table
subclass of: Restriction
  on property: has output
  some values from: Codon usage report
subclass of: Restriction
  on property: has output
  some values from: Codon usage table
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
has exact synonym: synon: Codon usage table analysis
has definition: Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences.
has exact synonym: synon: Codon usage data analysis
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Base position variability plotting
type: Class
subclass of: Codon usage analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence composition (base position variability)
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: bioinformatics
in subset: edam
in subset: operations

Sequence word comparison
type: Class
subclass of: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment (words)
Created in: beta12orEarlier
has definition: Find exact character or word matches between molecular sequences without full sequence alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence distance matrix generation
type: Class
subclass of: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence distance matrix
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
has definition: Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.
Created in: beta12orEarlier
has exact synonym: Phylogenetic distance matrix generation
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence redundancy removal
type: Class
subclass of: Sequence clustering
subclass of: Restriction
  on property: has output
  some values from: Sequence
subclass of: Restriction
  on property: has topic
  some values from: Sequence clustering
has definition: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence clustering
type: Class
subclass of: Sequence comparison
subclass of: Sequence cluster processing
subclass of: Sequence classification
subclass of: Restriction
  on property: has output
  some values from: Sequence cluster
has exact synonym: Sequence cluster generation
has definition: Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
Created in: beta12orEarlier
comment: The clusters may be output or used internally for some other purpose.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment construction
type: Class
subclass of: Sequence comparison
subclass of: Sequence alignment processing
subclass of: Alignment construction
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment
subclass of: Restriction
  on property: has input
  some values from: Sequence
has exact synonym: Sequence alignment computation
has exact synonym: Sequence alignment
has exact synonym: Sequence alignment generation
has definition: Align (identify equivalent sites within) molecular sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Hybrid sequence alignment construction
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).
Obsolete since: beta13
Created in: beta12orEarlier
deprecated: true
has exact synonym: Hybrid sequence alignment
consider: Sequence alignment construction
in subset: obsolete

Structure-based sequence alignment construction
type: Class
subclass of: Sequence alignment construction
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
has definition: Align molecular sequences using sequence and structural information.
Created in: beta12orEarlier
has exact synonym: Structure-based sequence alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Structure alignment construction
type: Class
subclass of: Structure comparison
subclass of: Alignment construction
subclass of: Structure alignment processing
subclass of: Restriction
  on property: has output
  some values from: Structure alignment
has exact synonym: Structure alignment
Created in: beta12orEarlier
has definition: Align (superimpose) molecular tertiary structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile generation
type: Class
subclass of: Sequence profile processing
subclass of: Sequence alignment processing
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
subclass of: Restriction
  on property: has output
  some values from: Sequence profile
has definition: Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structural (3D) profile generation
type: Class
subclass of: Structural (3D) profile processing
subclass of: Structure processing
subclass of: Structure alignment processing
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 (3D) 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 generation
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile alignment construction
type: Class
subclass of: Sequence profile processing
subclass of: Alignment construction
subclass of: Restriction
  on property: has input
  some values from: Sequence profile
subclass of: Restriction
  on property: has output
  some values from: Sequence profile alignment
has definition: Align sequence profiles (representing sequence alignments).
comment: See also 'Sequence alignment comparison'.
Created in: beta12orEarlier
has exact synonym: Sequence profile alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Structural (3D) profile alignment construction
type: Class
subclass of: Structural (3D) profile processing
subclass of: Alignment construction
subclass of: Restriction
  on property: has topic
  some values from: Structure alignment
subclass of: Restriction
  on property: has input
  some values from: Structural (3D) profile
subclass of: Restriction
  on property: has output
  some values from: Structural (3D) profile alignment
has exact synonym: Structural (3D) profile alignment
has definition: Align structural (3D) profiles or templates (representing structures or structure alignments).
has exact synonym: Structural profile alignment
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence-profile alignment construction
type: Class
subclass of: Sequence analysis
subclass of: Sequence profile processing
subclass of: Alignment construction
subclass of: Restriction
  on property: has input
  some values from: Sequence profile
subclass of: Restriction
  on property: has output
  some values from: Sequence-profile alignment
comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has exact synonym: Sequence-profile alignment
has definition: Align molecular sequence(s) to sequence profile(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence-3D profile alignment construction
type: Class
subclass of: Protein fold recognition
subclass of: Sequence analysis
subclass of: Alignment construction
subclass of: Restriction
  on property: has input
  some values from: Structural (3D) profile
subclass of: Restriction
  on property: has output
  some values from: Sequence-3D profile alignment
has exact synonym: Sequence-3D profile alignment
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has definition: Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein threading
type: Class
subclass of: Protein fold recognition
subclass of: Alignment construction
subclass of: Restriction
  on property: has output
  some values from: Sequence-structure alignment
subclass of: Restriction
  on property: has input
  some values from: Protein structure
subclass of: Restriction
  on property: has topic
  some values from: Homology modelling
has exact synonym: Sequence-structure alignment
has definition: Align molecular sequence to structure in 3D space (threading).
Created in: beta12orEarlier
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein fold recognition
type: Class
subclass of: Protein feature prediction (from sequence)
subclass of: Protein structure prediction
subclass of: Protein comparison
subclass of: Restriction
  on property: has topic
  some values from: Protein fold recognition
subclass of: Restriction
  on property: has output
  some values from: Protein features (domains)
has exact synonym: Protein fold prediction
has definition: Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).
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.
has exact synonym: Protein domain prediction
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (metadata and documentation)
type: Class
subclass of: Data retrieval
subclass of: Restriction
  on property: has output
  some values from: Metadata
comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
Created in: beta12orEarlier
has exact synonym: Data retrieval (metadata)
has definition: Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.
has exact synonym: Data retrieval (documentation)
in subset: bioinformatics
in subset: edam
in subset: operations

Literature search
type: Class
subclass of: Database search
subclass of: Restriction
  on property: has topic
  some values from: Literature and reference
subclass of: Restriction
  on property: has output
  some values from: Citation
has definition: Query the biomedical and informatics literature.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Text mining
type: Class
subclass of: Article analysis
subclass of: Restriction
  on property: has output
  some values from: Text mining report
subclass of: Restriction
  on property: has topic
  some values from: Text mining
subclass of: Restriction
  on property: has input
  some values from: Report
has definition: Process and analyse text (typically the biomedical and informatics literature) to extract information from it.
has exact synonym: Text data mining
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Virtual PCR
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
has definition: Perform in-silico (virtual) PCR.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design
type: Class
subclass of: Primer and probe design
subclass of: Restriction
  on property: has output
  some values from: PCR primers
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
subclass of: Restriction
  on property: has topic
  some values from: Sequence design
has definition: Design or predict oligonucleotide primers for PCR and DNA amplification etc.
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.
has exact synonym: PCR primer prediction
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray probe design
type: Class
subclass of: Primer and probe design
subclass of: Optimisation and refinement
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: Sequence design
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
has exact synonym: Microarray probe prediction
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly
type: Class
subclass of: Mapping and assembly
subclass of: Sequence processing (nucleic acid)
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
has definition: Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray data standardization and normalization
type: Class
subclass of: Evaluation and validation
subclass of: Gene expression data processing
subclass of: Restriction
  on property: has output
  some values from: Microarray hybridisation data
subclass of: Restriction
  on property: has input
  some values from: Microarray hybridisation data
comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.
has definition: Standardize or normalize microarray data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequencing-based expression profile data processing
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
has definition: Process (read and / or write) SAGE, MPSS or SBS experimental data.
consider: Gene expression data processing
in subset: obsolete

Gene expression profile clustering
type: Class
subclass of: Gene expression profile comparison
subclass of: Restriction
  on property: has output
  some values from: Processed microarray data
has definition: Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression profile generation
type: Class
subclass of: Gene expression profile processing
subclass of: Restriction
  on property: has output
  some values from: Gene expression profile
has exact synonym: Gene expression profiling
Created in: beta12orEarlier
has exact synonym: Expression profiling
has definition: Generate a gene expression profile or pattern, for example from microarray data.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression profile comparison
type: Class
subclass of: Gene expression profile analysis
subclass of: Nucleic acid comparison
subclass of: Restriction
  on property: has output
  some values from: Processed microarray data
has definition: Compare gene expression profiles or patterns.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Functional profiling
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Interpret (in functional terms) and annotate gene expression data.
Obsolete since: beta12orEarlier
deprecated: true
consider: Gene expression profile analysis
in subset: obsolete

EST and cDNA sequence analysis
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
has definition: Analyse EST or cDNA sequences.
consider: Sequence analysis
in subset: obsolete

Structural genomics target selection
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
comment: Methods will typically navigate a graph of protein families of known structure.
has definition: Identify and select targets for protein structural determination.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Protein structure analysis
in subset: obsolete

Protein secondary structure assignment
type: Class
subclass of: Protein secondary structure processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
subclass of: Restriction
  on property: has output
  some values from: Protein features (secondary structure)
has definition: Assign secondary structure from protein coordinate or experimental data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure assignment
type: Class
subclass of: Structure processing (protein)
subclass of: Restriction
  on property: has topic
  some values from: Structural biology
subclass of: Restriction
  on property: has output
  some values from: Protein structure
has definition: Assign a protein tertiary structure (3D coordinates) from raw experimental data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein model evaluation
type: Class
subclass of: Protein modelling
subclass of: Evaluation and 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: Protein tertiary structure
subclass of: Restriction
  on property: has topic
  some values from: Protein structure prediction
subclass of: Restriction
  on property: has topic
  some values from: Molecular modelling
subclass of: Restriction
  on property: has topic
  some values from: Homology modelling
Created in: beta12orEarlier
has db xref: WHATIF: UseFileDB
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.
has definition: Evaluate the quality or correctness a protein three-dimensional model.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein model refinement
type: Class
subclass of: Protein model evaluation
subclass of: Optimisation and refinement
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.
Created in: beta12orEarlier
has definition: Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc.
has db xref: WHATIF: CorrectedPDBasXML
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction
type: Class
subclass of: Phylogenetic tree processing
subclass of: Sequence classification
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
has exact synonym: Phylogenetic tree generation
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree.
comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.
has exact synonym: Phylogenetic tree construction
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree analysis
type: Class
subclass of: Phylogenetic tree processing
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree report
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic tree
has definition: Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree comparison
type: Class
subclass of: Phylogenetic tree analysis
subclass of: Comparison
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.
has definition: Compare two or more phylogenetic trees.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree editing
type: Class
subclass of: Phylogenetic tree processing
subclass of: Editing
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic tree
Created in: beta12orEarlier
has definition: Edit a phylogenetic tree.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic footprinting / shadowing
type: Class
subclass of: Phylogenetic tree construction (from molecular sequences)
subclass of: Restriction
  on property: has topic
  some values from: Phylogenomics
has definition: Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).
Created in: beta12orEarlier
comment: 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.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein folding simulation
type: Class
subclass of: Protein folding analysis
has definition: Simulate the folding of a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein folding pathway prediction
type: Class
subclass of: Protein folding analysis
subclass of: Prediction, detection and recognition (protein)
Created in: beta12orEarlier
has definition: Predict the folding pathway(s) or non-native structural intermediates of a protein.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein SNP mapping
type: Class
subclass of: Protein modelling (mutation)
subclass of: Restriction
  on property: has topic
  some values from: SNPs
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (polymorphism annotation)
has definition: Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein modelling (mutation)
type: Class
subclass of: Protein modelling
subclass of: Prediction, detection and recognition (protein)
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
comment: Methods might predict silent or pathological mutations.
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: Protein mutation modelling
in subset: bioinformatics
in subset: edam
in subset: operations

Immunogen design
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has definition: Design molecules that elicit an immune response (immunogens).
deprecated: true
consider: Peptide immunogen prediction and optimisation
in subset: obsolete

Zinc finger protein domain prediction and optimisation
type: Class
subclass of: Protein-nucleic acid binding prediction
subclass of: Optimisation and refinement
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
subclass of: Restriction
  on property: has output
  some values from: Protein-nucleic acid interaction
Created in: beta12orEarlier
has definition: Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
in subset: bioinformatics
in subset: edam
in subset: operations

Enzyme kinetics calculation
type: Class
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Enzyme kinetics data
subclass of: Restriction
  on property: has topic
  some values from: Enzymes
has definition: Calculate Km, Vmax and derived data for an enzyme reaction.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

File format conversion
type: Class
subclass of: File processing
has exact synonym: File reformatting
has definition: Reformat a file of data (or equivalent entity in memory).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

File validation
type: Class
subclass of: File processing
subclass of: Evaluation and validation
Created in: beta12orEarlier
has definition: Test and validate the format and content of a data file.
in subset: bioinformatics
in subset: edam
in subset: operations

Plotting and rendering
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has output
  some values from: Image
subclass of: Restriction
  on property: has input
  some values from: Data
subclass of: Restriction
  on property: has topic
  some values from: Data visualisation
has definition: Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.
has exact synonym: Visualisation
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search
type: Class
subclass of: Sequence analysis
subclass of: Database search
subclass of: Restriction
  on property: has output
  some values from: Database hits (sequence)
subclass of: Restriction
  on property: has topic
  some values from: Sequence comparison
Created in: beta12orEarlier
comment: This excludes direct retrieval methods (e.g. the dbfetch program).
has definition: Search a sequence database by sequence comparison and retrieve similar sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure database search
type: Class
subclass of: Database search
subclass of: Structure classification
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
subclass of: Restriction
  on property: has output
  some values from: Database hits (structure)
has definition: Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary database search
type: Class
subclass of: Database search
subclass of: Sequence screening
subclass of: Restriction
  on property: has topic
  some values from: Protein families
subclass of: Restriction
  on property: has output
  some values from: Database hits (secondary)
has exact synonym: Sequence profile database search
has definition: Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.
Created in: beta12orEarlier
comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.).
has exact synonym: Protein sequence classification
in subset: bioinformatics
in subset: edam
in subset: operations

Motif database search
type: Class
subclass of: Sequence motif recognition
subclass of: Database search
subclass of: Sequence screening
subclass of: Restriction
  on property: has output
  some values from: Sequence features (motifs)
has definition: Screen a sequence against a motif or pattern database.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile database search
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.4
has definition: Search a database of sequence profiles with a query sequence.
Created in: beta12orEarlier
deprecated: true
consider: Protein secondary database search
in subset: obsolete

Transmembrane protein database search
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Search a database of transmembrane proteins, for example for sequence or structural similarities.
deprecated: true
Obsolete since: beta12orEarlier
consider: Database search
in subset: obsolete

Sequence retrieval (by code)
type: Class
subclass of: Sequence retrieval
Created in: beta12orEarlier
has definition: Query a database and retrieve sequences with a given entry code or accession number.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence retrieval (by keyword)
type: Class
subclass of: Sequence retrieval
Created in: beta12orEarlier
has definition: Query a database and retrieve sequences containing a given keyword.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence)
type: Class
subclass of: Sequence database search
subclass of: Sequence comparison
subclass of: Sequence screening
Created in: beta12orEarlier
has definition: Search a sequence database and retrieve sequences that are similar to a query sequence.
has exact synonym: Sequence similarity search
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by motif or pattern)
type: Class
subclass of: Sequence motif recognition
subclass of: Sequence database search
subclass of: Restriction
  on property: has input
  some values from: Sequence motif
Created in: beta12orEarlier
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: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by amino acid composition)
type: Class
subclass of: Sequence database search
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
subclass of: Restriction
  on property: has input
  some values from: Amino acid frequencies
Created in: beta12orEarlier
has definition: Search a sequence database and retrieve sequences of a given amino acid composition.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by physicochemical property)
type: Class
subclass of: Sequence database search
Created in: beta12orEarlier
has definition: Search a sequence database and retrieve sequences with a specified physicochemical property.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence using word-based methods)
type: Class
subclass of: Sequence word comparison
subclass of: Sequence database search (by sequence)
has definition: Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.
has exact synonym: Sequence similarity search (word-based methods)
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence using profile-based methods)
type: Class
subclass of: Sequence-profile alignment construction
subclass of: Sequence database search (by sequence)
comment: This includes tools based on PSI-BLAST.
Created in: beta12orEarlier
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.
has exact synonym: Sequence similarity search (profile-based methods)
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence using local alignment-based methods)
type: Class
subclass of: Sequence database search (by sequence)
subclass of: Pairwise sequence alignment construction (local)
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
comment: This includes tools based on the Smith-Waterman algorithm or FASTA.
has exact synonym: Sequence similarity search (local alignment-based methods)
Created in: beta12orEarlier
has definition: Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence using global alignment-based methods)
type: Class
subclass of: Sequence database search (by sequence)
subclass of: Pairwise sequence alignment construction (global)
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
has exact synonym: Sequence similarity search (global alignment-based methods)
Created in: beta12orEarlier
has definition: Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.
comment: This includes tools based on the Needleman and Wunsch algorithm.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by sequence for primer sequences)
type: Class
subclass of: Sequence database search (by sequence)
subclass of: Restriction
  on property: has topic
  some values from: Sequence design
has exact synonym: Sequence similarity search (primer sequences)
comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
has definition: Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by molecular weight)
type: Class
subclass of: Sequence database search (by physicochemical property)
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
subclass of: Restriction
  on property: has input
  some values from: Peptide mass fingerprint
Created in: beta12orEarlier
has exact synonym: Peptide mass fingerprinting
has exact synonym: Protein fingerprinting
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: bioinformatics
in subset: edam
in subset: operations

Sequence database search (by isoelectric point)
type: Class
subclass of: Sequence database search (by physicochemical property)
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
has definition: Search sequence(s) or a sequence database for sequences of a given isoelectric point.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structure retrieval (by code)
type: Class
subclass of: Structure retrieval
Created in: beta12orEarlier
has definition: Query a tertiary structure database and retrieve entries with a given entry code or accession number.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure retrieval (by keyword)
type: Class
subclass of: Structure retrieval
Created in: beta12orEarlier
has definition: Query a tertiary structure database and retrieve entries containing a given keyword.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure database search (by sequence)
type: Class
subclass of: Structure database search
subclass of: Sequence comparison
subclass of: Sequence screening
has definition: Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.
has exact synonym: Structure retrieval by sequence
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structure database search (by structure)
type: Class
subclass of: Structure database search
subclass of: Restriction
  on property: has topic
  some values from: Structure comparison
has exact synonym: Structure retrieval by structure
has definition: Search a tertiary structure database and retrieve structures that are similar to a query structure.
has exact synonym: Structural similarity search
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
has definition: Annotate a molecular sequence record with terms from a controlled vocabulary.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Genome annotation
type: Class
subclass of: Sequence annotation
has definition: Annotate a genome sequence with terms from a controlled vocabulary.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid sequence reverse and complement
type: Class
subclass of: Sequence generation (nucleic acid)
has definition: Generate the reverse and / or complement of a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Nucleic acid restriction digest
type: Class
subclass of: Nucleic acid property calculation
subclass of: Sequence generation (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Restriction digest
has definition: Generate digest fragments for a nucleotide sequence containing restriction sites.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein sequence cleavage
type: Class
subclass of: Sequence generation (protein)
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
subclass of: Restriction
  on property: has output
  some values from: Proteolytic digest
has definition: Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence mutation and randomization
type: Class
subclass of: Sequence editing
has definition: Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence masking
type: Class
subclass of: Sequence editing
subclass of: Restriction
  on property: has input
  some values from: Sequence mask character
Created in: beta12orEarlier
comment: For example, SNPs or repeats in a DNA sequence might be masked.
has definition: Mask characters in a molecular sequence (replacing those characters with a mask character).
in subset: bioinformatics
in subset: edam
in subset: operations

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: bioinformatics
in subset: edam
in subset: operations

Restriction site creation
type: Class
subclass of: Sequence editing (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
Created in: beta12orEarlier
has definition: Create (or remove) restriction sites in sequences, for example using silent mutations.
in subset: bioinformatics
in subset: edam
in subset: operations

DNA translation
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
has definition: Translate a DNA sequence into protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

DNA transcription
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
has definition: Transcribe a nucleotide sequence into mRNA sequence(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence composition calculation (nucleic acid)
type: Class
subclass of: Sequence composition calculation
subclass of: Nucleic acid property calculation
Created in: beta12orEarlier
has definition: Calculate base frequency or word composition of a nucleotide sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence composition calculation (protein)
type: Class
subclass of: Sequence composition calculation
subclass of: Protein property calculation (from sequence)
Created in: beta12orEarlier
has definition: Calculate amino acid frequency or word composition of a protein sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Repeat sequence detection
type: Class
subclass of: Repeat sequence analysis
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has output
  some values from: Sequence features (repeats)
has definition: Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Repeat sequence organisation analysis
type: Class
subclass of: Sequence composition calculation
subclass of: Repeat sequence analysis
has definition: Analyse repeat sequence organization such as periodicity.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein hydropathy calculation (from structure)
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Protein hydropathy calculation
Created in: beta12orEarlier
has definition: Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein solvent accessibility calculation
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Restriction
  on property: has topic
  some values from: Protein properties
subclass of: Restriction
  on property: has output
  some values from: Protein solvent accessibility
has definition: Calculate solvent accessible or buried surface areas in protein structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein hydropathy cluster calculation
type: Class
subclass of: Protein hydropathy calculation (from structure)
subclass of: Protein residue cluster calculation
has definition: Identify clusters of hydrophobic or charged residues in a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein dipole moment calculation
type: Class
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein dipole moment
has definition: Calculate whether a protein structure has an unusually large net charge (dipole moment).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein surface and interior calculation
type: Class
subclass of: Protein solvent accessibility calculation
subclass of: Restriction
  on property: has topic
  some values from: Protein structural motifs and surfaces
has definition: Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Binding site prediction (from structure)
type: Class
subclass of: Protein structural motif recognition
subclass of: Binding site prediction
has exact synonym: Ligand-binding and active site prediction (from structure)
Created in: beta12orEarlier
has definition: Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein-nucleic acid binding site analysis
type: Class
subclass of: Protein interaction analysis
subclass of: Restriction
  on property: has input
  some values from: Protein-nucleic acid interaction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Analyse RNA or DNA-binding sites in protein structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein peeling
type: Class
subclass of: Protein domain recognition
subclass of: Restriction
  on property: has output
  some values from: Protein features (domains)
has definition: Decompose a structure into compact or globular fragments (protein peeling).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein distance matrix calculation
type: Class
subclass of: Residue interaction calculation
subclass of: Restriction
  on property: has output
  some values from: Protein distance matrix
has definition: Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein contact map calculation
type: Class
subclass of: Residue contact calculation (residue-residue)
subclass of: Restriction
  on property: has output
  some values from: Protein contact map
has definition: Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue cluster calculation
type: Class
subclass of: Residue contact calculation (residue-residue)
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.
comment: Cluster of contacting residues might be key structural residues.
in subset: bioinformatics
in subset: edam
in subset: operations

Hydrogen bond calculation
type: Class
subclass of: Residue interaction calculation
subclass of: Restriction
  on property: has output
  some values from: Protein hydrogen bonds
has definition: Identify potential hydrogen bonds between amino acids and other groups.
has db xref: WHATIF:ShowHydrogenBonds
has db xref: WHATIF:ShowHydrogenBondsM
Created in: beta12orEarlier
comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.
has db xref: WHATIF:HasHydrogenBonds
in subset: bioinformatics
in subset: edam
in subset: operations

Residue non-canonical interaction detection
type: Class
subclass of: Residue interaction calculation
subclass of: Protein model evaluation
has definition: Calculate non-canonical atomic interactions in protein structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Ramachandran plot calculation
type: Class
subclass of: Torsion angle 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: bioinformatics
in subset: edam
in subset: operations

