An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats
type: Ontology
idspace: EDAM_topic http://edamontology.org/topic_ "EDAM topics"
idspace: EDAM_operation http://edamontology.org/operation_ "EDAM operations"
date: 09:07:2015
next id: 3625
has subset: formats "EDAM data formats"
default-relationship-id-prefix: EDAM
has subset: identifiers "EDAM types of identifiers"
has subset: data "EDAM types of data"
has subset: relations "EDAM relations"
has subset: edam "EDAM"
remark: EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. 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.
has subset: operations "EDAM operations"
idspace: EDAM http://edamontology.org/ "EDAM relations and concept properties"
format: application/rdf+xml
idspace: EDAM_data http://edamontology.org/data_ "EDAM types of data"
has subset: concept_properties "EDAM concept properties"
creator: Jon Ison
creator: Matúš Kalaš
saved by: Jon Ison, Matus Kalas, Hervé Ménager
idspace: EDAM_format http://edamontology.org/format_ "EDAM data formats"
has subset: topics "EDAM topics"
version: 1.11
creator: Hervé Ménager
remark: EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.

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

Documentation
type: AnnotationProperty
has related synonym: Specification
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.
is metadata tag: true
in subset: concept_properties

Example
type: AnnotationProperty
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.
is metadata tag: true
in subset: concept_properties

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

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

has format
type: ObjectProperty
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'.
is cyclic: false
transitive over: OBO_REL:is_a
in subset: relations
is reflexive: false
is symmetric: false
in subset: edam
has definition: 'A has_format B' defines for the subject A, that it has the object B as its data format.
is anti symmetric: false
domain: data_0006
range: format 1915

has function
type: ObjectProperty
is anti symmetric: false
transitive over: OBO_REL:is_a
has related synonym: OBO_REL:bearer_of
in subset: edam
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
is cyclic: true
has definition: 'A has_function B' defines for the subject A, that it has the object B as its function.
in subset: relations
is reflexive: false
range: operation_0004

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

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

has identifier
type: ObjectProperty
is reflexive: false
is anti symmetric: false
in subset: relations
transitive over: OBO_REL:is_a
in subset: edam
has definition: 'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
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'.
is cyclic: false
is symmetric: false
domain: data_0006
range: data_0842

has input
type: ObjectProperty
has related synonym: OBO_REL:has_participant
is anti symmetric: false
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.
in subset: relations
transitive over: OBO_REL:is_a
is symmetric: 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 reflexive: false
is cyclic: true
in subset: edam
range: data_0006
domain: operation_0004

Axiom
annotated target: OBO_REL:has_participant
comment: 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.
annotated source: has input
annotated property: hasRelatedSynonym

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

has output
type: ObjectProperty
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.
in subset: edam
transitive over: OBO_REL:is_a
in subset: relations
has related synonym: OBO_REL:has_participant
is cyclic: true
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 symmetric: false
is reflexive: false
is anti symmetric: false
range: data_0006
domain: operation_0004

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
in subset: relations
is cyclic: true
comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
is symmetric: false
has definition: 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).
in subset: edam
transitive over: OBO_REL:is_a
is anti symmetric: false
is reflexive: false
range: topic_0003
domain: Class
  union of: data_0006
  union of: operation_0004

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

is format of
type: ObjectProperty
is anti symmetric: false
transitive over: OBO_REL:is_a
is reflexive: false
is symmetric: false
is cyclic: false
has definition: 'A is_format_of B' defines for the subject A, that it is a data format of the object B.
in subset: edam
in subset: relations
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.
has related synonym: OBO_REL:quality_of
range: data_0006
domain: format 1915
inverse of: has format

Axiom
annotated target: OBO_REL:quality_of
comment: Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.
annotated source: is format of
annotated property: hasRelatedSynonym

is function of
type: ObjectProperty
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.
has related synonym: OBO_REL:inheres_in
is cyclic: true
transitive over: OBO_REL:is_a
is reflexive: false
has definition: 'A is_function_of B' defines for the subject A, that it is a function of the object B.
has narrow synonym: OBO_REL:function_of
in subset: edam
in subset: relations
is anti symmetric: false
is symmetric: false
inverse of: has function
domain: operation_0004

Axiom
annotated target: OBO_REL:inheres_in
comment: Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.
annotated source: is function of
annotated property: hasRelatedSynonym

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

Axiom
annotated target: OBO_REL:function_of
comment: Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.
annotated source: is function of
annotated property: hasNarrowSynonym

is identifier of
type: ObjectProperty
is anti symmetric: false
is reflexive: false
in subset: edam
is cyclic: false
in subset: relations
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.
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
is symmetric: false
range: data_0006
domain: data_0842
inverse of: has identifier

is input of
type: ObjectProperty
is anti symmetric: false
in subset: relations
is cyclic: true
is reflexive: false
has related synonym: OBO_REL:participates_in
transitive over: OBO_REL:is_a
in subset: edam
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'.
is symmetric: false
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.
domain: data_0006
inverse of: has input
range: operation_0004

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
transitive over: OBO_REL:is_a
is reflexive: false
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_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.
in subset: edam
is anti symmetric: false
has definition: 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B.
has related synonym: OBO_REL:participates_in
is cyclic: true
in subset: relations
domain: data_0006
inverse of: has output
range: operation_0004

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

Axiom
annotated target: OBO_REL:participates_in
comment: 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.
annotated source: is output of
annotated property: hasRelatedSynonym

is topic of
type: ObjectProperty
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).
in subset: relations
has related synonym: OBO_REL:quality_of
is reflexive: false
is cyclic: true
is anti symmetric: false
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 symmetric: false
transitive over: OBO_REL:is_a
in subset: edam
inverse of: has topic
domain: topic_0003
range: Class
  union of: data_0006
  union of: operation_0004

Axiom
annotated target: OBO_REL:quality_of
comment: Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.
annotated source: is topic of
annotated property: hasRelatedSynonym

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

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

FASTA
type: Class
subclass of: FASTA-like (text)
subclass of: Alignment format (text)
Created in: beta12orEarlier
has exact synonym: FASTA format
has exact synonym: FASTA sequence format
has definition: FASTA format including NCBI-style IDs.
in subset: edam
in subset: formats

FASTA-like (text)
type: Class
subclass of: Textual format
subclass of: format 2546
comment: This concept may also be used for the many non-standard FASTA-like formats.
Created in: beta12orEarlier
has definition: A text format resembling FASTA format.
in subset: edam
in subset: formats

Textual format
type: Class
subclass of: format 1915
has definition: Textual format.
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 exact synonym: txt
has narrow synonym: Plain text
Created in: beta12orEarlier
in subset: edam
in subset: formats

Alignment format (text)
type: Class
subclass of: format 1921
has definition: Text format for molecular sequence alignment information.
Created in: beta12orEarlier
in subset: edam
in subset: formats

Obsolete concept (EDAM)
type: Class
subclass of: DeprecatedClass
Created in: 1.2
comment: Needed for conversion to the OBO format.
has definition: An obsolete concept (redefined in EDAM).
deprecated: true