emboss-test 6.6.0-1 / usr / share / EMBOSS / test / data / EDAM.obo

format-version: 1.2
data-version: 1.0
date: 13:01:2012 18:00 ! Always GMT (UTC) or British Summer Time
saved-by: Matus Kalas
subsetdef: operations "EDAM operations" {note="Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually."}
subsetdef: data "EDAM types of data" {note="Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals."}
subsetdef: topics "EDAM topics" {note="Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics."}
subsetdef: formats "EDAM data formats" {note="Data formats commonly used in - and specific to - bioinformatics. Many format concepts in EDAM include references to their definition and documentation."}
subsetdef: identifiers "EDAM types of identifiers" {note="Types of identifiers that identify biological or computational entities; including resource-specific data accessions. Several identifier concepts in EDAM include regular expressions and examples."}
subsetdef: relations "EDAM relations" {note="Types of relations - defined in EDAM - that apply between concepts, entities subject to semantic annotation, and entities and concepts (or possibly even vice versa)."}
subsetdef: concept_attributes "EDAM concept attributes" {note="Types of concept attributes and attribute modifiers or qualifiers, that are defined and used in EDAM in addition to the standard attributes of the OBO format."}
idspace: EDAM_operation http://edamontology.org/operation_ "EDAM Operations"
idspace: EDAM_data http://edamontology.org/data_ "EDAM Types of Data"
idspace: EDAM_topic http://edamontology.org/topic_ "EDAM Topics"
idspace: EDAM_format http://edamontology.org/format_ "EDAM Data Formats"
idspace: EDAM http://edamontology.org/ "EDAM Relations and Concept Attributes"
default-relationship-id-prefix: EDAM
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.
remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Hamish McWilliam, James Malone, Rodrigo Lopez, Helen Parkinson, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence.
next_id: 3168 {since=1.1}



!
! Relations
!

[Typedef]
id: has_input
name: has input
subset: relations
def: "'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument." [http://edamontology.org]
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. {note="In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined."}
synonym: "has input" EXACT [http://wsio.org/has_input]
synonym: "has_specified_input" NARROW [http://purl.obolibrary.org/obo/OBI_0000293] {note="'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)."}
synonym: "has_participant" RELATED [OBO_REL:has_participant] {note="'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."}
inverse_of: is_input_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_operation:0004 ! Operation
range: EDAM_data:0006 ! Data

[Typedef]
id: is_input_of
name: is input of
subset: relations
def: "'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." [http://edamontology.org]
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'. {note="In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'."}
synonym: "is input of" EXACT [http://wsio.org/is_input_of]
synonym: "is_specified_input_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000295] {note="'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)."}
synonym: "participates_in" RELATED [OBO_REL:participates_in] {note="'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."}
inverse_of: has_input
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_data:0006 ! Data
range: EDAM_operation:0004 ! Operation

[Typedef]
id: has_output
name: has output
subset: relations
def: "'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument." [http://edamontology.org]
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. {note="In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined."}
synonym: "has output" EXACT [http://wsio.org/has_output]
synonym: "has_specified_output" NARROW [http://purl.obolibrary.org/obo/OBI_0000299] {note="'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)."}
synonym: "has_participant" RELATED [OBO_REL:has_participant] {note="'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."}
inverse_of: is_output_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_operation:0004 ! Operation
range: EDAM_data:0006 ! Data
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "An operation has_output An error" implies "An error is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.

[Typedef]
id: is_output_of
name: is output of
subset: relations
def: "'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." [http://edamontology.org]
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'. {note="In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'."}
synonym: "is output of" EXACT [http://wsio.org/is_output_of]
synonym: "is_specified_output_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000312] {note="'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)."}
synonym: "participates_in" RELATED [OBO_REL:participates_in] {note="'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."}
inverse_of: has_output
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_data:0006 ! Data
range: EDAM_operation:0004 ! Operation
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statement, An error is_output_of An operation" implies "An error is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.

[Typedef]
id: has_topic
name: has topic
subset: relations
def: "'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)." [http://edamontology.org]
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'. {note="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."}
synonym: "hasTopic" RELATED [http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic] {note="'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."}
synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality]
synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] {note="'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."}
synonym: "is about" RELATED [http://purl.obolibrary.org/obo/IAO_0000136] {note="'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."}
inverse_of: is_topic_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_operation:0004 ! Operation
domain: EDAM_data:0006 ! Data
range: EDAM_topic:0003 ! Topic
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statements, "My experiment has_topic Molecular mimicry" implies "My experiment is an Operation" and "My experiment is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.
! NB: Second 'domain' line is not visible in OBO-Edit2