Ramachandran plot evaluation
type: Class
subclass of: Dihedral angle validation
subclass of: Restriction
  on property: has input
  some values from: Ramachandran plot
subclass of: Restriction
  on property: has output
  some values from: Protein structural quality report
has definition: Analyse (typically to validate) a Ramachandran plot of a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein molecular weight calculation
type: Class
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
subclass of: Restriction
  on property: has output
  some values from: Peptide molecular weights
Created in: beta12orEarlier
has definition: Calculate the molecular weight of a protein sequence or fragments.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein extinction coefficient calculation
type: Class
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein extinction coefficient
has definition: Predict extinction coefficients or optical density of a protein sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein pH-dependent property calculation
type: Class
subclass of: Protein property calculation (from sequence)
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein hydropathy calculation (from sequence)
type: Class
subclass of: Protein hydropathy calculation
Created in: beta12orEarlier
has definition: Hydropathy calculation on a protein sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein titration curve plotting
type: Class
subclass of: Protein pH-dependent property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein titration curve
has definition: Plot a protein titration curve.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein isoelectric point calculation
type: Class
subclass of: Protein pH-dependent property calculation
subclass of: Restriction
  on property: has output
  some values from: Protein isoelectric point
has definition: Calculate isoelectric point of a protein sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein hydrogen exchange rate calculation
type: Class
subclass of: Protein pH-dependent property 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: bioinformatics
in subset: edam
in subset: operations

Protein hydrophobic region calculation
type: Class
subclass of: Protein hydropathy calculation (from sequence)
Created in: beta12orEarlier
has definition: Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein aliphatic index calculation
type: Class
subclass of: Protein hydropathy calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein aliphatic index
has definition: Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein hydrophobic moment plotting
type: Class
subclass of: Protein hydropathy calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Peptide hydrophobic moment
has definition: Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein globularity prediction
type: Class
subclass of: Protein hydropathy calculation (from sequence)
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: bioinformatics
in subset: edam
in subset: operations

Protein solubility prediction
type: Class
subclass of: Protein hydropathy calculation (from sequence)
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: bioinformatics
in subset: edam
in subset: operations

Protein crystallizability prediction
type: Class
subclass of: Protein hydropathy calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein crystallizability
has definition: Predict crystallizability of a protein sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein signal peptide detection (eukaryotes)
type: Class
subclass of: Protein signal peptide detection
has definition: Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein signal peptide detection (bacteria)
type: Class
subclass of: Protein signal peptide detection
Created in: beta12orEarlier
has definition: Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins.
in subset: bioinformatics
in subset: edam
in subset: operations

MHC peptide immunogenicity prediction
type: Class
subclass of: Peptide immunogenicity prediction
Created in: beta12orEarlier
has definition: Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein feature prediction (from sequence)
type: Class
subclass of: Protein sequence analysis
subclass of: Protein feature prediction
has definition: Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.
has exact synonym: Sequence feature detection (protein)
Created in: beta12orEarlier
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid feature prediction
type: Class
subclass of: Sequence motif recognition
subclass of: Feature prediction
subclass of: Nucleic acid sequence analysis
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features
Created in: beta12orEarlier
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
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)
in subset: bioinformatics
in subset: edam
in subset: operations

Epitope mapping
type: Class
subclass of: Mapping and assembly
subclass of: Protein site detection
subclass of: Restriction
  on property: has output
  some values from: Protein features (binding sites)
subclass of: Restriction
  on property: has topic
  some values from: Immunology
Created in: beta12orEarlier
comment: Epitope mapping is commonly done during vaccine design.
has definition: Predict antigenic determinant sites (epitopes) in protein sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein post-translation modification site prediction
type: Class
subclass of: Protein site detection
subclass of: Restriction
  on property: has output
  some values from: Protein features (post-translation modifications)
subclass of: Restriction
  on property: has topic
  some values from: Protein modifications
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.
Created in: beta12orEarlier
has definition: Predict post-translation modification sites in protein sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein signal peptide detection
type: Class
subclass of: Protein subcellular localization prediction
subclass of: Protein site detection
subclass of: Restriction
  on property: has output
  some values from: Protein features (signal peptides)
subclass of: Restriction
  on property: has topic
  some values from: Protein targeting and localization
Created in: beta12orEarlier
has definition: Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.
comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Binding site prediction (from sequence)
type: Class
subclass of: Binding site prediction
subclass of: Protein site detection
Created in: beta12orEarlier
has exact synonym: Ligand-binding and active site prediction (from sequence)
has definition: Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein-nucleic acid binding prediction
type: Class
subclass of: Binding site prediction (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein features (binding sites)
has definition: Predict RNA and DNA-binding binding sites in protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein folding site prediction
type: Class
subclass of: Protein folding analysis
subclass of: Protein site detection
subclass of: Restriction
  on property: has output
  some values from: Protein features (key folding sites)
Created in: beta12orEarlier
has definition: Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein cleavage site prediction
type: Class
subclass of: Protein site detection
subclass of: Restriction
  on property: has topic
  some values from: Proteomics
subclass of: Restriction
  on property: has output
  some values from: Protein features (cleavage sites)
has definition: Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Epitope mapping (MHC Class I)
type: Class
subclass of: Epitope mapping
Created in: beta12orEarlier
has definition: Predict epitopes that bind to MHC class I molecules.
in subset: bioinformatics
in subset: edam
in subset: operations

Epitope mapping (MHC Class II)
type: Class
subclass of: Epitope mapping
Created in: beta12orEarlier
has definition: Predict epitopes that bind to MHC class II molecules.
in subset: bioinformatics
in subset: edam
in subset: operations

Whole gene prediction
type: Class
subclass of: Gene and gene component prediction
has definition: Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Gene component prediction
type: Class
subclass of: Gene and gene component prediction
has definition: Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.
Created in: beta12orEarlier
comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Transposon prediction
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (mobile genetic elements)
has definition: Detect or predict transposons, retrotransposons / retrotransposition signatures etc.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

PolyA signal detection
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (PolyA signal or site)
Created in: beta12orEarlier
has definition: Detect polyA signals in nucleotide sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Quadruplex formation site detection
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (quadruplexes)
has exact synonym: Quadruplex structure prediction
Created in: beta12orEarlier
comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
has definition: Detect quadruplex-forming motifs in nucleotide sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

CpG island and isochore detection
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has topic
  some values from: Sequence composition, complexity and repeats
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (CpG island and isochore)
has exact synonym: CpG island and isochores rendering
Created in: beta12orEarlier
has exact synonym: CpG island and isochores detection
has definition: Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Restriction site recognition
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (restriction sites)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
has definition: Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleosome formation or exclusion sequence prediction
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (nucleosome exclusion sequences)
has definition: Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Splice site prediction
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (splice sites)
comment: Methods might require a pre-mRNA or genomic DNA sequence.
has definition: Identify, predict or analyse splice sites in nucleotide sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Integrated gene prediction
type: Class
subclass of: Whole gene prediction
Created in: beta12orEarlier
has definition: Predict whole gene structure using a combination of multiple methods to achieve better predictions.
in subset: bioinformatics
in subset: edam
in subset: operations

Operon prediction
type: Class
subclass of: Whole gene prediction
Created in: beta12orEarlier
has definition: Find operons (operators, promoters and genes) in bacteria genes.
in subset: bioinformatics
in subset: edam
in subset: operations

Coding region prediction
type: Class
subclass of: Gene component prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (coding sequence)
Created in: beta12orEarlier
has definition: Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Selenocysteine insertion sequence (SECIS) prediction
type: Class
subclass of: Gene component prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (gene and transcript structure)
Created in: beta12orEarlier
comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.
has definition: Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Transcription regulatory element prediction
type: Class
subclass of: Gene component prediction
subclass of: Restriction
  on property: has topic
  some values from: Transcription factors and regulatory sites
Created in: beta12orEarlier
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.
has definition: Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Translation initiation site prediction
type: Class
subclass of: Coding region prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
has definition: Predict translation initiation sites, possibly by searching a database of sites.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Promoter prediction
type: Class
subclass of: Transcription regulatory element prediction
subclass of: Restriction
  on property: has output
  some values from: Gene features (promoter)
Created in: beta12orEarlier
comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.
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: bioinformatics
in subset: edam
in subset: operations

Transcription regulatory element prediction (DNA-cis)
type: Class
subclass of: Transcription regulatory element prediction
has definition: Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.
comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Transcription regulatory element prediction (RNA-cis)
type: Class
subclass of: Transcription regulatory element prediction
Created in: beta12orEarlier
has definition: Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.
comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
in subset: bioinformatics
in subset: edam
in subset: operations

Transcription regulatory element prediction (trans)
type: Class
subclass of: Transcription regulatory element prediction
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
has exact synonym: Functional RNA identification
has definition: Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.
comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Matrix/scaffold attachment site prediction
type: Class
subclass of: Transcription regulatory element prediction
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (matrix/scaffold attachment sites)
Created in: beta12orEarlier
has definition: Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.
comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
in subset: bioinformatics
in subset: edam
in subset: operations

Transcription factor binding site prediction
type: Class
subclass of: Promoter prediction
subclass of: Restriction
  on property: has output
  some values from: Gene features (TFBS)
has definition: Identify or predict transcription factor binding sites in DNA sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (exon)
Created in: beta12orEarlier
has definition: Identify or predict exonic splicing enhancers (ESE) in exons.
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment quality evaluation
type: Class
subclass of: Sequence alignment analysis
subclass of: Evaluation and validation
Created in: beta12orEarlier
has definition: Evaluate molecular sequence alignment accuracy.
comment: Evaluation might be purely sequence-based or use structural information.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (conservation)
type: Class
subclass of: Sequence alignment analysis
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.
has exact synonym: Residue conservation analysis
Created in: beta12orEarlier
has definition: Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (site correlation)
type: Class
subclass of: Sequence alignment analysis
Created in: beta12orEarlier
comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
has definition: Analyse correlations between sites in a molecular sequence alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (chimeric sequence detection)
type: Class
subclass of: Sequence alignment analysis (nucleic acid)
has definition: Detects chimeric sequences (chimeras) from a sequence alignment.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (recombination detection)
type: Class
subclass of: Sequence alignment analysis (nucleic acid)
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
has definition: Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (indel detection)
type: Class
subclass of: Sequence alignment analysis (nucleic acid)
has definition: Identify insertion, deletion and duplication events from a sequence alignment.
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleosome formation potential prediction
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Predict nucleosome formation potential of DNA sequences.
Obsolete since: beta12orEarlier
deprecated: true
consider: Nucleosome formation or exclusion sequence prediction
in subset: obsolete

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: bioinformatics
in subset: edam
in subset: operations

Nucleic acid melting profile plotting
type: Class
subclass of: Nucleic acid property calculation
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid melting profile
comment: A melting profile is used to visualise and analyse partly melted DNA conformations.
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA melting profile.
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid stitch profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid stitch profile
has definition: Calculate and plot a DNA or DNA/RNA stitch profile.
Created in: beta12orEarlier
comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid melting curve plotting
type: Class
subclass of: Nucleic acid melting profile plotting
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid melting curve
has definition: Calculate and plot a DNA or DNA/RNA melting curve.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid probability profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid probability profile
has definition: Calculate and plot a DNA or DNA/RNA probability profile.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid temperature profile plotting
type: Class
subclass of: Nucleic acid melting profile plotting
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid temperature profile
Created in: beta12orEarlier
has definition: Calculate and plot a DNA or DNA/RNA temperature profile.
in subset: bioinformatics
in subset: edam
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
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
comment: This includes properties such as.
Created in: beta12orEarlier
has definition: Calculate curvature and flexibility / stiffness of a nucleotide sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

microRNA detection
type: Class
subclass of: Transcription regulatory element prediction (trans)
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (microRNA)
Created in: beta12orEarlier
has definition: Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

tRNA gene prediction
type: Class
subclass of: Whole 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: bioinformatics
in subset: edam
in subset: operations

siRNA binding specificity prediction
type: Class
subclass of: Transcription regulatory element prediction (trans)
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: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure prediction (integrated)
type: Class
subclass of: Protein secondary structure prediction
Created in: beta12orEarlier
has definition: Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure prediction (helices)
type: Class
subclass of: Protein secondary structure prediction
has definition: Predict helical secondary structure of protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure prediction (coils)
type: Class
subclass of: Protein secondary structure prediction
has definition: Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure prediction (disulfide bonds)
type: Class
subclass of: Protein secondary structure prediction
has definition: Predict cysteine bonding state and disulfide bond partners in protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

GPCR prediction
type: Class
subclass of: Transmembrane protein prediction
subclass of: GPCR analysis
has definition: Predict G protein-coupled receptors (GPCR).
has exact synonym: G protein-coupled receptor (GPCR) prediction
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

GPCR analysis
type: Class
subclass of: Transmembrane protein analysis
subclass of: Restriction
  on property: has topic
  some values from: Membrane and lipoproteins
subclass of: Restriction
  on property: has output
  some values from: Protein features (membrane regions)
has exact synonym: G protein-coupled receptor (GPCR) analysis
Created in: beta12orEarlier
has definition: Analyse G-protein coupled receptor proteins (GPCRs).
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure prediction
type: Class
subclass of: Structure prediction
subclass of: Structure processing (protein)
subclass of: Protein sequence analysis
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Protein tertiary structure
subclass of: Restriction
  on property: has topic
  some values from: Protein structure prediction
subclass of: Restriction
  on property: has output
  some values from: Protein structure
has definition: Predict tertiary structure (backbone and side-chain conformation) of protein sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid structure prediction
type: Class
subclass of: Structure prediction
subclass of: Nucleic acid sequence analysis
subclass of: Structure processing (nucleic acid)
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid structure
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
comment: Methods might identify thermodynamically stable or evolutionarily conserved structures.
has definition: Predict tertiary structure of DNA or RNA.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Ab initio structure prediction
type: Class
subclass of: Protein structure prediction
subclass of: Restriction
  on property: has topic
  some values from: Ab initio structure prediction
Created in: beta12orEarlier
has definition: Predict tertiary structure of protein sequence(s) without homologs of known structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein modelling
type: Class
subclass of: Protein structure prediction
subclass of: Protein structure analysis
subclass of: Modelling and simulation
subclass of: Restriction
  on property: has topic
  some values from: Homology modelling
has exact synonym: Protein structure comparative modelling
has exact synonym: Homology structure modelling
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 minimization etc.
has exact synonym: Homology modelling
has definition: Build a three-dimensional protein model based on known (for example homologs) structures.
Created in: beta12orEarlier
has exact synonym: Comparative modelling
in subset: bioinformatics
in subset: edam
in subset: operations

Protein docking
type: Class
subclass of: Protein modelling
subclass of: Protein interaction prediction
subclass of: Restriction
  on property: has topic
  some values from: Molecular docking
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
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.
Created in: beta12orEarlier
has definition: Model the structure of a protein in complex with a small molecule or another macromolecule.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein modelling (backbone)
type: Class
subclass of: Protein modelling
Created in: beta12orEarlier
comment: Methods might require a preliminary C(alpha) trace.
has definition: Model protein backbone conformation.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein modelling (side chains)
type: Class
subclass of: Protein modelling
has definition: Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.
comment: Methods might use a residue rotamer library.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein modelling (loops)
type: Class
subclass of: Protein modelling
has definition: Model loop conformation in protein structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein-ligand docking
type: Class
subclass of: Protein docking
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
subclass of: Restriction
  on property: has output
  some values from: Protein-ligand complex
has exact synonym: Virtual ligand screening
comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.
Created in: beta12orEarlier
has definition: Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.
in subset: bioinformatics
in subset: edam
in subset: operations

Structured RNA prediction and optimisation
type: Class
subclass of: Optimisation and refinement
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: Sequence set (nucleic acid)
has definition: Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.
Created in: beta12orEarlier
has exact synonym: RNA inverse folding
has exact synonym: Nucleic acid folding family identification
in subset: bioinformatics
in subset: edam
in subset: operations

SNP detection
type: Class
subclass of: Sequence alignment analysis
subclass of: Nucleic acid feature prediction
subclass of: Mutation detection
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (polymorphism annotation)
comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
Created in: beta12orEarlier
has exact synonym: Single nucleotide polymorphism detection
has definition: Find single nucleotide polymorphisms (SNPs) between sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

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: bioinformatics
in subset: edam
in subset: operations

Functional mapping
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Map the genetic architecture of dynamic complex traits.
deprecated: true
comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
Created in: beta12orEarlier
consider: Genetic mapping
in subset: obsolete

Haplotype mapping
type: Class
subclass of: Genetic mapping
subclass of: Linkage analysis
subclass of: Restriction
  on property: has output
  some values from: Haplotype map
has exact synonym: Haplotype reconstruction
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 optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
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
in subset: bioinformatics
in subset: edam
in subset: operations

Linkage disequilibrium calculation
type: Class
subclass of: Linkage analysis
subclass of: Restriction
  on property: has output
  some values from: Gene annotation (linkage disequilibrium)
has definition: Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Genetic code prediction
type: Class
subclass of: Codon usage analysis
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has output
  some values from: Genetic code
has definition: Predict genetic code from analysis of codon usage data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Dotplot plotting
type: Class
subclass of: Sequence word comparison
subclass of: Sequence alignment rendering
subclass of: Restriction
  on property: has output
  some values from: Dotplot
has definition: Draw a dotplot of sequence similarities identified from word-matching or character comparison.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Pairwise sequence alignment construction
type: Class
subclass of: Sequence alignment construction
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment (pair)
Created in: beta12orEarlier
has definition: Align exactly two molecular sequences.
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has exact synonym: Pairwise sequence alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction
type: Class
subclass of: Sequence alignment construction
Created in: beta12orEarlier
has exact synonym: Multiple sequence alignment
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.
has definition: Align two or more molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Pairwise sequence alignment construction (local)
type: Class
subclass of: Pairwise sequence alignment construction
comment: Local alignment methods identify regions of local similarity.
has exact synonym: Local pairwise sequence alignment construction
Created in: beta12orEarlier
has exact synonym: Pairwise sequence alignment (local)
has definition: Locally align exactly two molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Pairwise sequence alignment construction (global)
type: Class
subclass of: Pairwise sequence alignment construction
Created in: beta12orEarlier
comment: Global alignment methods identify similarity across the entire length of the sequences.
has definition: Globally align exactly two molecular sequences.
has exact synonym: Pairwise sequence alignment (global)
has exact synonym: Global pairwise sequence alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction (local)
type: Class
subclass of: Multiple sequence alignment construction
has definition: Locally align two or more molecular sequences.
comment: Local alignment methods identify regions of local similarity.
Created in: beta12orEarlier
has exact synonym: Local multiple sequence alignment construction
has exact synonym: Multiple sequence alignment (local)
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction (global)
type: Class
subclass of: Multiple sequence alignment construction
Created in: beta12orEarlier
comment: Global alignment methods identify similarity across the entire length of the sequences.
has exact synonym: Multiple sequence alignment (global)
has exact synonym: Global multiple sequence alignment construction
has definition: Globally align two or more molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction (constrained)
type: Class
subclass of: Multiple sequence alignment construction
has exact synonym: Constrained multiple sequence alignment construction
has exact synonym: Multiple sequence alignment (constrained)
has definition: Align two or more molecular sequences with user-defined constraints.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction (consensus)
type: Class
subclass of: Multiple sequence alignment construction
has exact synonym: Multiple sequence alignment (consensus)
has definition: Align two or more molecular sequences using multiple methods to achieve higher quality.
Created in: beta12orEarlier
has exact synonym: Consensus multiple sequence alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple sequence alignment construction (phylogenetic tree-based)
type: Class
subclass of: Multiple sequence alignment construction
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
has exact synonym: Multiple sequence alignment (phylogenetic tree-based)
has definition: Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.
has exact synonym: Phylogenetic tree-based multiple sequence alignment construction
Created in: beta12orEarlier
comment: This is supposed to give a more biologically meaningful alignment than standard alignments.
in subset: bioinformatics
in subset: edam
in subset: operations

Secondary structure alignment construction
type: Class
subclass of: Structure-based sequence alignment construction
subclass of: Secondary structure processing
subclass of: Secondary structure comparison
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
subclass of: Restriction
  on property: has output
  some values from: Secondary structure alignment
has definition: Align molecular secondary structure (represented as a 1D string).
Created in: beta12orEarlier
has exact synonym: Secondary structure alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure alignment construction
type: Class
subclass of: Secondary structure alignment construction
subclass of: Protein secondary structure comparison
subclass of: Restriction
  on property: has output
  some values from: Secondary structure alignment (protein)
has exact synonym: Secondary structure alignment (protein)
has definition: Align protein secondary structures.
has exact synonym: Protein secondary structure alignment
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

RNA secondary structure alignment construction
type: Class
subclass of: Secondary structure alignment construction
subclass of: RNA secondary structure processing
subclass of: Restriction
  on property: has input
  some values from: RNA secondary structure record
subclass of: Restriction
  on property: has output
  some values from: Secondary structure alignment (RNA)
Created in: beta12orEarlier
has exact synonym: Secondary structure alignment (RNA)
has definition: Align RNA secondary structures.
has exact synonym: RNA secondary structure alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Pairwise structure alignment construction
type: Class
subclass of: Structure alignment construction
has definition: Align (superimpose) exactly two molecular tertiary structures.
has exact synonym: Pairwise structure alignment
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple structure alignment construction
type: Class
subclass of: Structure alignment construction
has exact synonym: Multiple structure alignment
Created in: beta12orEarlier
comment: This includes methods that use an existing alignment.
has definition: Align (superimpose) two or more molecular tertiary structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure alignment (protein)
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Align protein tertiary structures.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: Structure alignment construction
in subset: obsolete

Structure alignment (RNA)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Align RNA tertiary structures.
deprecated: true
Obsolete since: beta13
consider: Structure alignment construction
in subset: obsolete

Pairwise structure alignment construction (local)
type: Class
subclass of: Pairwise structure alignment construction
Created in: beta12orEarlier
comment: Local alignment methods identify regions of local similarity, common substructures etc.
has exact synonym: Pairwise structure alignment (local)
has definition: Locally align (superimpose) exactly two molecular tertiary structures.
has exact synonym: Local pairwise structure alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Pairwise structure alignment construction (global)
type: Class
subclass of: Pairwise structure alignment construction
Created in: beta12orEarlier
has exact synonym: Pairwise structure alignment (global)
has definition: Globally align (superimpose) exactly two molecular tertiary structures.
comment: Global alignment methods identify similarity across the entire structures.
has exact synonym: Global pairwise structure alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple structure alignment construction (local)
type: Class
subclass of: Multiple structure alignment construction
Created in: beta12orEarlier
has exact synonym: Multiple structure alignment (local)
comment: Local alignment methods identify regions of local similarity, common substructures etc.
has definition: Locally align (superimpose) two or more molecular tertiary structures.
has exact synonym: Local multiple structure alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Multiple structure alignment construction (global)
type: Class
subclass of: Multiple structure alignment construction
Created in: beta12orEarlier
has definition: Globally align (superimpose) two or more molecular tertiary structures.
has exact synonym: Global multiple structure alignment construction
has exact synonym: Multiple structure alignment (global)
comment: Global alignment methods identify similarity across the entire structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile alignment construction (pairwise)
type: Class
subclass of: Sequence profile alignment construction
has exact synonym: Pairwise sequence profile alignment construction
has definition: Align exactly two molecular profiles.
Created in: beta12orEarlier
has exact synonym: Sequence profile alignment (pairwise)
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile alignment construction (multiple)
type: Class
subclass of: Sequence profile alignment construction
has exact synonym: Sequence profile alignment (multiple)
has exact synonym: Multiple sequence profile alignment construction
Created in: beta12orEarlier
has definition: Align two or more molecular profiles.
in subset: bioinformatics
in subset: edam
in subset: operations

Structural (3D) profile alignment construction (pairwise)
type: Class
subclass of: Structural (3D) profile alignment construction
Created in: beta12orEarlier
has definition: Align exactly two molecular Structural (3D) profiles.
has exact synonym: Structural (3D) profile alignment (pairwise)
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has exact synonym: Pairwise structural (3D) profile alignment construction
in subset: bioinformatics
in subset: edam
in subset: operations

Structural (3D) profile alignment construction (multiple)
type: Class
subclass of: Structural (3D) profile alignment construction
has exact synonym: Structural (3D) profile alignment (multiple)
Created in: beta12orEarlier
has exact synonym: Multiple structural (3D) profile alignment construction
has definition: Align two or more molecular 3D profiles.
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (tool metadata)
type: Class
subclass of: Data retrieval (metadata and documentation)
subclass of: Restriction
  on property: has output
  some values from: Tool metadata
has exact synonym: Tool information retrieval
Created in: beta12orEarlier
has definition: Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.
has exact synonym: Data retrieval (tool annotation)
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (database metadata)
type: Class
subclass of: Data retrieval (metadata and documentation)
subclass of: Restriction
  on property: has output
  some values from: Database metadata
has exact synonym: Database information retrieval
has definition: Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.
has exact synonym: Data retrieval (database annotation)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (for large scale sequencing)
type: Class
subclass of: PCR primer design
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
Created in: beta12orEarlier
has definition: Predict primers for large scale sequencing.
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (for genotyping polymorphisms)
type: Class
subclass of: PCR primer design
has definition: Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (for gene transcription profiling)
type: Class
subclass of: PCR primer design
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
Created in: beta12orEarlier
has definition: Predict primers for gene transcription profiling.
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (for conserved primers)
type: Class
subclass of: PCR primer design
has definition: Predict primers that are conserved across multiple genomes or species.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (based on gene structure)
type: Class
subclass of: PCR primer design
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Predict primers based on gene structure, promoters, exon-exon junctions etc.
in subset: bioinformatics
in subset: edam
in subset: operations

PCR primer design (for methylation PCRs)
type: Class
subclass of: PCR primer design
has definition: Predict primers for methylation PCRs.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly (mapping assembly)
type: Class
subclass of: Sequence assembly
comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.
Created in: beta12orEarlier
has definition: Sequence assembly by combining fragments using an existing backbone sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly (de-novo assembly)
type: Class
subclass of: Sequence assembly
Created in: beta12orEarlier
comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers.
has definition: Sequence assembly by combining fragments into a new, previously unknown sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly (genome assembly)
type: Class
subclass of: Sequence assembly
Created in: beta12orEarlier
has definition: Sequence assembly capable on a very large scale such as assembly of whole genomes.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly (EST assembly)
type: Class
subclass of: Sequence assembly
comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.
has definition: Sequence assembly for EST sequences (transcribed mRNA).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Tag mapping
type: Class
subclass of: Gene expression profile annotation
subclass of: DNA mapping
subclass of: Restriction
  on property: has output
  some values from: Sequence tag profile (with gene assignment)
Created in: beta12orEarlier
comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.
has definition: Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts.
has exact synonym: Tag to gene assignment
in subset: bioinformatics
in subset: edam
in subset: operations

SAGE data processing
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Process (read and / or write) serial analysis of gene expression (SAGE) data.
Obsolete since: beta12orEarlier
has exact synonym: Serial analysis of gene expression data processing
Created in: beta12orEarlier
consider: Gene expression data processing
in subset: obsolete

MPSS data processing
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has exact synonym: Massively parallel signature sequencing data processing
deprecated: true
has definition: Process (read and / or write) massively parallel signature sequencing (MPSS) data.
Created in: beta12orEarlier
consider: Gene expression data processing
in subset: obsolete

SBS data processing
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Process (read and / or write) sequencing by synthesis (SBS) data.
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has exact synonym: Sequencing by synthesis data processing
consider: Gene expression data processing
in subset: obsolete

Heat map generation
type: Class
subclass of: Microarray data rendering
subclass of: Restriction
  on property: has output
  some values from: Heat map
has definition: Generate a heat map of gene expression from microarray data.
comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression profile analysis
type: Class
subclass of: Gene expression profile processing
subclass of: Restriction
  on property: has input
  some values from: Gene expression profile
has definition: Analyse one or more gene expression profiles, typically to interpret them in functional terms.
Created in: beta12orEarlier
has exact synonym: Functional profiling
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression profile pathway mapping
type: Class
subclass of: Gene expression profile analysis
subclass of: Pathway or network analysis
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
has definition: Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure assignment (from coordinate data)
type: Class
subclass of: Protein secondary structure assignment
subclass of: Protein feature prediction (from structure)
has definition: Assign secondary structure from protein coordinate data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure assignment (from CD data)
type: Class
subclass of: Protein secondary structure assignment
subclass of: Restriction
  on property: has input
  some values from: Protein circular dichroism (CD) spectroscopic data
Created in: beta12orEarlier
has definition: Assign secondary structure from circular dichroism (CD) spectroscopic data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure assignment (from X-ray crystallographic data)
type: Class
subclass of: Protein structure assignment
subclass of: Restriction
  on property: has input
  some values from: Protein X-ray crystallographic data
Created in: beta12orEarlier
has definition: Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure assignment (from NMR data)
type: Class
subclass of: Protein structure assignment
subclass of: Restriction
  on property: has input
  some values from: Protein NMR data
has definition: Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (data centric)
type: Class
subclass of: Phylogenetic tree construction
has definition: Construct a phylogenetic tree from a specific type of data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (method centric)
type: Class
subclass of: Phylogenetic tree construction
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree using a specific method.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (from molecular sequences)
type: Class
subclass of: Phylogenetic tree construction (data centric)
subclass of: Sequence analysis
comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.
Created in: beta12orEarlier
has definition: Phylogenetic tree construction from molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (from continuous quantitative characters)
type: Class
subclass of: Phylogenetic tree construction (data centric)
subclass of: Restriction
  on property: has input
  some values from: Phylogenetic continuous quantitative data
has definition: Phylogenetic tree construction from continuous quantitative character data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (from gene frequencies)
type: Class
subclass of: Phylogenetic tree construction (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.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (from polymorphism data)
type: Class
subclass of: Phylogenetic tree construction (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.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic species tree construction
type: Class
subclass of: Phylogenetic tree construction (from molecular sequences)
Created in: beta12orEarlier
has definition: Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (parsimony methods)
type: Class
subclass of: Phylogenetic tree construction (method centric)
Created in: beta12orEarlier
comment: This includes evolutionary parsimony (invariants) methods.
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (minimum distance methods)
type: Class
subclass of: Phylogenetic tree construction (method centric)
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.
Created in: beta12orEarlier
comment: This includes neighbor joining (NJ) clustering method.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (maximum likelihood and Bayesian methods)
type: Class
subclass of: Phylogenetic tree construction (method centric)
Created in: beta12orEarlier
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.
has definition: Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (quartet methods)
type: Class
subclass of: Phylogenetic tree construction (method centric)
has definition: Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (AI methods)
type: Class
subclass of: Phylogenetic tree construction (method centric)
Created in: beta12orEarlier
has definition: Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (phylogenetic modelling)
type: Class
subclass of: Modelling and simulation
subclass of: Sequence alignment analysis (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
subclass of: Restriction
  on property: has output
  some values from: DNA substitution model
has definition: Identify a plausible model of DNA substitution that explains a DNA sequence alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree analysis (shape)
type: Class
subclass of: Phylogenetic tree analysis
Created in: beta12orEarlier
has definition: Analyse the shape (topology) of a phylogenetic tree.
has exact synonym: Phylogenetic tree topology analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree bootstrapping
type: Class
subclass of: Phylogenetic tree analysis
subclass of: Evaluation and validation
Created in: beta12orEarlier
has definition: Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree analysis (gene family prediction)
type: Class
subclass of: Phylogenetic tree analysis
subclass of: Restriction
  on property: has topic
  some values from: Phylogenomics
subclass of: Restriction
  on property: has output
  some values from: Gene annotation
Created in: beta12orEarlier
has definition: Predict families of genes and gene function based on their position in a phylogenetic tree.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree analysis (natural selection)
type: Class
subclass of: Phylogenetic tree analysis
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).
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree construction (consensus)
type: Class
subclass of: Phylogenetic tree construction
subclass of: Phylogenetic tree comparison
Created in: beta12orEarlier
comment: Methods typically test for topological similarity between trees using for example a congruence index.
has definition: Compare two or more phylogenetic trees to produce a consensus tree.
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic sub/super tree detection
type: Class
subclass of: Phylogenetic tree comparison
has definition: Compare two or more phylogenetic trees to detect subtrees or supertrees.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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
has definition: Compare two or more phylogenetic trees to calculate distances between trees.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree annotation
type: Class
subclass of: Annotation
subclass of: Phylogenetic tree editing
has definition: Annotate a phylogenetic tree with terms from a controlled vocabulary.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations
has related synonym: CDAOAnnotation

Peptide immunogen prediction and optimisation
type: Class
subclass of: Peptide immunogenicity prediction
subclass of: Optimisation and refinement
subclass of: Restriction
  on property: has output
  some values from: Protein structure
subclass of: Restriction
  on property: has topic
  some values from: Immunology
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
has definition: Predict and optimise peptide ligands that elicit an immunological response.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

DNA vaccine prediction and optimisation
type: Class
subclass of: Optimisation and refinement
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure prediction
subclass of: Restriction
  on property: has topic
  some values from: Immunology
has definition: Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence reformatting
type: Class
subclass of: File format conversion
subclass of: Sequence file processing
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has output
  some values from: Sequence
has exact synonym: Sequence file format conversion
has definition: Reformat (a file or other report of) molecular sequence(s).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment reformatting
type: Class
subclass of: File format conversion
subclass of: Sequence alignment file processing
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment
Created in: beta12orEarlier
has definition: Reformat (a file or other report of) molecular sequence alignment(s).
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage table reformatting
type: Class
subclass of: File format conversion
subclass of: Codon usage table processing
subclass of: Restriction
  on property: has input
  some values from: Codon usage table
subclass of: Restriction
  on property: has output
  some values from: Codon usage table
Created in: beta12orEarlier
has definition: Reformat a codon usage table.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence rendering
type: Class
subclass of: Plotting and rendering
subclass of: Sequence processing
subclass of: Restriction
  on property: has output
  some values from: Sequence image
subclass of: Restriction
  on property: has input
  some values from: Sequence
has definition: Visualise, format or render a molecular sequence, possibly with sequence features or properties shown.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment rendering
type: Class
subclass of: Plotting and rendering
subclass of: Sequence alignment processing
subclass of: Restriction
  on property: has output
  some values from: Sequence alignment image
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment
Created in: beta12orEarlier
has definition: Visualise, format or print a molecular sequence alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence cluster rendering
type: Class
subclass of: Plotting and rendering
subclass of: Sequence cluster processing
subclass of: Restriction
  on property: has input
  some values from: Sequence cluster
has definition: Visualise, format or render sequence clusters.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree rendering
type: Class
subclass of: Plotting and rendering
subclass of: Phylogenetic tree processing
subclass of: Restriction
  on property: has output
  some values from: Phylogenetic tree
Created in: beta12orEarlier
has definition: Visualise or plot a phylogenetic tree.
in subset: bioinformatics
in subset: edam
in subset: operations

RNA secondary structure rendering
type: Class
subclass of: Plotting and rendering
subclass of: RNA secondary structure processing
subclass of: Restriction
  on property: has input
  some values from: RNA secondary structure record
Created in: beta12orEarlier
has definition: Visualise RNA secondary structure, knots, pseudoknots etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure rendering
type: Class
subclass of: Plotting and rendering
subclass of: Protein secondary structure processing
subclass of: Restriction
  on property: has input
  some values from: Protein features (secondary structure)
Created in: beta12orEarlier
has definition: Render and visualise protein secondary structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure rendering
type: Class
subclass of: Plotting and rendering
subclass of: Structure processing
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 a molecular tertiary structure, for example a high-quality static picture or animation.
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray data rendering
type: Class
subclass of: Plotting and rendering
subclass of: Gene expression profile processing
subclass of: Restriction
  on property: has input
  some values from: Microarray hybridisation data
subclass of: Restriction
  on property: has output
  some values from: Microarray image
Created in: beta12orEarlier
has definition: Visualise microarray data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction network rendering
type: Class
subclass of: Protein interaction network processing
subclass of: Pathway or network rendering
subclass of: Restriction
  on property: has input
  some values from: Pathway or network (protein-protein interaction)
has definition: Identify and analyse networks of protein interactions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Map rendering
type: Class
subclass of: Sequence rendering (nucleic acid)
subclass of: Map data processing
subclass of: Restriction
  on property: has input
  some values from: Map
has definition: Render and visualise a DNA map.
has exact synonym: DNA map rendering
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence motif rendering
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
deprecated: true
has definition: Render a sequence with motifs.
consider: Sequence rendering
in subset: obsolete

Restriction map rendering
type: Class
subclass of: Restriction site recognition
subclass of: Map rendering
subclass of: Restriction
  on property: has output
  some values from: Restriction map
Created in: beta12orEarlier
has definition: Visualise restriction maps in DNA sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

DNA linear map rendering
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Draw a linear maps of DNA.
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
consider: Map rendering
in subset: obsolete

DNA circular map rendering
type: Class
subclass of: Map rendering
has definition: Draw a circular maps of DNA, for example a plasmid map.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Operon rendering
type: Class
subclass of: Map rendering
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Visualise operon structure etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid folding family identification
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Identify folding families of related RNAs.
Obsolete since: beta12orEarlier
deprecated: true
consider: Structured RNA prediction and optimisation
in subset: obsolete

Nucleic acid folding energy calculation
type: Class
subclass of: 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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Annotation retrieval
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: Retrieve existing annotation (or documentation), typically annotation on a database entity.
comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Protein function prediction
type: Class
subclass of: Protein function analysis
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
has definition: Predict general functional properties of a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein function comparison
type: Class
subclass of: Protein function analysis
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: bioinformatics
in subset: edam
in subset: operations

Sequence submission
type: Class
subclass of: Sequence processing
subclass of: Restriction
  on property: has topic
  some values from: Data acquisition and deposition
subclass of: Restriction
  on property: has input
  some values from: Sequence
Created in: beta12orEarlier
has definition: Submit a molecular sequence to a database.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene regulatory network analysis
type: Class
subclass of: Gene regulatory network processing
subclass of: Pathway or network analysis
subclass of: Restriction
  on property: has input
  some values from: Pathway or network (gene regulation)
has definition: Analyse a known network of gene regulation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data loading
type: Class
subclass of: File processing
subclass of: Restriction
  on property: has input
  some values from: Identifier
has exact synonym: Data submission
Created in: beta12orEarlier
has definition: Prepare or load a user-specified data file so that it is available for use.
has exact synonym: Database submission
has db xref: WHATIF:UploadPDB
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence retrieval
type: Class
subclass of: Data retrieval
subclass of: Sequence processing
subclass of: Restriction
  on property: has output
  some values from: Sequence
Created in: beta12orEarlier
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
has definition: Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
has exact synonym: Data retrieval (sequences)
in subset: bioinformatics
in subset: edam
in subset: operations

Structure retrieval
type: Class
subclass of: Data retrieval
subclass of: Structure processing
subclass of: Restriction
  on property: has output
  some values from: Structure
has definition: Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.
has db xref: WHATIF:EchoPDB
comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
has db xref: WHATIF:DownloadPDB
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Surface rendering
type: Class
subclass of: Structure rendering
subclass of: Protein surface calculation
comment: A dot has three coordinates (x,y,z) and (typically) a color.
has definition: Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.
has db xref: WHATIF:GetSurfaceDots
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein atom surface calculation (accessible)
type: Class
subclass of: Protein atom surface calculation
comment: Waters are not considered.
has definition: Calculate the solvent accessibility ('accessible surface') for each atom in a structure.
has db xref: WHATIF:AtomAccessibilitySolvent
has db xref: WHATIF:AtomAccessibilitySolventPlus
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein atom surface calculation (accessible molecular)
type: Class
subclass of: Protein atom surface calculation
has db xref: WHATIF:AtomAccessibilityMolecularPlus
has db xref: WHATIF:AtomAccessibilityMolecular
comment: Waters are not considered.
has definition: Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue surface calculation (accessible)
type: Class
subclass of: Protein residue surface calculation
has definition: Calculate the solvent accessibility ('accessible surface') for each residue in a structure.
Created in: beta12orEarlier
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has db xref: WHATIF:ResidueAccessibilitySolvent
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue surface calculation (vacuum accessible)
type: Class
subclass of: Protein residue surface calculation
Created in: beta12orEarlier
has db xref: WHATIF:ResidueAccessibilityVacuum
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.
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue surface calculation (accessible molecular)
type: Class
subclass of: Protein residue surface calculation
Created in: beta12orEarlier
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has definition: Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure.
has db xref: WHATIF:ResidueAccessibilityMolecular
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue surface calculation (vacuum molecular)
type: Class
subclass of: Protein residue surface calculation
has db xref: WHATIF:ResidueAccessibilityVacuumMolecular
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.
Created in: beta12orEarlier
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
in subset: bioinformatics
in subset: edam
in subset: operations

Protein surface calculation (accessible molecular)
type: Class
subclass of: Protein surface calculation
has definition: Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole.
has db xref: WHATIF:TotAccessibilityMolecular
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein surface calculation (accessible)
type: Class
subclass of: Protein surface calculation
has definition: Calculate the solvent accessibility ('accessible surface') for a structure as a whole.
Created in: beta12orEarlier
has db xref: WHATIF:TotAccessibilitySolvent
in subset: bioinformatics
in subset: edam
in subset: operations

Backbone torsion angle calculation
type: Class
subclass of: Torsion angle calculation
has definition: Calculate for each residue in a protein structure all its backbone torsion angles.
has db xref: WHATIF:ResidueTorsionsBB
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Full torsion angle calculation
type: Class
subclass of: Torsion angle calculation
has db xref: WHATIF:ResidueTorsions
has definition: Calculate for each residue in a protein structure all its torsion angles.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Cysteine torsion angle calculation
type: Class
subclass of: Torsion angle calculation
has definition: Calculate for each cysteine (bridge) all its torsion angles.
has db xref: WHATIF:CysteineTorsions
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Tau angle calculation
type: Class
subclass of: Torsion angle calculation
has definition: For each amino acid in a protein structure calculate the backbone angle tau.
comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
Created in: beta12orEarlier
has db xref: WHATIF:ShowTauAngle
in subset: bioinformatics
in subset: edam
in subset: operations

Cysteine bridge detection
type: Class
subclass of: Protein cysteine and disulfide bond assignment
Created in: beta12orEarlier
has definition: Detect cysteine bridges (from coordinate data) in a protein structure.
has db xref: WHATIF:ShowCysteineBridge
in subset: bioinformatics
in subset: edam
in subset: operations

Free cysteine detection
type: Class
subclass of: Protein cysteine and disulfide bond assignment
has db xref: WHATIF:ShowCysteineFree
has definition: Detect free cysteines in a protein structure.
Created in: beta12orEarlier
comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.
in subset: bioinformatics
in subset: edam
in subset: operations

Metal-bound cysteine detection
type: Class
subclass of: Protein cysteine and disulfide bond assignment
has definition: Detect cysteines that are bound to metal in a protein structure.
has db xref: WHATIF:ShowCysteineMetal
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation (residue-nucleic acid)
type: Class
subclass of: Protein structural motif recognition
subclass of: Protein-nucleic acid binding site analysis
subclass of: Residue contact calculation
has definition: Calculate protein residue contacts with nucleic acids in a structure.
has db xref: WHATIF:ShowProteiNucleicContacts
has db xref: WHATIF:HasNucleicContacts
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation (residue-metal)
type: Class
subclass of: Binding site prediction (from structure)
subclass of: Residue contact calculation
has db xref: WHATIF:HasMetalContactsPlus
has definition: Calculate protein residue contacts with metal in a structure.
Created in: beta12orEarlier
has db xref: WHATIF:HasMetalContacts
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation (residue-negative ion)
type: Class
subclass of: Residue contact calculation
has db xref: WHATIF:HasNegativeIonContacts
Created in: beta12orEarlier
has db xref: WHATIF:HasNegativeIonContactsPlus
has definition: Calculate ion contacts in a structure (all ions for all side chain atoms).
in subset: bioinformatics
in subset: edam
in subset: operations

Residue bump detection
type: Class
subclass of: Residue non-canonical interaction detection
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.
Created in: beta12orEarlier
has db xref: WHATIF:ShowBumps
in subset: bioinformatics
in subset: edam
in subset: operations

Residue symmetry contact calculation
type: Class
subclass of: Residue contact calculation (residue-residue)
Created in: beta12orEarlier
comment: A symmetry contact is a contact between two atoms in different asymmetric unit.
has db xref: WHATIF:SymmetryContact
has definition: Calculate the number of symmetry contacts made by residues in a protein structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation (residue-ligand)
type: Class
subclass of: Binding site prediction (from structure)
subclass of: Residue contact calculation
has db xref: WHATIF:ShowDrugContacts
has db xref: WHATIF:ShowDrugContactsShort
Created in: beta12orEarlier
has db xref: WHATIF:ShowLigandContacts
has definition: Calculate contacts between residues and ligands in a protein structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Salt bridge calculation
type: Class
subclass of: Residue contact calculation (residue-residue)
has db xref: WHATIF:HasSaltBridgePlus
has definition: Calculate (and possibly score) salt bridges in a protein structure.
has db xref: WHATIF:ShowSaltBridgesH
has db xref: WHATIF:HasSaltBridge
Created in: beta12orEarlier
has db xref: WHATIF:ShowSaltBridges
comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
in subset: bioinformatics
in subset: edam
in subset: operations

Rotamer likelihood prediction
type: Class
subclass of: Protein modelling (side chains)
Created in: beta12orEarlier
has db xref: WHATIF:ShowLikelyRotamers100
has db xref: WHATIF:ShowLikelyRotamers200
has db xref: WHATIF:ShowLikelyRotamers300
has db xref: WHATIF:ShowLikelyRotamers400
has db xref: WHATIF:ShowLikelyRotamers700
comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
has db xref: WHATIF:ShowLikelyRotamers900
has db xref: WHATIF:ShowLikelyRotamers800
has db xref: WHATIF:ShowLikelyRotamers600
has definition: Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.
has db xref: WHATIF:ShowLikelyRotamers500
has db xref: WHATIF:ShowLikelyRotamers
in subset: bioinformatics
in subset: edam
in subset: operations

Proline mutation value calculation
type: Class
subclass of: Protein modelling (mutation)
Created in: beta12orEarlier
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: bioinformatics
in subset: edam
in subset: operations

Residue packing validation
type: Class
subclass of: Residue non-canonical interaction detection
has definition: Identify poorly packed residues in protein structures.
has db xref: WHATIF: PackingQuality
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Dihedral angle validation
type: Class
subclass of: Protein model evaluation
has db xref: WHATIF: ImproperQualityMax
Created in: beta12orEarlier
has definition: Identify for each residue in a protein structure any improper dihedral (phi/psi) angles.
has db xref: WHATIF: ImproperQualitySum
in subset: bioinformatics
in subset: edam
in subset: operations

PDB file sequence retrieval
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has db xref: WHATIF: PDB_sequence
Obsolete since: beta12orEarlier
has definition: Extract a molecular sequence from a PDB file.
consider: Sequence retrieval (by code)
in subset: obsolete

HET group detection
type: Class
subclass of: Residue contact calculation (residue-ligand)
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.
Created in: beta12orEarlier
has definition: Identify HET groups in PDB files.
has db xref: WHATIF: HETGroupNames
in subset: bioinformatics
in subset: edam
in subset: operations

DSSP secondary structure assignment
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: WHATIF: ResidueDSSP
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Determine for residue the DSSP determined secondary structure in three-state (HSC).
consider: Protein secondary structure assignment (from coordinate data)
in subset: obsolete

Structure reformatting
type: Class
subclass of: File format conversion
subclass of: Structure file processing
has db xref: WHATIF: PDBasXML
Created in: beta12orEarlier
has definition: Reformat (a file or other report of) tertiary structure data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein cysteine and disulfide bond assignment
type: Class
subclass of: Protein secondary structure assignment (from coordinate data)
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: bioinformatics
in subset: edam
in subset: operations