[Typedef]
id: is_topic_of
name: is topic of
subset: relations
def: "'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)." [http://edamontology.org]
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. {note="In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'."}
synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in]
synonym: "quality_of" RELATED [OBO_REL:quality_of] {note="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."}
inverse_of: has_topic
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_topic:0003 ! Topic
range: EDAM_operation:0004 ! Operation
range: EDAM_data:0006 ! Data
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statements, "Molecular mimicry is_topic_of My experiment" implies "My experiment is an Operation" and (even) "My experiment is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.
! NB: Second 'range' line is not visible in OBO-Edit2

[Typedef]
id: has_format
name: has format
subset: relations
def: "'A has_format B' defines for the subject A, that it has the object B as its data format." [http://edamontology.org]
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'. {note="In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'."}
synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality]
synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] {note="'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."}
inverse_of: is_format_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: false
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_data:0006 ! Data
range: EDAM_format:1915 ! Format

[Typedef]
id: is_format_of
name: is format of
subset: relations
def: "'A is_format_of B' defines for the subject A, that it is a data format of the object B." [http://edamontology.org]
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'. {note="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."}
synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in]
synonym: "quality_of" RELATED [OBO_REL:quality_of] {note="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."}
inverse_of: has_format
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: false
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_format:1915 ! Format
range: EDAM_data:0006 ! Data

[Typedef]
id: has_identifier
name: has identifier
subset: relations
def: "'A has_identifier B' defines for the subject A, that it has the object B as its identifier." [http://edamontology.org]
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'. {note="In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'."}
inverse_of: is_identifier_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: false
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_data:0006 ! Data
range: EDAM_data:0842 ! Identifier
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "My car has_identifier Licence plate number" implies "My car is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.

[Typedef]
id: is_identifier_of
name: is identifier of
subset: relations
def: "'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B." [http://edamontology.org]
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. {note="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."}
inverse_of: has_identifier
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: false
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_data:0842 ! Identifier
range: EDAM_data:0006 ! Data
! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "Licence plate number is_identifier_of My car" implies "My car is Data".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.

[Typedef]
id: has_function
name: has function
subset: relations
def: "'A has_function B' defines for the subject A, that it has the object B as its function." [http://edamontology.org]
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. {note="In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts."}
synonym: "has function" EXACT [http://wsio.org/has_function]
synonym: "has_function" NARROW [http://purl.obolibrary.org/obo/OBI_0000306] {note="'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."}
synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality]
synonym: "bearer_of" RELATED [OBO_REL:bearer_of] {note="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."}
inverse_of: is_function_of
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
range: EDAM_operation:0004 ! Operation
! NB. 'range' is defined in the following way in OBO format: According to that definition and the given 'range' statement, "My boss has_function Institute leadership" implies "Institute leadership is an Operation".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.

[Typedef]
id: is_function_of
name: is function of
subset: relations
def: "'A is_function_of B' defines for the subject A, that it is a function of the object B." [http://edamontology.org]
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. {note="Within EDAM itself, 'is_function_of' is not used."}
synonym: "is function of" EXACT [http://wsio.org/is_function_of]
synonym: "function_of" NARROW [OBO_REL:function_of] {note="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."}
synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in]
synonym: "inheres_in" RELATED [OBO_REL:inheres_in] {note="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."}
inverse_of: has_function
transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it?
is_cyclic: true {note="In very unusual cases"}
is_reflexive: false
is_symmetric: false
is_anti_symmetric: false
is_transitive: false
domain: EDAM_operation:0004 ! Operation
! NB. 'domain' is defined in the following way in OBO format: According to that definition and the given 'domain' statement, "Institute leadership is_function_of My boss" implies "Institute leadership is an Operation".
! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply.








!
! Concept metadata tags, modifiers, and qualifiers
!

[Typedef]
id: regex
name: Regular expression
subset: concept_attributes
def: "'Regular expression' concept attribute ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org]
is_metadata_tag: true

[Typedef]
id: example
name: Example
subset: concept_attributes
def: "'Example' concept attribute ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org]
is_metadata_tag: true

[Typedef]
id: documentation
name: Documentation
subset: concept_attributes
def: "'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." [http://edamontology.org]
synonym: "Specification" NARROW [http.//edamontology.org]
is_metadata_tag: true

[Typedef]
id: min_cardinality
name: Minimum cardinality
subset: concept_attributes
def: "'Minimum cardinality' trailing modifier ('min_cardinality') of 'has input' and 'has output' relations. Specificies the minimum number of data records consumed or produced by an operation." [http://edamontology.org]
is_metadata_tag: true

[Typedef]
id: max_cardinality
name: Maximum cardinality
subset: concept_attributes
def: "'Maximum cardinality' trailing modifier ('max_cardinality') of 'has input' and 'has output' relations. Specificies the maximum number of data records consumed or produced by an operation." [http://edamontology.org]
comment: 'max_cardinality' is not (yet) defined among concepts in EDAM.
is_metadata_tag: true