Residue validation
type: Class
subclass of: Protein model evaluation
comment: 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).
has db xref: WHATIF: UseResidueDB
Created in: beta12orEarlier
has definition: Identify poor quality amino acid positions in protein structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure retrieval (water)
type: Class
subclass of: Structure retrieval
has definition: Query a tertiary structure database and retrieve water molecules.
has db xref: WHATIF:MovedWaterPDB
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

siRNA duplex prediction
type: Class
subclass of: Transcription regulatory element prediction (trans)
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (siRNA)
subclass of: Restriction
  on property: has topic
  some values from: Functional, regulatory and non-coding RNA
has definition: Identify or predict siRNA duplexes in RNA.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Listfile processing
type: Class
subclass of: File processing
Created in: beta12orEarlier
has definition: Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence file processing
type: Class
subclass of: File processing
subclass of: Sequence processing
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, or create a file of sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment file processing
type: Class
subclass of: File processing
subclass of: Sequence alignment processing
has definition: Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Small molecule data processing
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Process (read and / or write) physicochemical property data for small molecules.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: Analysis and processing
in subset: obsolete

Data retrieval (ontology annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Search and retrieve documentation on a bioinformatics ontology.
deprecated: true
has exact synonym: Ontology information retrieval
Obsolete since: beta13
consider: Data retrieval
in subset: obsolete

Data retrieval (ontology concept)
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Ontology retrieval
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Query an ontology and retrieve concepts or relations.
deprecated: true
consider: Data retrieval
in subset: obsolete

Representative sequence identification
type: Class
subclass of: Sequence clustering
subclass of: Restriction
  on property: has topic
  some values from: Sequence clustering
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: bioinformatics
in subset: edam
in subset: operations

Structure file processing
type: Class
subclass of: File processing
subclass of: Structure processing
Created in: beta12orEarlier
has definition: Perform basic (non-analytical) operations on a file of molecular tertiary structural data.
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (sequence profile)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
Obsolete since: beta13
deprecated: true
has definition: Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.
consider: Data retrieval
in subset: obsolete

Statistical calculation
type: Class
subclass of: Analysis and processing
Created in: beta12orEarlier
has definition: Perform a statistical data operation of some type, e.g. calibration or validation.
in subset: bioinformatics
in subset: edam
in subset: operations

3D-1D scoring matrix generation
type: Class
subclass of: Protein property calculation (from structure)
subclass of: Protein property calculation (from sequence)
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 comparison
has definition: Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.
comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Transmembrane protein rendering
type: Class
subclass of: Transmembrane protein analysis
subclass of: Protein secondary structure rendering
subclass of: Restriction
  on property: has input
  some values from: Protein features (membrane regions)
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Demonstration
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: An operation performing purely illustrative (pedagogical) purposes.
deprecated: true
Created in: beta12orEarlier
in subset: obsolete

Data retrieval (pathway or network)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: Query a biological pathways database and retrieve annotation on one or more pathways.
deprecated: true
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Data retrieval (identifier)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
has definition: Query a database and retrieve one or more data identifiers.
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Nucleic acid density plotting
type: Class
subclass of: Sequence composition calculation (nucleic acid)
has definition: Calculate a density plot (of base composition) for a nucleotide sequence.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence analysis
type: Class
subclass of: Sequence processing
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has topic
  some values from: Sequence analysis
subclass of: Restriction
  on property: has output
  some values from: Sequence report
has exact synonym: Sequence analysis (general)
Created in: beta12orEarlier
has definition: Analyse one or more known molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence motif processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
Created in: beta12orEarlier
has definition: Process (read and / or write) molecular sequence motifs.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction data processing
type: Class
subclass of: Protein data processing
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
Created in: beta12orEarlier
has definition: Process (read and / or write) protein interaction data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure analysis
type: Class
subclass of: Structure processing (protein)
subclass of: Structure analysis
subclass of: Restriction
  on property: has output
  some values from: Protein property
subclass of: Restriction
  on property: has input
  some values from: Protein structure
Created in: beta12orEarlier
has exact synonym: Structure analysis (protein)
has definition: Analyse protein tertiary structural data.
in subset: bioinformatics
in subset: edam
in subset: operations

Annotation processing
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
deprecated: true
consider: Data retrieval
in subset: obsolete

Sequence feature analysis
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
has definition: Analyse features in molecular sequences.
deprecated: true
Created in: beta12orEarlier
consider: Feature prediction
in subset: obsolete

File processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Data processing and validation
has exact synonym: Data file processing
has exact synonym: File handling
has exact synonym: Report handling
Created in: beta12orEarlier
has definition: Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression analysis
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Analyse gene expression and regulation data.
Obsolete since: beta12orEarlier
consider: Gene expression data processing
in subset: obsolete

Structural (3D) profile processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Structure comparison
has definition: Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data index processing
type: Class
subclass of: File processing
Created in: beta12orEarlier
has definition: Process (read and / or write) an index of (typically a file of) biological data.
has exact synonym: Database index processing
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence profile processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
has definition: Process (read and / or write) some type of sequence profile.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein function analysis
type: Class
subclass of: Protein data processing
subclass of: Restriction
  on property: has output
  some values from: Protein report
Created in: beta12orEarlier
has definition: Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein folding analysis
type: Class
subclass of: Modelling and simulation
subclass of: Protein data processing
subclass of: Restriction
  on property: has topic
  some values from: Protein folding, stability and design
subclass of: Restriction
  on property: has output
  some values from: Protein folding report
Created in: beta12orEarlier
has exact synonym: Protein folding modelling
has definition: Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report.
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure analysis
type: Class
subclass of: Protein secondary structure processing
subclass of: Restriction
  on property: has input
  some values from: Protein features (secondary structure)
subclass of: Restriction
  on property: has output
  some values from: Protein secondary structure report
has exact synonym: Secondary structure analysis (protein)
Created in: beta12orEarlier
has definition: Analyse known protein secondary structure data.
in subset: bioinformatics
in subset: edam
in subset: operations

Physicochemical property data processing
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Process (read and / or write) data on the physicochemical property of a molecule.
deprecated: true
Obsolete since: beta13
consider: Analysis and processing
in subset: obsolete

Primer and probe design
type: Class
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Nucleic acid design
subclass of: Restriction
  on property: has topic
  some values from: Sequence design
has definition: Predict oligonucleotide primers or probes.
Created in: beta12orEarlier
has exact synonym: Primer and probe prediction
in subset: bioinformatics
in subset: edam
in subset: operations

Analysis and processing
type: Class
subclass of: Operation
Created in: beta12orEarlier
has definition: Process (read and / or write) data of a specific type, for example applying analytical methods.
has exact synonym: Calculation
has exact synonym: Computation
in subset: bioinformatics
in subset: edam
in subset: operations

Database search
type: Class
subclass of: Search and retrieval
subclass of: Comparison
subclass of: Restriction
  on property: has output
  some values from: Database hits
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.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval
type: Class
subclass of: Search and retrieval
subclass of: Restriction
  on property: has input
  some values from: Identifier
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.
Created in: beta12orEarlier
has broad synonym: Information retrieval
in subset: bioinformatics
in subset: edam
in subset: operations

Prediction, detection and recognition
type: Class
subclass of: Operation
has definition: Predict, recognise, detect or identify some properties of a biomolecule.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Comparison
type: Class
subclass of: Operation
has definition: Compare two or more things to identify similarities.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Optimisation and refinement
type: Class
subclass of: Operation
has definition: Refine or optimise some data model.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Modelling and simulation
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Molecular modelling
has definition: Model or simulate some biological entity or system.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Data handling
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Perform basic operations on some data or a database.
Obsolete since: beta12orEarlier
deprecated: true
consider: Analysis and processing
in subset: obsolete

Evaluation and validation
type: Class
subclass of: Operation
has definition: Validate or standardise some data.
has exact synonym: Validation and standardisation
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Mapping and assembly
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
in subset: bioinformatics
in subset: edam
in subset: operations

Design
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Design a biological entity (typically a molecular sequence or structure) with specific properties.
Obsolete since: beta13
Created in: beta12orEarlier
consider: Prediction, detection and recognition (nucleic acid)
in subset: obsolete

Microarray data processing
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
has definition: Process (read and / or write) microarray data.
Created in: beta12orEarlier
consider: Gene expression data processing
in subset: obsolete

Codon usage table processing
type: Class
subclass of: Codon usage analysis
Created in: beta12orEarlier
has definition: Process (read and / or write) a codon usage table.
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (codon usage table)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
deprecated: true
Created in: beta12orEarlier
has definition: Retrieve a codon usage table and / or associated annotation.
consider: Data retrieval
in subset: obsolete

Gene expression profile processing
type: Class
subclass of: Gene expression data processing
Created in: beta12orEarlier
has definition: Process (read and / or write) a gene expression profile.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression profile annotation
type: Class
subclass of: Annotation
subclass of: Gene expression profile analysis
subclass of: Restriction
  on property: has output
  some values from: Gene expression profile
has definition: Annotate a gene expression profile with concepts from an ontology of gene functions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Gene regulatory network prediction
type: Class
subclass of: Gene regulatory network processing
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has output
  some values from: Pathway or network (gene regulation)
Created in: beta12orEarlier
has definition: Predict a network of gene regulation.
in subset: bioinformatics
in subset: edam
in subset: operations

Pathway or network processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: Generate, analyse or handle a biological pathway or network.
in subset: bioinformatics
in subset: edam
in subset: operations

RNA secondary structure processing
type: Class
subclass of: Secondary structure processing
subclass of: Nucleic acid data processing
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
has definition: Process (read and / or write) RNA secondary structure data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structure processing (RNA)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Process (read and / or write) RNA tertiary structure data.
consider: Structure processing (nucleic acid)
in subset: obsolete

RNA structure prediction
type: Class
subclass of: Nucleic acid structure prediction
subclass of: Restriction
  on property: has output
  some values from: RNA structure record
has definition: Predict RNA tertiary structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Phylogenetic tree processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Phylogeny
has definition: Process (read and / or write) a phylogenetic tree.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure processing
type: Class
subclass of: Secondary structure processing
subclass of: Protein data processing
subclass of: Restriction
  on property: has topic
  some values from: Protein secondary structure
Created in: beta12orEarlier
has definition: Process (read and / or write) protein secondary structure data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction network processing
type: Class
subclass of: Protein interaction data processing
subclass of: Pathway or network processing
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
has definition: Process (read and / or write) a network of protein interactions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence processing
type: Class
subclass of: Analysis and processing
Created in: beta12orEarlier
has definition: Process (read and / or write) one or more molecular sequences and associated annotation.
has exact synonym: Sequence processing (general)
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence processing (protein)
type: Class
subclass of: Sequence processing
subclass of: Protein data processing
Created in: beta12orEarlier
has definition: Process (read and / or write) a protein sequence and associated annotation.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence processing (nucleic acid)
type: Class
subclass of: Sequence processing
subclass of: Nucleic acid data processing
has definition: Process (read and / or write) a nucleotide sequence and associated annotation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence comparison
type: Class
subclass of: Sequence analysis
subclass of: Comparison
subclass of: Restriction
  on property: has topic
  some values from: Sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Sequence report
subclass of: Restriction
  on property: has input
  some values from: Sequence
Created in: beta12orEarlier
has definition: Compare two or more molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence cluster processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Sequence clustering
Created in: beta12orEarlier
has definition: Process (read and / or write) a sequence cluster.
in subset: bioinformatics
in subset: edam
in subset: operations

Feature table processing
type: Class
subclass of: Sequence processing
subclass of: Restriction
  on property: has output
  some values from: Feature record
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
subclass of: Restriction
  on property: has input
  some values from: Sequence record full
subclass of: Restriction
  on property: has input
  some values from: Sequence feature table
Created in: beta12orEarlier
has definition: Process (read and / or write) a sequence feature table.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene and gene component prediction
type: Class
subclass of: Nucleic acid feature prediction
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (gene and transcript structure)
has exact synonym: Gene finding
has definition: Detect, predict and identify genes or components of genes in DNA sequences.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

GPCR classification
type: Class
subclass of: GPCR analysis
subclass of: Sequence classification
subclass of: Restriction
  on property: has output
  some values from: Protein family
has definition: Classify G-protein coupled receptors (GPCRs) into families and subfamilies.
has exact synonym: G protein-coupled receptor (GPCR) classification
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

GPCR coupling selectivity prediction
type: Class
subclass of: GPCR analysis
subclass of: Protein interaction prediction
subclass of: Protein property calculation (from sequence)
subclass of: Restriction
  on property: has output
  some values from: Protein report
Created in: beta12orEarlier
has definition: Predict G-protein coupled receptor (GPCR) coupling selectivity.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure processing (protein)
type: Class
subclass of: Structure processing
subclass of: Protein data processing
subclass of: Restriction
  on property: has topic
  some values from: Protein tertiary structure
has definition: Process (read and / or write) a protein tertiary structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein atom surface calculation
type: Class
subclass of: Protein surface and interior calculation
Created in: beta12orEarlier
has definition: Calculate the solvent accessibility for each atom in a structure.
comment: Waters are not considered.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein residue surface calculation
type: Class
subclass of: Protein surface and interior calculation
has definition: Calculate the solvent accessibility for each residue in a structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein surface calculation
type: Class
subclass of: Protein surface and interior calculation
Created in: beta12orEarlier
has definition: Calculate the solvent accessibility of a structure as a whole.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment processing
type: Class
subclass of: Alignment processing
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
has definition: Process (read and / or write) a molecular sequence alignment.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein-protein interaction prediction
type: Class
subclass of: Protein interaction prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
subclass of: Restriction
  on property: has output
  some values from: Protein-protein interaction
Created in: beta12orEarlier
has definition: Identify or predict protein-protein interactions, interfaces, binding sites etc.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure processing
type: Class
subclass of: Analysis and processing
Created in: beta12orEarlier
has definition: Process (read and / or write) a molecular tertiary structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Map annotation
type: Class
subclass of: Annotation
subclass of: Map data processing
subclass of: Restriction
  on property: has output
  some values from: Map
subclass of: Restriction
  on property: has input
  some values from: Map
Created in: beta12orEarlier
has definition: Annotate a DNA map of some type with terms from a controlled vocabulary.
in subset: bioinformatics
in subset: edam
in subset: operations

Data retrieval (protein annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: Protein information retrieval
deprecated: true
Obsolete since: beta13
has definition: Retrieve information on a protein.
consider: Data retrieval
in subset: obsolete

Data retrieval (phylogenetic tree)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Retrieve a phylogenetic tree from a data resource.
Obsolete since: beta13
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Data retrieval (protein interaction annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta13
deprecated: true
has definition: Retrieve information on a protein interaction.
consider: Data retrieval
in subset: obsolete

Data retrieval (protein family annotation)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Retrieve information on a protein family.
Obsolete since: beta13
has exact synonym: Protein family information retrieval
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Data retrieval (RNA family annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
Created in: beta12orEarlier
has exact synonym: RNA family information retrieval
deprecated: true
has definition: Retrieve information on an RNA family.
consider: Data retrieval
in subset: obsolete

Data retrieval (gene annotation)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: Retrieve information on a specific gene.
deprecated: true
has exact synonym: Gene information retrieval
Created in: beta12orEarlier
consider: Data retrieval
in subset: obsolete

Data retrieval (genotype and phenotype annotation)
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has exact synonym: Genotype and phenotype information retrieval
has definition: Retrieve information on a specific genotype or phenotype.
consider: Data retrieval
in subset: obsolete

Protein architecture comparison
type: Class
subclass of: Protein architecture analysis
subclass of: Protein secondary structure comparison
Created in: beta12orEarlier
has definition: Compare the architecture of two or more protein structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein architecture recognition
type: Class
subclass of: Protein architecture analysis
subclass of: Structure classification
subclass of: Prediction, detection and recognition (protein)
has definition: Identify the architecture of a protein structure.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Molecular dynamics simulation
type: Class
subclass of: Prediction, detection 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: Molecular dynamics
subclass of: Restriction
  on property: has topic
  some values from: Structure prediction
has definition: Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid sequence analysis
type: Class
subclass of: Sequence analysis
subclass of: Sequence processing (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid sequence
has exact synonym: Sequence analysis (nucleic acid)
Created in: beta12orEarlier
has definition: Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).
in subset: bioinformatics
in subset: edam
in subset: operations

Protein sequence analysis
type: Class
subclass of: Sequence analysis
subclass of: Sequence processing (protein)
subclass of: Restriction
  on property: has input
  some values from: Protein sequence
subclass of: Restriction
  on property: has topic
  some values from: Protein sequence analysis
Created in: beta12orEarlier
has exact synonym: Sequence analysis (protein)
has definition: Analyse a protein sequence (using methods that are only applicable to protein sequences).
in subset: bioinformatics
in subset: edam
in subset: operations

Structure analysis
type: Class
subclass of: Structure processing
subclass of: Restriction
  on property: has output
  some values from: Structure report
subclass of: Restriction
  on property: has input
  some values from: Structure
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
has definition: Analyse known molecular tertiary structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid structure analysis
type: Class
subclass of: Structure analysis
subclass of: Structure processing (nucleic acid)
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid property
subclass of: Restriction
  on property: has input
  some values from: Nucleic acid structure
Created in: beta12orEarlier
has definition: Analyse nucleic acid tertiary structural data.
in subset: bioinformatics
in subset: edam
in subset: operations

Secondary structure processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Structure analysis
Created in: beta12orEarlier
has definition: Process (read and / or write) a molecular secondary structure.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure comparison
type: Class
subclass of: Comparison
subclass of: Structure analysis
subclass of: Restriction
  on property: has topic
  some values from: Structure comparison
has definition: Compare two or more molecular tertiary structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Helical wheel rendering
type: Class
subclass of: Protein secondary structure rendering
subclass of: Restriction
  on property: has output
  some values from: Helical wheel
has definition: Render a helical wheel representation of protein secondary structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Topology diagram rendering
type: Class
subclass of: Protein secondary structure rendering
subclass of: Restriction
  on property: has output
  some values from: Protein structure image
has definition: Render a topology diagram of protein secondary structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Protein structure comparison
type: Class
subclass of: Structure processing (protein)
subclass of: Structure comparison
subclass of: Protein comparison
subclass of: Restriction
  on property: has input
  some values from: Protein structure
subclass of: Restriction
  on property: has output
  some values from: Protein property
has definition: Compare protein tertiary structures.
Created in: beta12orEarlier
comment: Methods might identify structural neighbors, find structural similarities or define a structural core.
has exact synonym: Structure comparison (protein)
in subset: bioinformatics
in subset: edam
in subset: operations

Protein secondary structure comparison
type: Class
subclass of: Protein secondary structure analysis
subclass of: Secondary structure comparison
subclass of: Protein comparison
subclass of: Restriction
  on property: has input
  some values from: Protein features (secondary structure)
has definition: Compare protein secondary structures.
Created in: beta12orEarlier
has exact synonym: Protein secondary structure
has exact synonym: Secondary structure comparison (protein)
in subset: bioinformatics
in subset: edam
in subset: operations

Protein subcellular localization prediction
type: Class
subclass of: Prediction, detection and recognition (protein)
subclass of: Protein function prediction (from sequence)
subclass of: Restriction
  on property: has topic
  some values from: Protein targeting and localization
has definition: Predict the subcellular localization of a protein sequence.
comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
Created in: beta12orEarlier
has exact synonym: Protein targeting prediction
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation (residue-residue)
type: Class
subclass of: Residue contact calculation
has definition: Calculate contacts between residues in a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Hydrogen bond calculation (inter-residue)
type: Class
subclass of: Hydrogen bond calculation
subclass of: Residue contact calculation (residue-residue)
Created in: beta12orEarlier
has definition: Identify potential hydrogen bonds between amino acid residues.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction prediction
type: Class
subclass of: Protein interaction data processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has output
  some values from: Protein interaction
Created in: beta12orEarlier
has definition: Predict the interactions of proteins with other molecules.
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage data processing
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Process (read and / or write) codon usage data.
Obsolete since: beta13
Created in: beta12orEarlier
consider: Codon usage analysis
in subset: obsolete

Gene expression data processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Gene expression
has definition: Process (read and / or write) gene expression (typically microarray) data.
has exact synonym: Microarray data processing
has exact synonym: Gene expression (microarray) data processing
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Gene regulatory network processing
type: Class
subclass of: Pathway or network processing
subclass of: Restriction
  on property: has topic
  some values from: Gene regulatory networks
has definition: Process (read and / or write) a network of gene regulation.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Pathway or network analysis
type: Class
subclass of: Pathway or network processing
subclass of: Restriction
  on property: has input
  some values from: Pathway or network
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
Created in: beta12orEarlier
has exact synonym: Network analysis
has definition: Analyse a known biological pathway or network.
has exact synonym: Pathway analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Sequencing-based expression profile data analysis
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.
consider: Gene expression data processing
in subset: obsolete

Splicing analysis
type: Class
subclass of: Modelling and simulation
subclass of: Nucleic acid sequence comparison
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (splice sites)
subclass of: Restriction
  on property: has topic
  some values from: Gene structure
Created in: beta12orEarlier
has definition: Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences.
has exact synonym: Splicing modelling
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray raw data analysis
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Analyse raw microarray data.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Gene expression data processing
in subset: obsolete

Nucleic acid data processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
Created in: beta12orEarlier
has definition: Process (read and / or write) nucleic acid sequence or structural data.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein data processing
type: Class
subclass of: Analysis and processing
subclass of: Restriction
  on property: has topic
  some values from: Proteins
has definition: Process (read and / or write) protein sequence or structural data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence data processing
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Process (read and / or write) molecular sequence data.
in subset: obsolete

Structural data processing
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
has definition: Process (read and / or write) molecular structural data.
consider: Structure processing
in subset: obsolete

Text processing
type: Class
subclass of: Analysis and processing
has definition: Process (read and / or write) text.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (protein)
type: Class
subclass of: Sequence alignment analysis
subclass of: Protein data processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment (protein)
Created in: beta12orEarlier
has definition: Analyse a protein sequence alignment, typically to detect features or make predictions.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence alignment analysis (nucleic acid)
type: Class
subclass of: Sequence alignment analysis
subclass of: Nucleic acid data processing
subclass of: Prediction, detection and recognition (nucleic acid)
subclass of: Restriction
  on property: has input
  some values from: Sequence alignment (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Sequence alignment
has definition: Analyse a protein sequence alignment, typically to detect features or make predictions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid sequence comparison
type: Class
subclass of: Sequence comparison
subclass of: Nucleic acid sequence analysis
subclass of: Nucleic acid comparison
Created in: beta12orEarlier
has definition: Compare two or more nucleic acid sequences.
has exact synonym: Sequence comparison (nucleic acid)
in subset: bioinformatics
in subset: edam
in subset: operations

Protein sequence comparison
type: Class
subclass of: Sequence comparison
subclass of: Protein sequence analysis
subclass of: Protein comparison
has definition: Compare two or more protein sequences.
has exact synonym: Sequence comparison (protein)
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

DNA back-translation
type: Class
subclass of: Sequence conversion
subclass of: Restriction
  on property: has topic
  some values from: Protein expression
has definition: Back-translate a protein sequence into DNA.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence editing (nucleic acid)
type: Class
subclass of: Sequence editing
subclass of: Sequence processing (nucleic acid)
Created in: beta12orEarlier
has definition: Edit or change a nucleic acid sequence, either randomly or specifically.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence editing (protein)
type: Class
subclass of: Sequence editing
subclass of: Sequence processing (protein)
Created in: beta12orEarlier
has definition: Edit or change a protein sequence, either randomly or specifically.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence generation (nucleic acid)
type: Class
subclass of: Sequence generation
subclass of: Sequence processing (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
Created in: beta12orEarlier
has definition: Generate a nucleic acid sequence by some means.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence generation (protein)
type: Class
subclass of: Sequence generation
subclass of: Sequence processing (protein)
subclass of: Restriction
  on property: has topic
  some values from: Protein sequence analysis
Created in: beta12orEarlier
has definition: Generate a protein sequence by some means.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence rendering (nucleic acid)
type: Class
subclass of: Sequence rendering
subclass of: Sequence processing (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid sequence analysis
Created in: beta12orEarlier
comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
has definition: Visualise, format or render a nucleic acid sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence rendering (protein)
type: Class
subclass of: Sequence rendering
subclass of: Sequence processing (protein)
has exact synonym: Protein sequence visualisation
Created in: beta12orEarlier
comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
has exact synonym: Protein sequence rendering
has definition: Visualise, format or render a protein sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid structure comparison
type: Class
subclass of: Nucleic acid structure analysis
subclass of: Structure comparison
subclass of: Nucleic acid comparison
has exact synonym: Structure comparison (nucleic acid)
Created in: beta12orEarlier
has definition: Compare nucleic acid tertiary structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure processing (nucleic acid)
type: Class
subclass of: Structure processing
subclass of: Nucleic acid data processing
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acid structure analysis
has definition: Process (read and / or write) nucleic acid tertiary structure data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

DNA mapping
type: Class
subclass of: Mapping and assembly
subclass of: Map data processing
subclass of: Restriction
  on property: has output
  some values from: Map
has definition: Generate a map of a DNA sequence annotated with positional or non-positional features of some type.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Map data processing
type: Class
subclass of: Nucleic acid data processing
subclass of: Restriction
  on property: has topic
  some values from: Mapping
Created in: beta12orEarlier
has definition: Process (read and / or write) a DNA map of some type.
has exact synonym: DNA map data processing
in subset: bioinformatics
in subset: edam
in subset: operations

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
has definition: Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Binding site prediction
type: Class
subclass of: Protein interaction prediction
subclass of: Restriction
  on property: has topic
  some values from: Protein interactions
subclass of: Restriction
  on property: has output
  some values from: Protein features (binding sites)
subclass of: Restriction
  on property: has output
  some values from: Protein features (active sites)
has definition: Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.
Created in: beta12orEarlier
has exact synonym: Ligand-binding and active site prediction
in subset: bioinformatics
in subset: edam
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
has definition: Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
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.
Created in: beta12orEarlier
has exact synonym: Sequence mapping
in subset: bioinformatics
in subset: edam
in subset: operations

Alignment construction
type: Class
subclass of: Alignment processing
subclass of: Restriction
  on property: has output
  some values from: Alignment
Created in: beta12orEarlier
has exact synonym: Alignment
has definition: Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein fragment weight comparison
type: Class
subclass of: Protein molecular weight calculation
subclass of: Protein property comparison
has definition: Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Secondary structure comparison
type: Class
subclass of: Comparison
subclass of: Restriction
  on property: has output
  some values from: Secondary structure report
subclass of: Restriction
  on property: has input
  some values from: Secondary structure
subclass of: Restriction
  on property: has topic
  some values from: Structure comparison
Created in: beta12orEarlier
has definition: Compare two or more molecular secondary structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Hopp and Woods plotting
type: Class
subclass of: Peptide immunogenicity prediction
has definition: Generate a Hopp and Woods plot of antigenicity of a protein.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray cluster textual view rendering
type: Class
subclass of: Microarray data rendering
has definition: Visualise gene clusters with gene names.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray wave graph rendering
type: Class
subclass of: Microarray data rendering
has definition: Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.
comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.
Created in: beta12orEarlier
has exact synonym: Microarray cluster temporal graph rendering
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray dendrograph rendering
type: Class
subclass of: Microarray data rendering
has exact synonym: Microarray view rendering
has exact synonym: Microarray checks view rendering
Created in: beta12orEarlier
has definition: Generate a dendrograph of raw, preprocessed or clustered microarray data.
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray proximity map rendering
type: Class
subclass of: Microarray data rendering
has definition: Generate a plot of distances (distance matrix) between genes.
has exact synonym: Microarray distance map rendering
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray tree or dendrogram view rendering
type: Class
subclass of: Microarray data rendering
has exact synonym: Microarray matrix tree plot rendering
has exact synonym: Microarray 2-way dendrogram rendering
has definition: Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray principal component rendering
type: Class
subclass of: Microarray data rendering
has definition: Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray scatter plot rendering
type: Class
subclass of: Microarray data rendering
Created in: beta12orEarlier
has definition: Generate a scatter plot of microarray data, typically after principal component analysis.
in subset: bioinformatics
in subset: edam
in subset: operations

Whole microarray graph view rendering
type: Class
subclass of: Microarray data rendering
Created in: beta12orEarlier
has definition: Visualise gene expression data where each band (or line graph) corresponds to a sample.
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray tree-map rendering
type: Class
subclass of: Microarray data rendering
has definition: Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Microarray Box-Whisker plot rendering
type: Class
subclass of: Microarray data rendering
has definition: Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Physical mapping
type: Class
subclass of: DNA mapping
subclass of: Restriction
  on property: has topic
  some values from: Mapping
subclass of: Restriction
  on property: has output
  some values from: Physical map
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Analysis
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
comment: For non-analytical operations, see the 'Processing' branch.
has definition: Apply analytical methods to existing data of a specific type.
consider: Analysis and processing
in subset: obsolete

Alignment analysis
type: Class
subclass of: Alignment processing
subclass of: Restriction
  on property: has output
  some values from: Alignment report
subclass of: Restriction
  on property: has input
  some values from: Alignment
has definition: Analyse an existing alignment of two or more molecular sequences, structures or derived data.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Article analysis
type: Class
subclass of: Text processing
subclass of: Restriction
  on property: has topic
  some values from: Literature and reference
subclass of: Restriction
  on property: has input
  some values from: Article
subclass of: Restriction
  on property: has output
  some values from: Article report
Created in: beta12orEarlier
has definition: Analyse a body of scientific text (typically a full text article from a scientific journal.)
in subset: bioinformatics
in subset: edam
in subset: operations

Molecular interaction analysis
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.
in subset: obsolete

Protein interaction analysis
type: Class
subclass of: Protein interaction data processing
subclass of: Restriction
  on property: has output
  some values from: Protein interaction
has definition: Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Residue contact calculation
type: Class
subclass of: Residue interaction calculation
has definition: Calculate contacts between residues and some other group in a protein structure.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Alignment processing
type: Class
subclass of: Analysis and processing
Created in: beta12orEarlier
has definition: Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.
in subset: bioinformatics
in subset: edam
in subset: operations

Structure alignment processing
type: Class
subclass of: Alignment processing
subclass of: Restriction
  on property: has topic
  some values from: Structure alignment
Created in: beta12orEarlier
has definition: Process (read and / or write) a molecular tertiary (3D) structure alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

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.
in subset: bioinformatics
in subset: edam
in subset: operations

Codon usage bias plotting
type: Class
subclass of: Codon usage bias calculation
subclass of: Restriction
  on property: has output
  some values from: Codon usage bias plot
has definition: Generate a codon usage bias plot.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

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: bioinformatics
in subset: edam
in subset: operations

Classification
type: Class
subclass of: Operation
subclass of: Restriction
  on property: has output
  some values from: Classification
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Molecular interaction data processing
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Process (read and / or write) molecular interaction data.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
in subset: obsolete

Sequence classification
type: Class
subclass of: Sequence analysis
subclass of: Classification
has definition: Assign molecular sequence(s) to a group or category.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
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: bioinformatics
in subset: edam
in subset: operations

Nucleic acid comparison
type: Class
subclass of: Comparison
has definition: Compare two or more nucleic acids to identify similarities.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Prediction, detection and recognition (protein)
type: Class
subclass of: Prediction, detection and recognition
has definition: Predict, recognise, detect or identify some properties of proteins.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Prediction, detection and recognition (nucleic acid)
type: Class
subclass of: Prediction, detection and recognition
has definition: Predict, recognise, detect or identify some properties of nucleic acids.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Structure editing
type: Class
subclass of: Structure file processing
subclass of: 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: bioinformatics
in subset: edam
in subset: operations

Sequence alignment editing
type: Class
subclass of: Sequence alignment file processing
subclass of: Editing
Created in: beta13
has definition: Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.
in subset: bioinformatics
in subset: edam
in subset: operations

Pathway or network rendering
type: Class
subclass of: Plotting and rendering
subclass of: Pathway or network processing
subclass of: Restriction
  on property: has input
  some values from: Pathway or network
Created in: beta13
has definition: Render (visualise) a biological pathway or network.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein function prediction (from sequence)
type: Class
subclass of: Protein function prediction
subclass of: Protein sequence analysis
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Function analysis
has definition: Predict general (non-positional) functional properties of a protein from analysing its sequence.
comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Protein site detection
type: Class
subclass of: Sequence motif recognition
subclass of: Protein feature prediction (from sequence)
Created in: beta13
has exact synonym: name: Sequence motif recognition (protein)
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: bioinformatics
in subset: edam
in subset: operations

Protein property calculation (from sequence)
type: Class
subclass of: Protein property calculation
subclass of: 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.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Protein feature prediction (from structure)
type: Class
subclass of: Protein structure analysis
subclass of: Protein feature prediction
has definition: Predict, recognise and identify positional features in proteins from analysing protein structure.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Protein feature prediction
type: Class
subclass of: Feature prediction
subclass of: Protein data processing
subclass of: Prediction, detection and recognition (protein)
subclass of: Restriction
  on property: has topic
  some values from: Sequence sites, features and motifs
subclass of: Restriction
  on property: has output
  some values from: Protein features
subclass of: Restriction
  on property: has topic
  some values from: Protein sequence analysis
Created in: beta13
has definition: Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence screening
type: Class
subclass of: Sequence classification
Created in: beta13
has definition: Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein interaction network prediction
type: Class
subclass of: Protein interaction network processing
subclass of: Restriction
  on property: has output
  some values from: Pathway or network (protein-protein interaction)
has definition: Predict a network of protein interactions.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Nucleic acid design
type: Class
subclass of: Nucleic acid sequence analysis
has definition: Design (or predict) nucleic acid sequences with specific chemical or physical properties.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Editing
type: Class
subclass of: Operation
has definition: Edit, convert or otherwise change a data entity, either randomly or specifically.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly evaluation
type: Class
subclass of: Optimisation and refinement
subclass of: Sequence processing (nucleic acid)
subclass of: Nucleic acid sequence analysis
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.
in subset: bioinformatics
in subset: edam
in subset: operations

Genome alignment construction
type: Class
subclass of: Sequence alignment construction
has exact synonym: Genome alignment
Created in: 1.1
has definition: Align two or more (tpyically huge) molecular sequences that represent genomes.
in subset: bioinformatics
in subset: edam
in subset: operations

Localized reassembly
type: Class
subclass of: Sequence assembly
Created in: 1.1
has definition: Reconstruction of a sequence assembly in a localised area.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence assembly rendering
type: Class
subclass of: Sequence rendering (nucleic acid)
has exact synonym: Assembly visualisation
Created in: 1.1
has definition: Render and visualise a DNA sequence assembly.
has exact synonym: Assembly rendering
has exact synonym: Sequence assembly visualisation
in subset: bioinformatics
in subset: edam
in subset: operations

Base-calling
type: Class
subclass of: Sequence processing (nucleic acid)
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
has exact synonym: Base calling
Created in: 1.1
has exact synonym: Phred base calling
has exact synonym: Phred base-calling
has definition: Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer.
in subset: bioinformatics
in subset: edam
in subset: operations

Bisulfite mapping
type: Class
subclass of: Physical mapping
has exact synonym: Bisulfite sequence mapping
has exact synonym: Bisulfite sequence alignment
has definition: The mapping of methylation sites in a DNA (genome) sequence.
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.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence contamination filtering
type: Class
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Nucleic acids
has definition: Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: operations

Trim ends
type: Class
subclass of: Sequence trimming
comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
Created in: 1.1
has definition: Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
in subset: bioinformatics
in subset: edam
in subset: operations

Trim vector
type: Class
subclass of: Sequence trimming
Created in: 1.1
has definition: Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Trim to reference
type: Class
subclass of: Sequence trimming
has definition: Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence trimming
type: Class
subclass of: Sequence cutting
has definition: Cut (remove) the end from a molecular sequence.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Genome feature comparison
type: Class
subclass of: Feature comparison
Created in: 1.1
has definition: Compare the features of two genome sequences.
comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequencing error detection
type: Class
subclass of: Nucleic acid sequence comparison
subclass of: Restriction
  on property: has topic
  some values from: Sequencing
has definition: Detect errors in DNA sequences generated from sequencing projects).
Created in: beta12orEarlier
has exact synonym: Short-read error correction
has exact synonym: Short read error correction
in subset: bioinformatics
in subset: edam
in subset: operations

Genotyping
type: Class
subclass of: Genetic variation analysis
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.
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.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Genetic variation analysis
type: Class
subclass of: Nucleic acid sequence comparison
subclass of: Restriction
  on property: has output
  some values from: Nucleic acid features (variation)
has exact synonym: Genetic variation annotation
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.
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.
has exact synonym: Sequence variation analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Read mapping
type: Class
subclass of: Sequence alignment construction
subclass of: Physical mapping
has exact synonym: Short sequence read mapping
has definition: Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
has exact synonym: Short read alignment
Created in: 1.1
has exact synonym: Read alignment
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.
has exact synonym: Oligonucleotide alignment
has exact synonym: Oligonucleotide alignment construction
has exact synonym: Short read mapping
has exact synonym: Oligonucleotide mapping
has exact synonym: Short oligonucleotide alignment
in subset: bioinformatics
in subset: edam
in subset: operations

Split read mapping
type: Class
subclass of: Read mapping
Created in: 1.1
has definition: A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.
in subset: bioinformatics
in subset: edam
in subset: operations

DNA barcoding
type: Class
subclass of: Nucleic acid feature prediction
has exact synonym: Sample barcoding
Created in: 1.1
has definition: Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.
in subset: bioinformatics
in subset: edam
in subset: operations

SNP calling
type: Class
subclass of: SNP detection
Created in: 1.1
comment: Operations usually score confidence in the prediction or some other statistical measure of evidence.
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: bioinformatics
in subset: edam
in subset: operations

Mutation detection
type: Class
subclass of: Genetic variation analysis
Created in: 1.1
has definition: Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.
has exact synonym: Polymorphism detection
in subset: bioinformatics
in subset: edam
in subset: operations

Chromatogram visualisation
type: Class
subclass of: Plotting and rendering
Created in: 1.1
has exact synonym: Chromatogram viewing
has definition: Visualise, format or render an image of a Chromatogram.
in subset: bioinformatics
in subset: edam
in subset: operations

Methylation analysis
type: Class
subclass of: Nucleic acid feature prediction
has definition: Determine cytosine methylation states in nucleic acid sequences.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Methylation calling
type: Class
subclass of: Methylation analysis
has definition: Determine cytosine methylation status of specific positions in a nucleic acid sequences.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Methylation level analysis (global)
type: Class
subclass of: Methylation calling
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: Global methylation analysis
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Methylation level analysis (gene-specific)
type: Class
subclass of: Methylation calling
comment: Many different techniques are available for this.
has definition: Measure the level of methyl cytosines in specific genes.
Created in: 1.1
has exact synonym: Gene-specific methylation analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Genome rendering
type: Class
subclass of: Sequence rendering (nucleic acid)
has exact synonym: Genome browsing
has exact synonym: Genome viewing
has exact synonym: Genome visualisation
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 visualization
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Genome comparison
type: Class
subclass of: Nucleic acid sequence comparison
has exact synonym: Genomic region matching
Created in: 1.1
has definition: Compare the sequence or features of two or more genomes, for example, to find matching regions.
in subset: bioinformatics
in subset: edam
in subset: operations

Genome indexing
type: Class
subclass of: Data indexing
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.
comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
in subset: bioinformatics
in subset: edam
in subset: operations

Genome indexing (Burrows-Wheeler)
type: Class
subclass of: Genome indexing
Created in: 1.1
has definition: Generate an index of a genome sequence using the Burrows-Wheeler algorithm.
comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
in subset: bioinformatics
in subset: edam
in subset: operations

Genome indexing (suffix arrays)
type: Class
subclass of: Genome indexing
comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome.
has exact synonym: suffix arrays
has definition: Generate an index of a genome sequence using a suffix arrays algorithm.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Spectrum analysis
type: Class
subclass of: Analysis and processing
has exact synonym: Mass spectrum analysis
has definition: Analyse a spectrum from a mass spectrometry (or other) experiment.
Created in: 1.1
has exact synonym: Spectral analysis
in subset: bioinformatics
in subset: edam
in subset: operations

Peak detection
type: Class
subclass of: Spectrum analysis
subclass of: Restriction
  on property: has input
  some values from: Mass spectrometry spectra
has definition: Identify peaks in a spectrum from a mass spectrometry experiment.
has exact synonym: Peak finding
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Scaffolding
type: Class
subclass of: Mapping and assembly
subclass of: Sequence processing (nucleic acid)
subclass of: Nucleic acid sequence analysis
comment: Scaffold may be positioned along a chromosome physical map to create a "golden path".
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
in subset: bioinformatics
in subset: edam
in subset: operations

Scaffold gap completion
type: Class
subclass of: Mapping and assembly
subclass of: Sequence processing (nucleic acid)
subclass of: Nucleic acid sequence analysis
Created in: 1.1
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.
has definition: Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequencing quality control
type: Class
subclass of: Evaluation and validation
subclass of: Nucleic acid sequence analysis
has exact synonym: Analyse raw sequence data from a sequencing pipeline and identify problems.
Created in: 1.1
has exact synonym: Sequencing QC
has definition: Raw sequence data quality control.
in subset: bioinformatics
in subset: edam
in subset: operations

Read pre-processing
type: Class
subclass of: Nucleic acid sequence analysis
Created in: 1.1
has definition: Pre-process sequence reads to ensure (or improve) quality and reliability.
comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
has exact synonym: Sequence read pre-processing
in subset: bioinformatics
in subset: edam
in subset: operations

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: bioinformatics
in subset: edam
in subset: operations

Peak calling
type: Class
subclass of: Nucleic acid feature prediction
Created in: 1.1
has exact synonym: Protein binding peak detection
has definition: Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.
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').
in subset: bioinformatics
in subset: edam
in subset: operations

Differential expression analysis
type: Class
subclass of: Gene expression profile comparison
Created in: 1.1
comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
has exact synonym: Differentially expressed gene identification
has definition: Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.
in subset: bioinformatics
in subset: edam
in subset: operations

Gene set testing
type: Class
subclass of: Gene expression profile processing
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.
comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Variant classification
type: Class
subclass of: Sequence classification
subclass of: Genetic variation analysis
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.)
Created in: 1.1
has definition: Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.
in subset: bioinformatics
in subset: edam
in subset: operations

Variant prioritization
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.
comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
in subset: bioinformatics
in subset: edam
in subset: operations

Variant mapping
type: Class
subclass of: Genetic variation analysis
has exact synonym: Variant calling
has definition: Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.
comment: Methods often utilise a database of aligned reads.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Structural variation discovery
type: Class
subclass of: Genetic variation analysis
comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
Created in: 1.1
has definition: Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).
in subset: bioinformatics
in subset: edam
in subset: operations

Exome analysis
type: Class
subclass of: Nucleic acid sequence analysis
has definition: Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.
has exact synonym: Exome sequence analysis
comment: Exome sequencing is considered a cheap alternative to whole genome sequencing.
has exact synonym: Targeted exome capture
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Read depth analysis
type: Class
subclass of: Nucleic acid sequence analysis
has definition: Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: operations

Gene expression QTL analysis
type: Class
subclass of: Gene expression profile analysis
subclass of: Restriction
  on property: has output
  some values from: Pathway or network report
Created in: 1.1
has exact synonym: expression quantitative trait loci profiling
has exact synonym: expression QTL profiling
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: eQTL profiling
in subset: bioinformatics
in subset: edam
in subset: operations

Copy number estimation
type: Class
subclass of: Nucleic acid sequence analysis
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 hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.
Created in: 1.1
has exact synonym: Transcript copy number estimation
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).
in subset: bioinformatics
in subset: edam
in subset: operations

Primer removal
type: Class
subclass of: Sequence cutting
subclass of: Sequence editing (nucleic acid)
has definition: Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).
Created in: 1.2
in subset: bioinformatics
in subset: edam
in subset: operations

Transcriptome assembly
type: Class
subclass of: Mapping and assembly
subclass of: Sequence processing (nucleic acid)
subclass of: Nucleic acid sequence analysis
subclass of: Restriction
  on property: has topic
  some values from: Sequence assembly
subclass of: Restriction
  on property: has output
  some values from: Sequence assembly
has definition: Infer a transcriptome sequence by analysis of short sequence reads.
Created in: 1.2
in subset: bioinformatics
in subset: edam
in subset: operations

Transcriptome assembly (de novo)
type: Class
subclass of: Transcriptome assembly
has definition: Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.
Created in: 1.2
has exact synonym: de novo transcriptome assembly
in subset: bioinformatics
in subset: edam
in subset: operations

Transcriptome assembly (mapping)
type: Class
subclass of: Transcriptome assembly
Created in: 1.2
has definition: Infer a transcriptome sequence by mapping short reads to a reference genome.
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence coordinate conversion
type: Class
subclass of: File processing
subclass of: Restriction
  on property: has output
  some values from: Sequence coordinates
subclass of: Restriction
  on property: has input
  some values from: Sequence coordinates
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.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: operations

Document similarity calculation
type: Class
subclass of: Article analysis
Created in: 1.3
has definition: Calculate similarity between 2 or more documents.
in subset: bioinformatics
in subset: edam
in subset: operations

Document clustering
type: Class
subclass of: Article analysis
Created in: 1.3
has definition: Cluster (group) documents on the basis of their calculated similarity.
in subset: bioinformatics
in subset: edam
in subset: operations

Named entity recognition
type: Class
subclass of: Article analysis
has definition: Recognise named entities (text tokens) within documents.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: operations

ID mapping
type: Class
subclass of: Data retrieval (metadata and documentation)
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
Created in: 1.3
has exact synonym: Identifier mapping
in subset: bioinformatics
in subset: edam
in subset: operations

Data anonymisation
type: Class
subclass of: File processing
Created in: 1.3
has exact synonym: Data anonymization
has definition: Process data in such a way that makes it hard to trace to the person which the data concerns.
in subset: bioinformatics
in subset: edam
in subset: operations

ID retrieval
type: Class
subclass of: Data retrieval (metadata and documentation)
subclass of: Restriction
  on property: has output
  some values from: Identifier
Created in: 1.3
has definition: Search for and retrieve a data identifier of some kind, e.g. a database entry accession.
has exact synonym: Accession retrieval
has exact synonym: Data retrieval (id)
has exact synonym: Identifier retrieval
has exact synonym: Data retrieval (ID)
has exact synonym: Data retrieval (accession)
has exact synonym: id retrieval
in subset: bioinformatics
in subset: edam
in subset: operations

Sequence checksum generation
type: Class
subclass of: Sequence processing
subclass of: Restriction
  on property: has input
  some values from: Sequence
subclass of: Restriction
  on property: has topic
  some values from: Data acquisition and deposition
Created in: 1.4
has definition: Generate a checksum of a molecular sequence.
in subset: bioinformatics
in subset: edam
in subset: operations

Bibliography construction
type: Class
subclass of: Text processing
Created in: 1.4
has definition: Construct a bibliography from the scientific literature.
in subset: bioinformatics
in subset: edam
in subset: operations

Protein quaternary structure prediction
type: Class
subclass of: Protein structure prediction
has definition: Predict the structure of a multi-subunit protein and particularly how the subunits fit together.
Created in: 1.4
in subset: bioinformatics
in subset: edam
in subset: operations

Protein surface analysis
type: Class
subclass of: Protein property calculation (from structure)
has definition: Analyse the surface properties of proteins.
Created in: 1.4
in subset: bioinformatics
in subset: edam
in subset: operations

Ontology comparison
type: Class
subclass of: Comparison
has definition: Compare two or more ontologies, e.g. identify differences.
Created in: 1.4
in subset: bioinformatics
in subset: edam
in subset: operations

Semantic analysis
type: Class
subclass of: Text processing
has definition: Analyse set(s) of terms from a controlled vocabulary to make scientific inferences.
has definition: Compare two or more ontologies, e.g. identify differences.
Created in: 1.4
in subset: bioinformatics
in subset: edam
in subset: operations

Format detection
type: Class
subclass of: File processing
subclass of: Restriction
  on property: has input
  some values from: Data
subclass of: Restriction
  on property: has output
  some values from: Format identifier
has exact synonym: Format inference
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.
has exact synonym: Format recognition
has exact synonym: Format identification
Created in: 1.4
has definition: Recognition of which format the given data is in.
no clue: noClue
in subset: bioinformatics
in subset: edam
in subset: operations

Axiom
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.
annotated property: noClue
annotated target: noClue
annotated source: Format detection

File splitting
type: Class
subclass of: File processing
Created in: 1.4
has definition: split a file containing multiple data items into many files, each containing one item
in subset: bioinformatics
in subset: edam
in subset: operations

Topic
type: Class
disjoint with: DeprecatedClass
has related synonym: sumo:FieldOfStudy
Created in: beta12orEarlier
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: Area of Research
has related synonym: Method
in subset: bioinformatics
in subset: edam
in subset: topics
has broad synonym: Quality
has broad synonym: Continuant
has related synonym: Quality
has related synonym: quality
has related synonym: Category
has related synonym: Perpetuant

Axiom
comment: BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic.
annotated source: Topic
annotated property: hasRelatedSynonym
annotated target: Quality

Axiom
comment: Topic can be a quality of an entity.
annotated source: Topic
annotated property: hasRelatedSynonym
annotated target: quality

Axiom
comment: GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials.
annotated source: Topic
annotated property: hasRelatedSynonym
annotated target: Perpetuant

Axiom
comment: GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated.
annotated source: Topic
annotated property: hasRelatedSynonym
annotated target: Category

Nucleic acids
type: Class
subclass of: Biochemistry
has definition: Topic concerning the processing and analysis of nucleic acid sequence, structural and other data.
Created in: beta12orEarlier
has narrow synonym: Nucleic acid physicochemistry
has narrow synonym: Nucleic acid properties
has exact synonym: Nucleic acid informatics
has exact synonym: Nucleic acid analysis
has exact synonym: Nucleic acid bioinformatics
has narrow synonym: D017422
has narrow synonym: D017423
in subset: bioinformatics
in subset: edam
in subset: topics

Proteins
type: Class
subclass of: Biochemistry
Created in: beta12orEarlier
has exact synonym: Protein analysis
has narrow synonym: Protein databases
has exact synonym: Protein bioinformatics
has definition: Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data.
has exact synonym: Protein informatics
has narrow synonym: D020539
in subset: bioinformatics
in subset: edam
in subset: topics

Metabolites
type: Class
subclass of: Small molecules
Created in: beta12orEarlier
comment: This concept excludes macromolecules such as proteins and nucleic acids.
has definition: Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.
has exact synonym: Metabolite structures
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence analysis
type: Class
subclass of: Computational biology
has db xref: BioCatalogue:Sequence Analysis
has exact synonym: Sequences
has narrow synonym: Sequence databases
has definition: Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.
Created in: beta12orEarlier
has exact synonym: D017421
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structure analysis
type: Class
subclass of: Computational biology
Created in: beta12orEarlier
has narrow synonym: Structure data resources
comment: This includes related concepts such as structural properties, alignments and structural motifs.
has narrow synonym: Structure databases
has exact synonym: Structural bioinformatics
has exact synonym: Structure analysis
has definition: Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.
has narrow synonym: Computational structural biology
has related synonym: D015394
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structure prediction
type: Class
subclass of: Structure analysis
Created in: beta12orEarlier
has definition: Topic concerning the prediction of molecular (secondary or tertiary) structure.
in subset: bioinformatics
in subset: edam
in subset: topics

Alignment
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).
deprecated: true
Obsolete since: beta12orEarlier
consider: Sequence alignment
consider: Structure alignment
consider: Threading
in subset: obsolete

Phylogeny
type: Class
subclass of: Evolutionary biology
has db xref: BioCatalogue:Evolutionary Distance Measurements
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.
has db xref: BioCatalogue:Phylogeny
has narrow synonym: Phylogenetic simulation
has db xref: BioCatalogue:Statistical Robustness
has definition: Topic concerning the study of evolutionary relationships amongst organisms.
has narrow synonym: Phylogenetic clocks
has narrow synonym: Phylogenetic dating
Created in: beta12orEarlier
has db xref: BioCatalogue:Tree Inference
has narrow synonym: Phylogenetic stratigraphy
has narrow synonym: Phylogeny reconstruction
has narrow synonym: D010802
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Functional genomics
type: Class
subclass of: Genomics
subclass of: Function analysis
has db xref: BioCatalogue:Functional Genomics
has definition: Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Ontology and terminology
type: Class
subclass of: Topic
has narrow synonym: Ontologies
has db xref: BioCatalogue:Ontology Lookup
has definition: Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.
has narrow synonym: Ontology
has narrow synonym: Applied ontology
Created in: beta12orEarlier
has narrow synonym: Terminology
has db xref: BioCatalogue:Ontology
has narrow synonym: D002965
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data search, query and retrieval
type: Class
subclass of: Data management
has definition: Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information.
has exact synonym: Data query
has db xref: BioCatalogue:Structure Retrieval
has db xref: BioCatalogue:Image Retrieval
has db xref: BioCatalogue:Sequence Retrieval
has db xref: BioCatalogue:Data Retrieval
has db xref: BioCatalogue:Identifier Retrieval
has narrow synonym: Data search
comment: This includes, for example, search, query and retrieval of molecular sequences and associated data.
has exact synonym: Data retrieval
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Bioinformatics
type: Class
subclass of: Biology
subclass of: Computer science
comment: This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation.
has definition: Topic concerning the archival, curation, processing and analysis of complex biological data.
Created in: beta12orEarlier
has narrow synonym: D016247
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data visualisation
type: Class
subclass of: Data management
Created in: beta12orEarlier
has exact synonym: Data rendering and visualisation
has exact synonym: Data rendering
has exact synonym: Data plotting
has definition: Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data.
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid thermodynamics
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning the study of the thermodynamic properties of a nucleic acid.
consider: Nucleic acid structure analysis
in subset: obsolete

Nucleic acid structure analysis
type: Class
subclass of: Structure analysis
has narrow synonym: RNA structure
has exact synonym: Nucleic acid structure
has narrow synonym: Nucleic acid thermodynamics
Created in: beta12orEarlier
has narrow synonym: RNA structure alignment
has definition: Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.
has narrow synonym: RNA alignment
has narrow synonym: Nucleic acid denaturation
has narrow synonym: DNA melting
comment: Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.
in subset: bioinformatics
in subset: edam
in subset: topics

RNA
type: Class
subclass of: Nucleic acids
has definition: Topic concerning RNA sequences and structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid restriction
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.
Created in: beta12orEarlier
Obsolete since: 1.3
consider: Nucleic acid sites and features
in subset: obsolete

Mapping
type: Class
subclass of: Nucleic acid sequence analysis
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.
Created in: beta12orEarlier
has narrow synonym: Linkage mapping
has narrow synonym: Linkage
has narrow synonym: Genetic linkage
has definition: Topic concerning the mapping of complete (typically nucleotide) sequences.
in subset: bioinformatics
in subset: edam
in subset: topics

Genetic codes and codon usage
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Codon usage analysis
Obsolete since: 1.3
has definition: Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on.
deprecated: true
Created in: beta12orEarlier
consider: Gene expression
in subset: obsolete

Protein expression
type: Class
subclass of: Proteins
Created in: beta12orEarlier
has definition: Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell.
has narrow synonym: Translation
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Gene finding
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: BioCatalogue:Gene Prediction
has exact synonym: Gene discovery
has definition: Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.
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.
Obsolete since: 1.3
deprecated: true
has exact synonym: Gene prediction
Created in: beta12orEarlier
consider: Gene structure
in subset: obsolete

Transcription
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning the transcription of DNA into mRNA.
Obsolete since: 1.3
consider: Gene expression
in subset: obsolete

Promoters
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
has definition: Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).
has db xref: BioCatalogue:Promoter Prediction
Created in: beta12orEarlier
deprecated: true
consider: Transcription factors and regulatory sites
in subset: obsolete

Nucleic acid folding
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning the folding (in 3D space) of nucleic acid molecules.
deprecated: true
Obsolete since: beta12orEarlier
consider: Nucleic acid structure prediction
in subset: obsolete

Gene structure
type: Class
subclass of: Molecular genetics
has definition: Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion.
Created in: beta12orEarlier
comment: This includes the study of promoters, coding regions etc.
in subset: bioinformatics
in subset: edam
in subset: topics

Proteomics
type: Class
subclass of: Omics
has db xref: BioCatalogue:Proteomics
has narrow synonym: Protein expression
has definition: Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms.
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 expression data, for example in different cells or tissues.
has narrow synonym: Peptide identification
has narrow synonym: Protein and peptide identification
Created in: beta12orEarlier
has exact synonym: D040901
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structural genomics
type: Class
subclass of: Genomics
subclass of: Structural biology
has definition: Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism.
Created in: beta12orEarlier
has db xref: BioCatalogue:Structural Genomics
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Protein properties
type: Class
subclass of: Proteins
Created in: beta12orEarlier
has exact synonym: Protein physicochemistry
has narrow synonym: Protein hydropathy
has definition: Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.
in subset: bioinformatics
in subset: edam
in subset: topics

Protein interactions
type: Class
subclass of: Proteins
subclass of: Molecular interactions, pathways and networks
has db xref: BioCatalogue:Protein Interaction
has definition: Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.
has narrow synonym: Protein-DNA interaction
has db xref: BioCatalogue:Ligand Interaction
has narrow synonym: Protein-ligand interactions
Created in: beta12orEarlier
has narrow synonym: Protein-protein interactions
comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
has narrow synonym: Protein-nucleic acid interactions
has narrow synonym: Protein-RNA interaction
in subset: bioinformatics
in subset: edam
in subset: topics

Protein folding, stability and design
type: Class
subclass of: Protein structure analysis
has narrow synonym: Rational protein design
has narrow synonym: Protein stability
has narrow synonym: Protein folding
has narrow synonym: Protein design
has narrow synonym: Protein residue interactions
Created in: beta12orEarlier
has definition: Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
in subset: bioinformatics
in subset: edam
in subset: topics

Two-dimensional gel electrophoresis
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: beta13
has definition: Topic concerning two-dimensional gel electrophoresis image and related data.
consider: Proteomics
in subset: obsolete

Mass spectrometry
type: Class
subclass of: Laboratory techniques
has definition: Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase.
Created in: beta12orEarlier
in subset: edam
in subset: events
in subset: topics

Protein microarrays
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta13
Created in: beta12orEarlier
deprecated: true
has definition: Topic concerning protein microarray data.
consider: Proteomics
consider: Microarrays
in subset: obsolete

Protein hydropathy
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
Created in: beta12orEarlier
has definition: Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein.
consider: Protein properties
in subset: obsolete

Protein targeting and localization
type: Class
subclass of: Protein expression
Created in: beta12orEarlier
has narrow synonym: Protein localization
has narrow synonym: Protein targeting
has narrow synonym: Protein sorting
has definition: Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export.
in subset: bioinformatics
in subset: edam
in subset: topics

Protein cleavage sites and proteolysis
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
Created in: beta12orEarlier
has definition: Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.
deprecated: true
consider: Protein and peptide identification
in subset: obsolete

Protein structure comparison
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
comment: Use this concept for methods that are exclusively for protein structure.
Created in: beta12orEarlier
has definition: Topic concerning the comparison of two or more protein structures.
consider: Protein tertiary structure
consider: Structure comparison
in subset: obsolete

Protein residue interactions
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.3
has exact synonym: Protein residue interactions
deprecated: true
has definition: The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.
consider: Protein folding, stability and design
in subset: obsolete

Protein-protein interactions
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.
Obsolete since: 1.3
Created in: beta12orEarlier
deprecated: true
has narrow synonym: Protein interaction networks
consider: Protein interactions
in subset: obsolete

Protein-ligand interactions
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning protein-ligand (small molecule) interactions.
Created in: beta12orEarlier
consider: Protein interactions
in subset: obsolete

Protein-nucleic acid interactions
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning protein-DNA/RNA interactions.
Created in: beta12orEarlier
consider: Protein interactions
in subset: obsolete

Protein design
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
Created in: beta12orEarlier
Obsolete since: 1.3
consider: Protein folding, stability and design
in subset: obsolete

G protein-coupled receptors (GPCR)
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Topic concerning G-protein coupled receptors (GPCRs).
deprecated: true
consider: Membrane and lipoproteins
in subset: obsolete

Carbohydrates
type: Class
subclass of: Biochemistry
has definition: Topic concerning carbohydrates, typically including structural information.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Lipids
type: Class
subclass of: Biochemistry
has definition: Topic concerning lipids and their structures.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Small molecules
type: Class
subclass of: Biochemistry
Created in: beta12orEarlier
has related synonym: CHEBI:23367
has definition: Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information.
comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included.
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence editing
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Edit, convert or otherwise change a molecular sequence, either randomly or specifically.
deprecated: true
Obsolete since: beta12orEarlier
consider: Sequence analysis
consider: Bioinformatics
in subset: obsolete

Sequence composition, complexity and repeats
type: Class
subclass of: Sequence analysis
has db xref: BioCatalogue:Repeats
has narrow synonym: Sequence composition
has definition: Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.
has narrow synonym: Sequence repeats
has narrow synonym: Low complexity sequences
has narrow synonym: Sequence complexity
Created in: beta12orEarlier
has narrow synonym: Repeat sequences
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence motifs
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.
Obsolete since: 1.3
deprecated: true
has exact synonym: Motifs
Created in: beta12orEarlier
consider: Sequence sites, features and motifs
in subset: obsolete

Sequence comparison
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
has db xref: BioCatalogue:Protein Sequence Similarity
has db xref: BioCatalogue:Nucleotide Sequence Similarity
comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
has definition: Topic concerning the comparison of two or more molecular sequences.
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence sites, features and motifs
type: Class
subclass of: Sequence analysis
has narrow synonym: HMMs
Created in: beta12orEarlier
has narrow synonym: Sequence sites
has narrow synonym: Sequence profiles
has narrow synonym: Protein sequence features
has definition: Topic concerning the archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
has narrow synonym: Sequence feature detection
has narrow synonym: Sequence motifs
has narrow synonym: Functional sites
has narrow synonym: Protein functional sites
has narrow synonym: Sequence features
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence database search
type: Class
subclass of: Obsolete concept (EDAM)
comment: The query is a sequence-based entity such as another sequence, a motif or profile.
deprecated: true
Created in: beta12orEarlier
has definition: Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).
Obsolete since: beta12orEarlier
consider: Sequence comparison
in subset: obsolete

Sequence clustering
type: Class
subclass of: Sequence comparison
has exact synonym: Sequence clusters
has definition: Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities.
Created in: beta12orEarlier
comment: This includes systems that generate, process and analyse sequence clusters.
in subset: bioinformatics
in subset: edam
in subset: topics

Protein structural motifs and surfaces
type: Class
subclass of: Protein structure analysis
has narrow synonym: Protein surfaces
has narrow synonym: Protein structural motifs
Created in: beta12orEarlier
has definition: Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.
comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on.
has narrow synonym: Protein structural features
has narrow synonym: Structural motifs
in subset: bioinformatics
in subset: edam
in subset: topics

Structural (3D) profiles
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Structural profiles
Obsolete since: 1.3
Created in: beta12orEarlier
deprecated: true
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.
consider: Structure comparison
in subset: obsolete

Protein structure prediction
type: Class
subclass of: Structure prediction
subclass of: Protein structure analysis
has db xref: BioCatalogue:Protein Structure Prediction
has definition: Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid structure prediction
type: Class
subclass of: Structure prediction
subclass of: Nucleic acid structure analysis
has definition: Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
has narrow synonym: Nucleic acid folding
has db xref: BioCatalogue:Nucleotide Structure Prediction
has db xref: BioCatalogue:Nucleotide Tertiary Structure
has db xref: BioCatalogue:Nucleotide Secondary Structure
Created in: beta12orEarlier
has exact synonym: RNA structure prediction
has narrow synonym: Nucleic acid design
has narrow synonym: DNA structure prediction
in subset: bioinformatics
in subset: edam
in subset: topics

Ab initio structure prediction
type: Class
subclass of: Structure prediction
Created in: beta12orEarlier
has exact synonym: de novo protein structure prediction
has definition: Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.
in subset: bioinformatics
in subset: edam
in subset: topics

Homology modelling
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data.
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.4
consider: Molecular modelling
in subset: obsolete

Molecular dynamics
type: Class
subclass of: Structure prediction
Created in: beta12orEarlier
has broad synonym: Molecular motions
has broad synonym: Molecular flexibility
has definition: Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
comment: This includes resources concerning flexibility and motion in protein and other molecular structures.
in subset: bioinformatics
in subset: edam
in subset: topics

Molecular docking
type: Class
subclass of: Structure prediction
has definition: Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Protein secondary structure prediction
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.3
has definition: Topic concerning the prediction of secondary or supersecondary structure of protein sequences.
consider: Protein structure prediction
consider: Protein secondary structure
in subset: obsolete

Protein tertiary structure prediction
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning the prediction of tertiary structure of protein sequences.
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.3
consider: Protein structure prediction
consider: Protein tertiary structure
in subset: obsolete

Protein fold recognition
type: Class
subclass of: Structure prediction
Created in: beta12orEarlier
has definition: Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).
comment: For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence alignment
type: Class
subclass of: Sequence comparison
has db xref: BioCatalogue:Protein Multiple Alignment
has definition: Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments).
has db xref: BioCatalogue:Protein Pairwise Alignment
Created in: beta12orEarlier
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.
has db xref: BioCatalogue:Nucleotide Multiple Alignment
has db xref: BioCatalogue:Protein Sequence Alignment
has db xref: BioCatalogue:Nucleotide Pairwise Alignment
has db xref: BioCatalogue:Nucleotide Sequence Alignment
has exact synonym: D016415
in subset: bioinformatics
in subset: edam
in subset: topics

Structure alignment
type: Class
subclass of: Structure comparison
Created in: beta12orEarlier
comment: This includes the generation, storage, analysis, rendering etc. of structure alignments.
has definition: Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).
has exact synonym: Structure alignment generation
in subset: bioinformatics
in subset: edam
in subset: topics

Threading
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
Obsolete since: 1.3
has exact synonym: Sequence-structure alignment
consider: Protein fold recognition
in subset: obsolete

Sequence profiles and HMMs
type: Class
subclass of: Obsolete concept (EDAM)
comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
Obsolete since: 1.3
Created in: beta12orEarlier
has definition: Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment.
deprecated: true
consider: Sequence sites, features and motifs
in subset: obsolete

Phylogeny reconstruction
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: BioCatalogue:Tree Inference
comment: Currently too specific for the topic sub-ontology (but might be unobsoleted).
has definition: Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.
has db xref: BioCatalogue:Evolutionary Distance Measurements
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.3
consider: Phylogeny
in subset: obsolete

Phylogenomics
type: Class
subclass of: Genomics
subclass of: Phylogenetics
has definition: Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Virtual PCR
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning simulated polymerase chain reaction (PCR).
deprecated: true
has exact synonym: PCR
Created in: beta12orEarlier
has exact synonym: Polymerase chain reaction
Obsolete since: beta13
consider: Nucleic acids
in subset: obsolete

Sequence assembly
type: Class
subclass of: Nucleic acid sequence analysis
has definition: Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence.
Created in: beta12orEarlier
comment: This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.
has narrow synonym: Assembly
in subset: bioinformatics
in subset: edam
in subset: topics

Genetic variation
type: Class
subclass of: Genotype and phenotype
has exact synonym: DNA variation
Created in: beta12orEarlier
has narrow synonym: Polymorphism
has narrow synonym: Mutation
has definition: Topic concerning DNA sequence variation (mutation and polymorphism) data.
has exact synonym: D014644
in subset: bioinformatics
in subset: edam
in subset: topics

Microarrays
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning microarrays, for example, to process microarray data or design probes and experiments.
Obsolete since: 1.3
has db xref: BioCatalogue:Microarrays
has narrow synonym: DNA microarrays
deprecated: true
consider: Gene expression
has narrow synonym: D046228
in subset: obsolete

Pharmacology
type: Class
subclass of: Biomedical science
has definition: Topic concerning the study of drugs and their effects or responses in living systems.
has narrow synonym: Pharmacoinformatics
Created in: beta12orEarlier
has narrow synonym: Computational pharmacology
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Gene expression
type: Class
subclass of: Genetics
has narrow synonym: Codon usage
has narrow synonym: DNA microarrays
has exact synonym: Gene expression analysis
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.
has alternative id: http://edamontology.org/topic_0197
has definition: Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.
Created in: beta12orEarlier
has narrow synonym: Expression profiling
has narrow synonym: Gene expression profiling
has db xref: BioCatalogue:Microarrays
comment: This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.
has related synonym: D015870
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Gene regulation
type: Class
subclass of: Gene expression
Created in: beta12orEarlier
has definition: Topic concerning primarily the regulation of gene expression.
in subset: bioinformatics
in subset: edam
in subset: topics

Pharmacogenomics
type: Class
subclass of: Pharmacology
subclass of: Genomics
has definition: Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Medicinal chemistry
type: Class
subclass of: Drug discovery
subclass of: Synthetic chemistry
has exact synonym: Drug design
Created in: beta12orEarlier
has definition: Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.
comment: This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Fish
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation.
Created in: beta12orEarlier
consider: Vertebrates
in subset: obsolete

Flies
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation.
consider: Invertebrates
in subset: obsolete

Mice or rats
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation.
Obsolete since: 1.3
Created in: beta12orEarlier
deprecated: true
comment: The resource may be specific to a group of mice / rats or all mice / rats.
consider: Vertebrates
in subset: obsolete

Worms
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation.
consider: Invertebrates
in subset: obsolete

Literature analysis
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.
Obsolete since: 1.3
Created in: beta12orEarlier
consider: Text mining
in subset: obsolete

Text mining
type: Class
subclass of: Literature and reference
has db xref: BioCatalogue:Document Clustering
has db xref: BioCatalogue:Document Similarity
has exact synonym: Text data mining
has db xref: BioCatalogue:Text Mining
Created in: beta12orEarlier
has definition: Topic concerning the analysis of the biomedical and informatics literature.
has exact synonym: Literature mining
has broad synonym: Literature analysis
has db xref: BioCatalogue:Named Entity Recognition
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data curation and annotation
type: Class
subclass of: Data management
has narrow synonym: Annotation
has narrow synonym: Ontology annotation
has definition: Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary.
has db xref: BioCatalogue:Ontology Annotation
has db xref: BioCatalogue:Genome Annotation
has narrow synonym: Genome annotation
Created in: beta12orEarlier
has narrow synonym: Curation
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data processing and validation
type: Class
subclass of: Data management
Created in: beta12orEarlier
has exact synonym: Data file handling
has exact synonym: Report processing
has narrow synonym: Datatypes
has narrow synonym: Data types
has exact synonym: Report handling
comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.
has definition: Topic concerning basic manipulations of files or reports of generic biological data.
has exact synonym: File handling
in subset: bioinformatics
in subset: edam
in subset: topics

Sequence annotation
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Annotate a molecular sequence.
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
consider: Data curation and annotation
in subset: obsolete

Genome annotation
type: Class
subclass of: Obsolete concept (EDAM)
has db xref: BioCatalogue:Genome Annotation
has definition: Annotate a genome.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
consider: Data curation and annotation
consider: Organisms
in subset: obsolete

NMR spectroscopy
type: Class
subclass of: Structural biology
subclass of: Imaging
has definition: Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.
has broad synonym: Spectroscopy
has exact synonym: Nuclear magnetic resonance spectroscopy
Created in: beta12orEarlier
has exact synonym: NMR
in subset: edam
in subset: events
in subset: topics

Sequence classification
type: Class
subclass of: Sequence analysis
comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
has definition: Topic concerning the classification of molecular sequences based on some measure of their similarity.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Protein classification
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.
deprecated: true
Obsolete since: 1.3
consider: Protein families
in subset: obsolete

Sequence motif or profile
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.
Obsolete since: beta12orEarlier
comment: This includes comparison, discovery, recognition etc. of sequence motifs.
deprecated: true
Created in: beta12orEarlier
consider: Sequence motifs
consider: Sequence profiles and HMMs
in subset: obsolete

Protein modifications
type: Class
subclass of: Protein expression
Created in: beta12orEarlier
has related synonym: MOD:00000
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)
has exact synonym: Protein post-translational modification
has definition: Topic concerning protein chemical modifications, e.g. post-translational modifications.
has related synonym: GO:0006464
in subset: bioinformatics
in subset: edam
in subset: topics

Molecular interactions, pathways and networks
type: Class
subclass of: Systems biology
has db xref: BioCatalogue:Pathways
has alternative id: http://edamontology.org/topic_3076
has definition: Topic concerning molecular interactions, biological pathways, networks and other models.
has narrow synonym: Biological pathways
has narrow synonym: Biological models
has narrow synonym: Molecular interactions
Created in: beta13
has narrow synonym: Network or pathway analysis
has narrow synonym: Biological networks
has db xref: BioCatalogue:Pathway Retrieval
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Informatics
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area.
deprecated: true
consider: Bioinformatics
in subset: obsolete

Literature data resources
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
Created in: beta12orEarlier
deprecated: true
has definition: Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.
consider: Literature and reference
in subset: obsolete

Laboratory information management
type: Class
subclass of: Data management
has narrow synonym: Laboratory resources
Created in: beta12orEarlier
has definition: Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.
consider: Data management
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Cell and tissue culture
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has narrow synonym: Cell culture
has definition: Topic concerning general cell culture or data on a specific cell lines.
deprecated: true
Obsolete since: 1.3
has narrow synonym: Tissue culture
consider: Sample collections
in subset: obsolete

Ecology
type: Class
subclass of: Biology
has broad synonym: Environmental science
has narrow synonym: Ecoinformatics
has narrow synonym: Computational ecology
Created in: beta12orEarlier
has narrow synonym: Ecological informatics
has definition: Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics).
has related synonym: D004777
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Electron microscopy
type: Class
subclass of: Structural biology
subclass of: Imaging
has definition: Topic concerning the use of electrons to analyse structures at resolutions higher than can be achieved using light.
Created in: beta12orEarlier
in subset: edam
in subset: events
in subset: topics

Cell cycle
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning the cell cycle including key genes and proteins.
Obsolete since: beta13
consider: Cell biology
in subset: obsolete

Peptides and amino acids
type: Class
subclass of: Small molecules
has narrow synonym: Peptides
has narrow synonym: Amino acids
has definition: Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Organelles
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has narrow synonym: Rough endoplasmic reticulum
has narrow synonym: Golgi apparatus
has narrow synonym: Mitochondria
deprecated: true
has narrow synonym: Nucleus
has narrow synonym: Ribosome
has narrow synonym: Lysosome
has narrow synonym: Centriole
Created in: beta12orEarlier
has definition: Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).
has narrow synonym: Smooth endoplasmic reticulum
has narrow synonym: Cell membrane
has narrow synonym: Cytoplasm
has narrow synonym: Organelle genes and proteins
consider: Cell biology
in subset: obsolete

Ribosomes
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning ribosomes, typically of ribosome-related genes and proteins.
has narrow synonym: Ribosome genes and proteins
Created in: beta12orEarlier
consider: Organelles
in subset: obsolete

Scents
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has definition: A database about scents.
consider: Small molecules
in subset: obsolete

Drugs and target structures
type: Class
subclass of: Small molecules
subclass of: Drug discovery
has narrow synonym: Target structures
Created in: beta12orEarlier
has definition: Topic concerning the structures of drugs, drug target, their interactions and binding affinities.
has narrow synonym: Drug structures
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Organisms
type: Class
subclass of: Biology
has narrow synonym: Model organisms
has definition: Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology.
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.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Genomics
type: Class
subclass of: Omics
Created in: beta12orEarlier
has definition: Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
has db xref: BioCatalogue:Genomics
has exact synonym: D023281
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Gene families
type: Class
subclass of: Sequence classification
subclass of: Genetics
has exact synonym: Genes, gene family or system
has exact synonym: Gene and protein families
has definition: Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins.
has exact synonym: Gene system
has exact synonym: Gene family
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Chromosomes
type: Class
subclass of: DNA
has definition: Topic concerning chromosomes.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Genotype and phenotype
type: Class
subclass of: Genetics
Created in: beta12orEarlier
has exact synonym: Genotyping
has definition: Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.
has exact synonym: Genotype and phenotype resources
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Gene expression and microarray
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta12orEarlier
has definition: Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.
consider: Microarrays
consider: Gene expression
in subset: obsolete

Sequence design
type: Class
subclass of: Sequence analysis
Created in: beta12orEarlier
has narrow synonym: Primers
has narrow synonym: Primer design
has narrow synonym: in silico cloning
has definition: Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR).
has narrow synonym: Probe design
has narrow synonym: Gene design
comment: This includes the design of primers for PCR and DNA amplification or the design of molecular probes.
has narrow synonym: Probes
has related synonym: D015335
in subset: bioinformatics
in subset: edam
in subset: topics

Pathology
type: Class
subclass of: Medicine
has exact synonym: Diseases
Created in: beta12orEarlier
has definition: Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Specific protein resources
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: Specific protein
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning a particular protein, protein family or other group of proteins.
consider: Protein families
in subset: obsolete

Taxonomy
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning organism classification, identification and naming.
Created in: beta12orEarlier
consider: Phylogeny
in subset: obsolete

Protein sequence analysis
type: Class
subclass of: Sequence analysis
has exact synonym: Protein sequences
has definition: Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.
has db xref: BioCatalogue:Protein Sequence Analysis
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid sequence analysis
type: Class
subclass of: Sequence analysis
has definition: Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.
has db xref: BioCatalogue:Nucleotide Sequence Analysis
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Repeat sequences
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has definition: Topic concerning the repetitive nature of molecular sequences.
Created in: beta12orEarlier
deprecated: true
consider: Sequence composition, complexity and repeats
in subset: obsolete

Low complexity sequences
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.3
has definition: Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity.
deprecated: true
consider: Sequence composition, complexity and repeats
in subset: obsolete

Proteome
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta13
Created in: beta12orEarlier
has definition: Topic concerning a specific proteome including protein sequences and annotation.
consider: Sequence analysis
in subset: obsolete

DNA
type: Class
subclass of: Nucleic acids
comment: The DNA sequences might be coding or non-coding sequences.
has definition: Topic concerning DNA sequences and structure, including processes such as methylation and replication.
Created in: beta12orEarlier
has exact synonym: DNA analysis
in subset: bioinformatics
in subset: edam
in subset: topics

Coding RNA
type: Class
subclass of: RNA
Created in: beta12orEarlier
has narrow synonym: mRNA
has narrow synonym: cDNA
has definition: Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences.
has narrow synonym: EST
in subset: bioinformatics
in subset: edam
in subset: topics

Functional, regulatory and non-coding RNA
type: Class
subclass of: RNA
Created in: beta12orEarlier
has definition: Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).
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).
has narrow synonym: Regulatory RNA
has narrow synonym: Functional RNA
has narrow synonym: Non-coding RNA
in subset: bioinformatics
in subset: edam
in subset: topics

rRNA
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning one or more ribosomal RNA (rRNA) sequences.
deprecated: true
Obsolete since: 1.3
consider: Functional, regulatory and non-coding RNA
in subset: obsolete

tRNA
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning one or more transfer RNA (tRNA) sequences.
Obsolete since: 1.3
deprecated: true
consider: Functional, regulatory and non-coding RNA
in subset: obsolete

Protein secondary structure
type: Class
subclass of: Protein structure analysis
comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
has db xref: BioCatalogue:Protein Secondary Structure
has definition: Topic concerning protein secondary structure or secondary structure alignments.
has exact synonym: Protein secondary structure analysis
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

RNA structure
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Topic concerning RNA secondary or tertiary structure and alignments.
Obsolete since: 1.3
consider: Nucleic acid structure analysis
in subset: obsolete

Protein tertiary structure
type: Class
subclass of: Protein structure analysis
Created in: beta12orEarlier
has exact synonym: Protein tertiary structure analysis
has definition: Topic concerning protein tertiary structures.
has db xref: BioCatalogue:Protein Tertiary Structure
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid classification
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning classification of nucleic acid sequences and structures.
deprecated: true
Obsolete since: 1.3
consider: Gene families
in subset: obsolete

Protein families
type: Class
subclass of: Proteins
subclass of: Sequence classification
comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
has narrow synonym: Protein secondary databases
has narrow synonym: Protein sequence classification
Created in: beta12orEarlier
has definition: Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Protein domains and folds
type: Class
subclass of: Protein structure analysis
has db xref: BioCatalogue:Domains
has narrow synonym: Protein domains
has narrow synonym: Protein folds
has definition: Topic concerning protein tertiary structural domains and folds.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Nucleic acid sequence alignment
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has definition: Topic concerning nucleotide sequence alignments.
deprecated: true
Created in: beta12orEarlier
consider: Sequence alignment
in subset: obsolete

Protein sequence alignment
type: Class
subclass of: Obsolete concept (EDAM)
comment: A sequence profile typically represents a sequence alignment.
has definition: Topic concerning protein sequence alignments.
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.3
consider: Sequence alignment
in subset: obsolete

Nucleic acid sites and features
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning the archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences.
deprecated: true
Obsolete since: 1.3
Created in: beta12orEarlier
consider: Sequence sites, features and motifs
consider: Nucleic acid sequence analysis
in subset: obsolete

Protein sites and features
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites.
Obsolete since: 1.3
Created in: beta12orEarlier
consider: Sequence sites, features and motifs
consider: Protein sequence analysis
in subset: obsolete

Transcription factors and regulatory sites
type: Class
subclass of: Gene expression
subclass of: Protein families
has narrow synonym: Transcription factor binding sites
Created in: beta12orEarlier
has narrow synonym: Transcription factors
has narrow synonym: Transcriptional regulatory sites
has definition: Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.
has db xref: BioCatalogue:Transcription Factors
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.
in subset: bioinformatics
in subset: edam
in subset: topics

Phosphorylation sites
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning protein phosphorylation and phosphorylation sites in protein sequences.
deprecated: true
Obsolete since: 1.0
consider: Protein modifications
consider: Protein sites and features
in subset: obsolete

Metabolic pathways
type: Class
subclass of: Molecular interactions, pathways and networks
has definition: Topic concerning metabolic pathways.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Signaling pathways
type: Class
subclass of: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: Topic concerning signaling pathways.
in subset: bioinformatics
in subset: edam
in subset: topics

Protein and peptide identification
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.3
consider: Proteomics
in subset: obsolete

Workflows
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.0
Created in: beta12orEarlier
deprecated: true
has definition: Topic concerning biological or biomedical analytical workflows or pipelines.
in subset: obsolete

Data types and objects
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.0
Created in: beta12orEarlier
has definition: Topic concerning structuring data into basic types and (computational) objects.
consider: Bioinformatics
in subset: obsolete

Theoretical biology
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
consider: Computational biology
in subset: obsolete

Mitochondria
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has definition: Topic concerning mitochondria, typically of mitochondrial genes and proteins.
deprecated: true
Created in: beta12orEarlier
consider: Organelles
in subset: obsolete

Plants
type: Class
subclass of: Eukaryotes
Created in: beta12orEarlier
has definition: Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.
has exact synonym: Plant
has broad synonym: Botany
has broad synonym: Plant biology
comment: The resource may be specific to a plant, a group of plants or all plants.
in subset: bioinformatics
in subset: edam
in subset: topics

Viruses
type: Class
subclass of: Organisms
comment: The resource may be specific to a virus, a group of viruses or all viruses.
Created in: beta12orEarlier
has definition: Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.
has broad synonym: Virology
in subset: bioinformatics
in subset: edam
in subset: topics

Fungi
type: Class
subclass of: Eukaryotes
comment: The resource may be specific to a fungus, a group of fungi or all fungi.
has definition: Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.
Created in: beta12orEarlier
has broad synonym: Mycology
in subset: bioinformatics
in subset: edam
in subset: topics

Pathogens
type: Class
subclass of: Organisms
has definition: Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Arabidopsis
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning Arabidopsis-specific data.
consider: Plants
in subset: obsolete

Rice
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning rice-specific data.
Obsolete since: 1.3
deprecated: true
consider: Plants
in subset: obsolete

Genetic mapping and linkage
type: Class
subclass of: Obsolete concept (EDAM)
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.
has exact synonym: Genetic linkage
deprecated: true
Obsolete since: 1.3
Created in: beta12orEarlier
has exact synonym: Linkage mapping
consider: Mapping
in subset: obsolete

Comparative genomics
type: Class
subclass of: Genomics
has db xref: BioCatalogue:Comparative Genomics
Created in: beta12orEarlier
has definition: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Mobile genetic elements
type: Class
subclass of: DNA
has definition: Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Human disease
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease.
Created in: beta12orEarlier
deprecated: true
Obsolete since: beta13
consider: Pathology
in subset: obsolete

Immunology
type: Class
subclass of: Biomedical science
has narrow synonym: Computational immunology
Created in: beta12orEarlier
has narrow synonym: Immunoinformatics
has definition: Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.
has related synonym: D007120
has related synonym: D007125
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Membrane and lipoproteins
type: Class
subclass of: Protein families
has definition: Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.
has narrow synonym: Lipoproteins
has narrow synonym: Transmembrane proteins
Created in: beta12orEarlier
has narrow synonym: Membrane proteins
in subset: bioinformatics
in subset: edam
in subset: topics

Enzymes
type: Class
subclass of: Protein families
has exact synonym: Enzymology
Created in: beta12orEarlier
has definition: Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.
in subset: bioinformatics
in subset: edam
in subset: topics

Structural biology
type: Class
subclass of: Biology
has narrow synonym: Structural determination
consider: This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen.
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.
Created in: 1.3
has narrow synonym: Structure determination
has narrow synonym: Structural assignment
has definition: Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structure comparison
type: Class
subclass of: Structure analysis
Created in: beta12orEarlier
has definition: Topic concerning the comparison of two or more molecular structures.
comment: This might involve comparison of secondary or tertiary (3D) structural information.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Function analysis
type: Class
subclass of: Computational biology
has definition: Topic concerning the study of gene and protein function including the prediction of functional properties of a protein.
Created in: beta12orEarlier
has narrow synonym: Protein function analysis
has db xref: BioCatalogue:Function Prediction
has narrow synonym: Protein function prediction
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Prokaryotes and archae
type: Class
subclass of: Organisms
has definition: Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.
Created in: beta12orEarlier
comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
in subset: bioinformatics
in subset: edam
in subset: topics

Protein databases
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Protein data resources
has definition: Topic concerning protein data resources.
Created in: beta12orEarlier
Obsolete since: 1.3
deprecated: true
consider: Proteins
in subset: obsolete

Structure determination
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
Created in: beta12orEarlier
consider: Structural biology
in subset: obsolete

Cell biology
type: Class
subclass of: Biology
has definition: Topic concerning cells, such as key genes and proteins involved in the cell cycle.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Classification
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has definition: Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.
Created in: beta12orEarlier
Obsolete since: beta13
consider: Ontologies, nomenclature and classification
in subset: obsolete

Lipoproteins
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning lipoproteins (protein-lipid assemblies).
Obsolete since: 1.3
deprecated: true
consider: Membrane and lipoproteins
in subset: obsolete

Phylogeny visualisation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: beta12orEarlier
has db xref: BioCatalogue:Tree Display
has definition: Visualise a phylogeny, for example, render a phylogenetic tree.
deprecated: true
consider: Phylogeny
in subset: obsolete

Cheminformatics
type: Class
subclass of: Chemistry
subclass of: Computer science
has exact synonym: Chemical informatics
has db xref: BioCatalogue:Chemoinformatics
has exact synonym: Chemoinformatics
Created in: beta12orEarlier
has definition: Topic concerning the application of information technology to chemistry in biological research environment.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Systems biology
type: Class
subclass of: Biology
has narrow synonym: Biological modelling
has narrow synonym: Biological system modelling
Created in: beta12orEarlier
has db xref: BioCatalogue:Systems Biology
has db xref: BioCatalogue:Model Analysis
has narrow synonym: Biological models
has definition: Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein.
has db xref: BioCatalogue:Model Creation
has db xref: BioCatalogue:Model Execution
comment: This includes databases of models and methods to construct or analyse a model.
has exact synonym: Systems biology
has exact synonym: D049490
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Statistics
type: Class
subclass of: Mathematics
has definition: Topic concerning the application of statistical methods to biological problems.
Created in: beta12orEarlier
has db xref: BioCatalogue:Biostatistics
has narrow synonym: Biostatistics
has exact synonym: Biostatistics
has exact synonym: D056808
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structure database search
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
has definition: Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).
Obsolete since: beta12orEarlier
comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
consider: Structure comparison
in subset: obsolete

Molecular modelling
type: Class
subclass of: Structure prediction
has definition: Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour.
has narrow synonym: Comparative modeling
has exact synonym: Molecular modeling
has narrow synonym: Homology modelling
Created in: beta12orEarlier
has narrow synonym: Comparative modelling
has narrow synonym: Homology modeling
in subset: bioinformatics
in subset: edam
in subset: topics

Protein function prediction
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning the prediction of functional properties of a protein.
deprecated: true
has db xref: BioCatalogue:Function Prediction
Created in: beta12orEarlier
Obsolete since: 1.2
consider: Function analysis
in subset: obsolete

SNPs
type: Class
subclass of: Genetic variation
comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.
has definition: Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Transmembrane protein prediction
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Predict transmembrane domains and topology in protein sequences.
consider: Protein secondary structure prediction
consider: Membrane and lipoproteins
in subset: obsolete

Nucleic acid structure comparison
type: Class
subclass of: Obsolete concept (EDAM)
comment: Use this concept for methods that are exclusively for nucleic acid structures.
Obsolete since: beta12orEarlier
has definition: Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.
deprecated: true
Created in: beta12orEarlier
consider: Nucleic acid structure analysis
consider: Structure comparison
in subset: obsolete

Oncology
type: Class
subclass of: Medicine
has exact synonym: Cancer biology
has narrow synonym: Cancer
Created in: beta12orEarlier
has definition: Topic concerning the study of cancer, for example, genes and proteins implicated in cancer.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Toxins and targets
type: Class
subclass of: Small molecules
subclass of: Toxicology
has narrow synonym: Toxins
Created in: beta12orEarlier
has narrow synonym: Targets
has definition: Topic concerning structural and associated data for toxic chemical substances.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Tool topic
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.
Obsolete since: beta12orEarlier
consider: Topic
in subset: obsolete

Study topic
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: beta12orEarlier
deprecated: true
Created in: beta12orEarlier
has definition: A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.
consider: Topic
in subset: obsolete

Nomenclature
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
Obsolete since: 1.3
has definition: Topic concerning biological nomenclature (naming), symbols and terminology.
deprecated: true
consider: Ontology and terminology
in subset: obsolete

Disease genes and proteins
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning the genes, gene variations and proteins involved in one or more specific diseases.
deprecated: true
Obsolete since: 1.3
consider: Pathology
in subset: obsolete

Protein structure analysis
type: Class
subclass of: Structure analysis
has definition: Topic concerning protein secondary or tertiary structural data and/or associated annotation.
Created in: beta12orEarlier
has alternative id: http://edamontology.org/topic_3040
has exact synonym: Protein structure
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Humans
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has definition: Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general.
deprecated: true
Created in: beta12orEarlier
consider: Vertebrates
in subset: obsolete

Gene resources
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has exact synonym: Gene database
has definition: Informatics resource (typically a database) primarily focussed on genes.
Obsolete since: 1.3
Created in: beta12orEarlier
has exact synonym: Gene resource
consider: Genetics
in subset: obsolete

Yeast
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.
consider: Fungi
in subset: obsolete

Eukaryotes
type: Class
subclass of: Organisms
Created in: beta12orEarlier
comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
has definition: Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.
has exact synonym: Eukaryote
in subset: bioinformatics
in subset: edam
in subset: topics

Invertebrates
type: Class
subclass of: Eukaryotes
has definition: Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.
Created in: beta12orEarlier
comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
in subset: bioinformatics
in subset: edam
in subset: topics

Vertebrates
type: Class
subclass of: Eukaryotes
Created in: beta12orEarlier
has definition: Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
in subset: bioinformatics
in subset: edam
in subset: topics

Unicellular eukaryotes
type: Class
subclass of: Eukaryotes
has definition: Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.
comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
Created in: beta12orEarlier
in subset: bioinformatics
in subset: edam
in subset: topics

Protein structure alignment
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
deprecated: true
Created in: beta12orEarlier
has definition: Topic concerning protein secondary or tertiary structure alignments.
consider: Structure alignment
in subset: obsolete

X-ray crystallography
type: Class
subclass of: Structural biology
subclass of: Imaging
has exact synonym: Crystallography
Created in: beta12orEarlier
has definition: Topic concerning the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials.
in subset: edam
in subset: events
in subset: topics

Ontologies, nomenclature and classification
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.
Created in: beta12orEarlier
Obsolete since: 1.3
deprecated: true
consider: Ontology and terminology
has narrow synonym: D002965
in subset: obsolete

Immunoproteins, genes and antigens
type: Class
subclass of: Protein families
subclass of: Immunology
has narrow synonym: Immunogenes
has narrow synonym: Immunoproteins
Created in: beta12orEarlier
comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
has narrow synonym: Antigens
has narrow synonym: Immunopeptides
has definition: Topic concerning immunity-related genes, proteins and their ligands.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Molecules
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: beta12orEarlier
Created in: beta12orEarlier
has definition: Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.
has related synonym: CHEBI:23367
consider: Molecular biology
in subset: obsolete

Toxicology
type: Class
subclass of: Medicine
subclass of: Safety sciences
has narrow synonym: Computational toxicology
Created in: beta12orEarlier
has broad synonym: Toxicology
has narrow synonym: Toxicoinformatics
has definition: Topic concerning toxins and the adverse effects of these chemical substances on living organisms.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

High-throughput sequencing
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has definition: Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously.
deprecated: true
Obsolete since: beta13
has exact synonym: Next-generation sequencing
consider: Sequencing
in subset: obsolete

Structural clustering
type: Class
subclass of: Structure comparison
Created in: beta12orEarlier
has definition: Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.
has exact synonym: Structure classification
in subset: bioinformatics
in subset: edam
in subset: topics

Gene regulatory networks
type: Class
subclass of: Gene regulation
subclass of: Molecular interactions, pathways and networks
Created in: beta12orEarlier
has definition: Topic concerning gene regulatory networks.
in subset: bioinformatics
in subset: edam
in subset: topics

Disease (specific)
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
deprecated: true
has definition: Informatics resources dedicated to one or more specific diseases (not diseases in general).
Obsolete since: beta12orEarlier
consider: Pathology
in subset: obsolete

Nucleic acid design
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta12orEarlier
Obsolete since: 1.3
has definition: Topic for the design of nucleic acid sequences with specific conformations.
consider: Nucleic acid structure prediction
in subset: obsolete

Primer or probe design
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta13
deprecated: true
has definition: Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes.
Obsolete since: 1.3
consider: Sequence design
in subset: obsolete

Structure databases
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.
has exact synonym: Structure data resources
Obsolete since: 1.2
deprecated: true
Created in: beta13
consider: Structure analysis
in subset: obsolete

Nucleic acid structure
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.2
has definition: Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.
Created in: beta13
deprecated: true
consider: Nucleic acid structure analysis
in subset: obsolete

Sequence databases
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
has exact synonym: Sequence data resources
Created in: beta13
has definition: Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles.
has exact synonym: Sequence data resource
has exact synonym: Sequence data
deprecated: true
consider: Sequence analysis
in subset: obsolete

Nucleic acid sequences
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Nucleotide sequences
deprecated: true
has definition: Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
Obsolete since: 1.3
Created in: beta13
consider: Nucleic acid sequence analysis
in subset: obsolete

Protein sequences
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
Created in: beta13
has definition: Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
consider: Protein sequence analysis
in subset: obsolete

Protein interaction networks
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
consider: Protein-protein interactions
in subset: obsolete

Molecular biology
type: Class
subclass of: Biology
has definition: Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Mammals
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.
Obsolete since: 1.3
Created in: beta13
deprecated: true
consider: Vertebrates
in subset: obsolete

Biodiversity
type: Class
subclass of: Ecology
has definition: Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet.
Created in: beta13
has exact synonym: D044822
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Sequence clusters and classification
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta13
has exact synonym: Sequence clusters
Obsolete since: 1.3
has exact synonym: Sequence families
has definition: Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity.
deprecated: true
comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
consider: Sequence classification
in subset: obsolete

Genetics
type: Class
subclass of: Biology
has narrow synonym: Gene resource
Created in: beta13
has exact synonym: Genetics data resources
has narrow synonym: Gene database
has definition: Topic concerning the study of genes, genetic variation and heredity in living organisms.
has exact synonym: D005823
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Quantitative genetics
type: Class
subclass of: Genotype and phenotype
has definition: Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: topics

Population genetics
type: Class
subclass of: Genetics
Created in: beta13
has definition: Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Regulatory RNA
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta13
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).
consider: Functional, regulatory and non-coding RNA
in subset: obsolete

Documentation and help
type: Class
subclass of: Literature and reference
has narrow synonym: Documentation
Created in: beta13
has narrow synonym: Help
has definition: Topic concerning the documentation of resources such as tools, services and databases and how to get help.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Genetic organisation
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Created in: beta13
has definition: Topic concerning the structural and functional organisation of genes and other genetic elements.
Obsolete since: 1.3
consider: Gene structure
in subset: obsolete

Medical informatics
type: Class
subclass of: Medicine
subclass of: Computer science
has broad synonym: Molecular medicine
has exact synonym: Health and disease
Created in: beta13
has exact synonym: Healthcare informatics
has broad synonym: Translational medicine
has exact synonym: Biomedical informatics
has exact synonym: Clinical informatics
has exact synonym: Health informatics
has definition: Topic concerning the application of information technology to health, disease and biomedicine.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Developmental biology
type: Class
subclass of: Biology
Created in: beta13
has definition: Topic concerning how organisms grow and develop.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Embryology
type: Class
subclass of: Developmental biology
has definition: Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Anatomy
type: Class
subclass of: Biomedical science
has definition: Topic concerning the form and function of the structures of living organisms.
Created in: beta13
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Literature and reference
type: Class
subclass of: Topic
has narrow synonym: Literature sources
has narrow synonym: Literature search
has definition: Topic concerning the scientific literature, reference information and documentation.
Created in: beta13
has related synonym: D011642
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biology
type: Class
subclass of: Topic
has definition: Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on.
Created in: beta13
has exact synonym: Biological science
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data management
type: Class
subclass of: Topic
has narrow synonym: Knowledge management
has exact synonym: Databases
has narrow synonym: Data handling
Created in: beta13
has narrow synonym: Databases
has definition: Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
has narrow synonym: D030541
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Sequence feature detection
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta13
deprecated: true
has definition: Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences.
Obsolete since: 1.3
consider: Sequence sites, features and motifs
has related synonym: D058977
in subset: obsolete

Nucleic acid feature detection
type: Class
subclass of: Obsolete concept (EDAM)
Obsolete since: 1.3
Created in: beta13
has definition: Topic concerning the detection of positional features such as functional sites in nucleotide sequences.
deprecated: true
has definition: Nucleic acid sites and features
in subset: obsolete

Protein feature detection
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
Obsolete since: 1.3
has definition: Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites.
Created in: beta13
consider: Protein sites and features
in subset: obsolete

Biological system modelling
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic for modelling biological systems in mathematical terms.
Created in: beta13
deprecated: true
has db xref: BioCatalogue:Model Execution
Obsolete since: 1.2
has db xref: BioCatalogue:Model Analysis
consider: Theoretical biology
in subset: obsolete

Data acquisition and deposition
type: Class
subclass of: Data management
has definition: Topic concerning the acquisition and deposition of biological data.
has narrow synonym: Data deposition
has narrow synonym: Data acquisition
has exact synonym: Database submission
Created in: beta13
has narrow synonym: Deposition
in subset: bioinformatics
in subset: edam
in subset: topics

Genes and proteins resources
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has exact synonym: Gene and protein families
Created in: beta13
has exact synonym: Gene family
has definition: Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.
Obsolete since: 1.3
consider: Gene families
in subset: obsolete

Sequencing
type: Class
subclass of: Laboratory techniques
has narrow synonym: Next generation sequencing
Created in: 1.1
has definition: Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
has narrow synonym: Next gen sequencing
has narrow synonym: D059014
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

ChIP-seq
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: Chip-sequencing
Created in: 1.1
has exact synonym: Chip seq
Obsolete since: 1.3
has definition: Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
has exact synonym: Chip sequencing
deprecated: true
consider: Protein-nucleic acid interactions
in subset: obsolete

RNA-Seq
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
has exact synonym: WTSS
has exact synonym: Small RNA-Seq
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.
Obsolete since: 1.3
Created in: 1.1
has exact synonym: Whole transcriptome shotgun sequencing
has exact synonym: RNA-seq
has exact synonym: Small RNA-seq
consider: Gene expression
in subset: obsolete

DNA methylation
type: Class
subclass of: Obsolete concept (EDAM)
Created in: 1.1
Obsolete since: 1.3
deprecated: true
has definition: Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.
consider: Epigenetics
has exact synonym: D019175
in subset: obsolete

Metabolomics
type: Class
subclass of: Omics
Created in: 1.1
has definition: Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.
has exact synonym: D055432
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Epigenomics
type: Class
subclass of: Genomics
subclass of: Epigenetics
has definition: Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc.
comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.
Created in: 1.1
has exact synonym: D057890
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Metagenomics
type: Class
subclass of: Ecology
subclass of: Genomics
Created in: 1.1
has definition: Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data.
has broad synonym: Environmental genomics
has broad synonym: Community genomics
has broad synonym: Ecogenomics
has exact synonym: D056186
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Structural variation
type: Class
subclass of: Genetic variation
has exact synonym: Genomic structural variation
has definition: Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
Created in: 1.1
in subset: bioinformatics
in subset: edam
in subset: topics

DNA packaging
type: Class
subclass of: DNA
has definition: Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.
Created in: beta12orEarlier
has exact synonym: D042003
in subset: bioinformatics
in subset: edam
in subset: topics

DNA-Seq
type: Class
subclass of: Obsolete concept (EDAM)
deprecated: true
has exact synonym: DNA-seq
Obsolete since: 1.3
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.
Created in: 1.1
consider: Sequencing
in subset: obsolete

RNA-Seq alignment
type: Class
subclass of: Obsolete concept (EDAM)
Created in: beta12orEarlier
has exact synonym: RNA-seq alignment
Obsolete since: 1.3
has definition: Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.
deprecated: true
consider: Sequence assembly
in subset: obsolete

ChIP-on-chip
type: Class
subclass of: Obsolete concept (EDAM)
has exact synonym: ChIP-chip
Created in: 1.1
has definition: Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions.
Obsolete since: 1.3
deprecated: true
consider: Protein-nucleic acid interactions
in subset: obsolete

Data security
type: Class
subclass of: Data management
has exact synonym: Security
has broad synonym: Security
Created in: 1.3
has exact synonym: Privacy
has definition: Topic concerning the protection of data, for example, patient health data.
in subset: bioinformatics
in subset: edam
in subset: topics

Sample collections
type: Class
subclass of: Biomedical science
has exact synonym: Specimen collections
has narrow synonym: biosamples
Created in: 1.3
has definition: Topic concerning biological samples and specimens.
has exact synonym: biobanking
has narrow synonym: samples
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biochemistry
type: Class
subclass of: Biology
subclass of: Chemistry
has definition: Topic concerning chemical substances and physico-chemical processes and that occur within living organisms.
has exact synonym: Biological chemistry
Created in: 1.3
has exact synonym: Chemical biology
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Phylogenetics
type: Class
subclass of: Sequence analysis
subclass of: Phylogeny
Created in: 1.3
has definition: Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).
has narrow synonym: D010802
in subset: bioinformatics
in subset: edam
in subset: topics

Epigenetics
type: Class
subclass of: Molecular genetics
Created in: 1.3
has narrow synonym: Histone modification
has narrow synonym: DNA methylation
comment: This includes sub-topics such as histone modification and DNA methylation.
has narrow synonym: 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 narrow synonym: D019175
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biotechnology
type: Class
subclass of: Biology
Created in: 1.3
has definition: Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Phenomics
type: Class
subclass of: Genotype and phenotype
subclass of: Evolutionary biology
Created in: 1.3
has definition: Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Evolutionary biology
type: Class
subclass of: Biology
Created in: 1.3
has definition: Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Physiology
type: Class
subclass of: Medicine
has definition: Topic concerning the functions of living organisms and their constituent parts.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Microbiology
type: Class
subclass of: Biomedical science
Created in: 1.3
has definition: Topic concerning the biology of microorganisms.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Parasitology
type: Class
subclass of: Biomedical science
Created in: 1.3
has definition: Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system.
has definition: Topic concerning the biology of parasites.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Medicine
type: Class
subclass of: Topic
has exact synonym: Biomedical research
Created in: 1.3
has definition: Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease.
has exact synonym: Experimental medicine
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Neurobiology
type: Class
subclass of: Biomedical science
has definition: Topic concerning the study of the nervous system and brain; its anatomy, physiology and function.
Created in: 1.3
has broad synonym: Neuroscience
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Public health and epidemiology
type: Class
subclass of: Medicine
has narrow synonym: Epidemiology
has narrow synonym: Public health
Created in: 1.3
has alternative id: Topic concerning the the patterns, cause, and effect of disease within populations.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biophysics
type: Class
subclass of: Biology
subclass of: Physics
has definition: Topic concerning the use of physics to study biological system.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Computational biology
type: Class
subclass of: Biology
subclass of: Computer science
has narrow synonym: Biomathematics
Created in: 1.3
has narrow synonym: Theoretical biology
has definition: Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.
has narrow synonym: Mathematical biology
comment: This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).
has db xref: BioCatalogue:Model Execution
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Transcriptomics
type: Class
subclass of: Gene expression
subclass of: Genomics
has definition: Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.
Created in: 1.3
has narrow synonym: Transcriptome
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Chemistry
type: Class
subclass of: Topic
has definition: Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Mathematics
type: Class
subclass of: Topic
Created in: 1.3
has exact synonym: Maths
has definition: Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Computer science
type: Class
subclass of: Topic
Created in: 1.3
has definition: Topic concerning the theory and practical use of computer systems.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Physics
type: Class
subclass of: Topic
Created in: 1.3
has definition: Topic concerning the study of matter, space and time, and related concepts such as energy and force.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

RNA splicing
type: Class
subclass of: RNA
subclass of: Molecular genetics
Created in: 1.3
comment: This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.
has definition: Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.
in subset: bioinformatics
in subset: edam
in subset: topics

Molecular genetics
type: Class
subclass of: Genetics
Created in: 1.3
has definition: Topic concerning the structure and function of genes at a molecular level.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Respiratory medicine
type: Class
subclass of: Medicine
has narrow synonym: Pulmonary disorders
Created in: 1.3
has exact synonym: Pulmonary medicine
has narrow synonym: Respiratory disease
has definition: Topic concerning the study of respiratory system.
has exact synonym: Pulmonology
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Metabolic disease
type: Class
subclass of: Obsolete concept (EDAM)
has definition: Topic concerning the study of metabolic diseases.
Created in: 1.3
Obsolete since: 1.4
deprecated: true
consider: Endocrinology and metabolism
in subset: obsolete

Infectious disease
type: Class
subclass of: Pathology
Created in: 1.3
has exact synonym: Communicable disease
has definition: Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).
has exact synonym: Transmissable disease
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Rare diseases
type: Class
subclass of: Pathology
has definition: Topic concerning the study of rare diseases.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Computational chemistry
type: Class
subclass of: Chemistry
subclass of: Computer science
has db xref: Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Neurology
type: Class
subclass of: Medicine
Created in: 1.3
has narrow synonym: Neurological disorders
has definition: Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Cardiology
type: Class
subclass of: Medicine
has narrow synonym: Heart disease
has definition: Topic concerning the diseases and abnormalities of the heart and circulatory system.
Created in: 1.3
has exact synonym: Cardiovascular medicine
has narrow synonym: Cardiovascular disease
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Drug discovery
type: Class
subclass of: Chemistry
subclass of: Medicine research and development
Created in: 1.3
comment: This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
has definition: Topic concerning the discovery and design of drugs or potential drug compounds.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biobank
type: Class
subclass of: Sample collections
has exact synonym: Tissue collection
has definition: Topic concerning repositories of biological samples, typically human, for basic biological and clinical research.
Created in: 1.3
has exact synonym: biobanking
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Mouse clinic
type: Class
subclass of: Sample collections
has definition: Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Microbial collection
type: Class
subclass of: Sample collections
has definition: Topic concerning collections of microbial cells including bacteria, yeasts and moulds.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Cell culture collection
type: Class
subclass of: Sample collections
Created in: 1.3
has definition: Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Clone library
type: Class
subclass of: Sample collections
has definition: Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Translational medicine
type: Class
subclass of: Medicine
Created in: 1.3
has definition: Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Compound libraries and screening
type: Class
subclass of: Drug discovery
Created in: 1.3
has narrow synonym: Chemical screening
has narrow synonym: Compound library
has definition: Topic concerning collections of chemicals, typically for use in high-throughput screening experiments.
has narrow synonym: Chemical library
has broad synonym: Translational medicine
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Biomedical science
type: Class
subclass of: Biology
subclass of: Medicine
Created in: 1.3
has exact synonym: Topic concerning biological science that is (typically) performed in the context of medicine.
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Data identity and mapping
type: Class
subclass of: Data management
has exact synonym: Topic concerning the identity of biological data and the mapping of entities in different databases.
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: events
in subset: topics

Sequence search
type: Class
subclass of: Sequence analysis
subclass of: Sequence comparison
has definition: Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity.
has exact synonym: Sequence database search
Created in: 1.3
in subset: bioinformatics
in subset: edam
in subset: topics

Biomarkers
type: Class
subclass of: Biology
has definition: Topic concerning objective indicators of biological state often used to assess health, and determinate treatment.
Created in: 1.4
has exact synonym: Diagnostic markers
in subset: edam
in subset: topics

Laboratory techniques
type: Class
subclass of: Topic
Created in: 1.4
has exact synonym: Lab techniques
has definition: Topic concerning the procedures used to conduct an experiment.
in subset: edam
in subset: events
in subset: topics

Data analysis
type: Class
subclass of: Data management
Created in: 1.4
has definition: Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data.
in subset: edam
in subset: events
in subset: topics

Data integration
type: Class
subclass of: Data management
Created in: 1.4
has definition: Topic concerning the combination of data from different sources to provide users with a unified view of these data.
in subset: edam
in subset: events
in subset: topics

Biomaterials
type: Class
subclass of: Biotechnology
has definition: Topic concerning any matter, surface or construct that interacts with a biological system.
Created in: 1.4
has exact synonym: Diagnostic markers
in subset: edam
in subset: events
in subset: topics

Chemical biology
type: Class
subclass of: Biology
subclass of: Synthetic chemistry
has definition: Topic concerning the use of synthetic chemistry to study and manipulate biological systems.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Analytical chemistry
type: Class
subclass of: Chemistry
has definition: Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Synthetic chemistry
type: Class
subclass of: Chemistry
has definition: Topic concerning the use of chemistry to create new compounds.
Created in: 1.4
has exact synonym: Synthetic organic chemistry
in subset: edam
in subset: events
in subset: topics

Computer programming
type: Class
subclass of: Computer science
has exact synonym: Software development
Created in: 1.4
has definition: Topic concerning the process that leads from an original formulation of a computing problem to executable programs.
in subset: edam
in subset: events
in subset: topics

Drug development
type: Class
subclass of: Medicine research and development
has exact synonym: Medicines development
has exact synonym: Drug development science
has exact synonym: Medicine development
has definition: Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Drug formulation and delivery
type: Class
subclass of: Medicine research and development
Created in: 1.4
has definition: Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect.
has narrow synonym: Drug formulation
has narrow synonym: Drug delivery
in subset: edam
in subset: events
in subset: topics

Pharmacokinetics and pharmacodynamics
type: Class
subclass of: Medicine research and development
has narrow synonym: Drug metabolism
has broad synonym: Drug metabolism
has exact synonym: ADME
has narrow synonym: Drug absorption
has narrow synonym: Drug excretion
Created in: 1.4
has narrow synonym: Drug distribution
has definition: Topic concerning the study of how a drug interacts with the body.
has narrow synonym: Pharmacokinetics
has narrow synonym: Pharmacodynamics
in subset: edam
in subset: events
in subset: topics

Medicine research and development
type: Class
label: Medicines research and development
subclass of: Biomedical science
has definition: Topic concerning the discovery, development and approval of medicines.
Created in: 1.4
has exact synonym: Drug discovery and development
has broad synonym: Health care research
in subset: edam
in subset: events
in subset: topics

Safety sciences
type: Class
subclass of: Medicine research and development
has definition: Topic concerning the safety (or lack) of drugs and other medical interventions.
has narrow synonym: Drug safety
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Pharmacovigilence
type: Class
subclass of: Safety sciences
has definition: Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines.
comment: Pharmacovigilence concerns safety once a drug has gone to market.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Preclinical and clinical studies
type: Class
subclass of: Medicine research and development
has narrow synonym: Clinical studies
Created in: 1.4
has narrow synonym: Preclinical studies
has definition: Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.
in subset: edam
in subset: events
in subset: topics

Imaging
type: Class
subclass of: Laboratory techniques
has definition: Topic concerning the visual representation of an object.
has narrow synonym: Microscopy
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Biological imaging
type: Class
subclass of: Imaging
has definition: Topic concerning the use of imaging techniques to understand biology.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Medical imaging
type: Class
subclass of: Imaging
has definition: Topic concerning the use of imaging techniques for clinical purposes for medical research.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Light microscopy
type: Class
subclass of: Imaging
Created in: 1.4
has definition: Topic concerning the use of optical instruments to magnify the image of an object.
in subset: edam
in subset: events
in subset: topics

Laboratory animal science
type: Class
subclass of: Biomedical science
has definition: Topic concerning the use of animals and alternatives in experimental research.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Marine biology
type: Class
subclass of: Biology
has definition: Topic concerning the study of organisms in the ocean or brackish waters.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Molecular medicine
type: Class
subclass of: Translational medicine
has definition: Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Nutritional science
type: Class
subclass of: Biomedical science
has exact synonym: Nutrition science
Created in: 1.4
has definition: Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices.
in subset: edam
in subset: events
in subset: topics

Omics
type: Class
subclass of: Biology
has definition: Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Quality affairs
type: Class
subclass of: Medicine research and development
Created in: 1.4
has narrow synonym: Good laboratory practice
has exact synonym: Quality assurance
has narrow synonym: Good clinical practice
has definition: Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use.
has narrow synonym: Good manufacturing practice
in subset: edam
in subset: events
in subset: topics

Regulatory affairs
type: Class
subclass of: Medicine research and development
Created in: 1.4
has definition: Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.
in subset: edam
in subset: events
in subset: topics

Regnerative medicine
type: Class
subclass of: Biomedical science
has definition: Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells.
Created in: 1.4
has exact synonym: Stem cell research
in subset: edam
in subset: events
in subset: topics

Systems medicine
type: Class
subclass of: Medicine
has definition: Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Veterinary medicine
type: Class
subclass of: Medicine
has alternative id: Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Bioengineering
type: Class
subclass of: Biotechnology
has definition: Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering.
has exact synonym: Diagnostic markers
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Geriatric medicine
type: Class
subclass of: Medicine
has exact synonym: Geriatrics
Created in: 1.4
has exact synonym: Aging
has exact synonym: Ageing
has definition: Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.
in subset: edam
in subset: events
in subset: topics

Allergy, clinical immunology and immunotherapeutics.
type: Class
subclass of: Medicine
has narrow synonym: Immunotherapeutics
has narrow synonym: Allergy
has narrow synonym: Immunomodulators
has narrow synonym: Clinical immunology
has narrow synonym: Immune disorders
Created in: 1.4
has definition: Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement.
in subset: edam
in subset: events
in subset: topics

Pain medicine
type: Class
subclass of: Medicine
has exact synonym: Algiatry
Created in: 1.4
has exact synonym: Ageing
has definition: Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.
in subset: edam
in subset: events
in subset: topics

Anaesthesiology
type: Class
subclass of: Medicine
has definition: Topic concerning anaesthesia and anaesthetics.
Created in: 1.4
has exact synonym: Anaesthetics
in subset: edam
in subset: events
in subset: topics

Critical care medicine
type: Class
subclass of: Cardiology
has definition: Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury.
Created in: 1.4
has exact synonym: Emergency medicine
has exact synonym: Acute medicine
has exact synonym: Geriatrics
in subset: edam
in subset: events
in subset: topics

Dermatology
type: Class
subclass of: Medicine
Created in: 1.4
has definition: Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.
has narrow synonym: Dermatological disorders
in subset: edam
in subset: events
in subset: topics

Dentistry
type: Class
subclass of: Medicine
has definition: Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Ear, nose and throat medicine
type: Class
subclass of: Medicine
has exact synonym: Audiovestibular medicine
has narrow synonym: Head and neck disorders
Created in: 1.4
has exact synonym: Otolaryngology
has definition: Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.
in subset: edam
in subset: events
in subset: topics

Endocrinology and metabolism
type: Class
subclass of: Medicine
has narrow synonym: Endocrine disorders
has narrow synonym: Endocrinology
has definition: Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.
has narrow synonym: Metabolism
has narrow synonym: Metabolic disorders
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Haematology
type: Class
subclass of: Medicine
has narrow synonym: Blood disorders
Created in: 1.4
has narrow synonym: Haematological disorders
has definition: Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases.
in subset: edam
in subset: events
in subset: topics

Gastroenterology
type: Class
subclass of: Medicine
has definition: Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.
Created in: 1.4
has narrow synonym: Gastrointestinal disorders
in subset: edam
in subset: events
in subset: topics

Gender medicine
type: Class
subclass of: Medicine
Created in: 1.4
has definition: Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.
in subset: edam
in subset: events
in subset: topics

Gynaecology and obstetrics
type: Class
subclass of: Medicine
has narrow synonym: Obstetrics
has narrow synonym: Gynaecological disorders
has narrow synonym: Gynaecology
has definition: Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Hepatic and biliary medicine
type: Class
subclass of: Medicine
has definition: Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile.
Created in: 1.4
has narrow synonym: Liver disorders
has exact synonym: Hepatobiliary medicine
in subset: edam
in subset: events
in subset: topics

Infectious tropical disease
type: Class
subclass of: Infectious disease
has definition: Topic concerning the branch of medicine that deals with the infectious diseases of the tropics.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Trauma medicine
type: Class
subclass of: Medicine
has definition: Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Medical toxicology
type: Class
subclass of: Medicine
Created in: 1.4
has definition: Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.
in subset: edam
in subset: events
in subset: topics

Musculoskeletal medicine
type: Class
subclass of: Medicine
Created in: 1.4
has narrow synonym: Musculoskeletal disorders
has definition: Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.
in subset: edam
in subset: events
in subset: topics

Opthalmology
type: Class
subclass of: Medicine
has definition: Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.
has exact synonym: Audiovestibular medicine
has narrow synonym: Eye disoders
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Paediatrics
type: Class
subclass of: Medicine
has exact synonym: Child health
has definition: Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents.
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Psychiatry
type: Class
subclass of: Medicine
has broad synonym: Mental health
has definition: Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.
has narrow synonym: Psychiatric disorders
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Reproductive health
type: Class
subclass of: Medicine
has narrow synonym: Fertility medicine
has narrow synonym: Family planning
has definition: Topic concerning the health of the reproductive processes, functions and systems at all stages of life.
Created in: 1.4
has exact synonym: Audiovestibular medicine
has narrow synonym: Reproductive disorders
in subset: edam
in subset: events
in subset: topics

Surgery
type: Class
subclass of: Medicine
Created in: 1.4
has definition: Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.
in subset: edam
in subset: events
in subset: topics

Urology and nephrology
type: Class
subclass of: Medicine
has narrow synonym: Nephrology
has narrow synonym: Urological disorders
has definition: Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.
has narrow synonym: Kidney disease
has narrow synonym: Urology
Created in: 1.4
in subset: edam
in subset: events
in subset: topics

Complementary medicine
type: Class
subclass of: Medicine
has broad synonym: Alternative medicine
Created in: 1.4
has broad synonym: Holistic medicine
has definition: Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.
in subset: edam
in subset: events
in subset: topics

Obsolete concept (EDAM)
type: Class
subclass of: DeprecatedClass
deprecated: true
has definition: An obsolete concept (redefined in EDAM).
comment: Needed for conversion to the OBO format.
Created in: 1.2