[Typedef]
id: cardinality
name: Cardinality
subset: concept_attributes
def: "'Cardinality' trailing modifier ('cardinality') of 'has input' and 'has output' relations. Specificies the number of data records consumed or produced by an operation." [http://edamontology.org]
comment: 'cardinality' is not (yet) defined among concepts in EDAM.
is_metadata_tag: true
is_a: min_cardinality
is_a: max_cardinality

[Typedef]
id: note
name: Note
subset: concept_attributes
def: "'Note' trailing modifier ('note') of any concept or ontology attributes. Contains a note for a human reader related to the given attribute." [http://edamontology.org]
is_metadata_tag: true

[Typedef]
id: since
name: Since
subset: concept_attributes
def: "'Since' trailing modifier ('since') of 'id' and 'is_obsolete: true' attributes (may be applicable to other attributes, too). Specificies the released version of the ontology in which the attribute received its current value/started to be valid. In case of 'id' this is the version in which the concept has been introduced, and in case of 'is_obsolete: true' the version in which the concept became obsolete." [http://edamontology.org]
is_metadata_tag: true




[Term]
id: EDAM_operation:0004
name: Operation
namespace: operation
subset: operations
def: "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs)." [http://edamontology.org]
comment: A singular case is a constant operation (constant function) that consumes no input (has no input arguments).
xref: WSIO_operation:operation, http://wsio.org/operation
synonym: "Function" BROAD [http://edamontology.org] {note="Operation is a function that has input(s) and output(s) that are data."}
synonym: "Computational operation" NARROW [http://edamontology.org]
synonym: "Computational procedure" NARROW [http://edamontology.org]
synonym: "Computational method" NARROW [http://edamontology.org]
synonym: "Computational subroutine" NARROW [http://edamontology.org]
synonym: "Function (programming)" NARROW [http://edamontology.org]
synonym: "Lambda abstraction" NARROW [http://edamontology.org]
synonym: "Mathematical operation" NARROW [http://edamontology.org]
synonym: "Mathematical function" NARROW [http://edamontology.org]
synonym: "Process" RELATED [http://edamontology.org] {note="Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs."}
synonym: "Computational tool" RELATED [http://edamontology.org] {note="Computational tool provides an operation with inputs and outputs."}
synonym: "Operation" EXACT [http://wsio.org/operation_001]
synonym: "function" BROAD [http://purl.org/biotop/biotop.owl#Function] {note="Operation is a function that has input(s) and output(s) that are data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'."}
synonym: "function" BROAD [http://semanticscience.org/resource/SIO_000017]
synonym: "continuant" BROAD [snap:Continuant]
synonym: "Function" BROAD [http://www.onto-med.de/ontologies/gfo.owl#Function] {note="However, operation is not a GFO 'Concept' present only in someone's mind."}
synonym: "Subroutine" NARROW [http://en.wikipedia.org/wiki/Subroutine, http://en.wikipedia.org/wiki/Function_(computer_science)]
synonym: "Function (mathematics)" NARROW [http://en.wikipedia.org/wiki/Function_(mathematics)]
synonym: "function" RELATED [sumo:Function] ! Related external synonyms in EDAM without a note is usually almost exact.
synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] {note="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."}
synonym: "function" RELATED [snap:Function] {note="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)."}
synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] {note="Function, including an operation, can be a quality/attribute of e.g. a computational tool."}
synonym: "quality" RELATED [snap:Quality] {note="Function, including an operation, can have a role of a quality/attribute in semantic annotation of e.g. a computational tool."}
synonym: "process" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process] {note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."}
synonym: "process" RELATED [span:Process] {note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."}
synonym: "Process" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Process] {note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."}
synonym: "information processing" RELATED [http://www.ebi.ac.uk/swo/SWO_0000003] {note="However, one may think that an operation is not a process."}
synonym: "information processing" RELATED [http://semanticscience.org/resource/SIO_000649] {note="However, one may think that an operation is not a process and not a physical entity."}
synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] {note="Method may in addition focus on how to achieve the result, not just on what to achieve as with operation."}
relationship: has_input EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option.
relationship: has_output EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option.
relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option.


[Term]
id: EDAM_data:0006
name: Data
namespace: data
subset: data
! alt_id: EDAM_data:3030 {since=beta13} ! Not released
def: "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." [http://edamontology.org]
synonym: "Datum" EXACT [http://edamontology.org] {note="The multiplicity is not taken into account."}
synonym: "Data record" EXACT [http://edamontology.org] {note="Currently we are for practical purposes not distinguishing a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable information)."}
synonym: "Data set" EXACT [http://edamontology.org] {note="The multiplicity is not taken into account."}
synonym: "Data" EXACT [http://wsio.org/data_002]
synonym: "continuant" BROAD [snap:Continuant]
synonym: "digital entity" RELATED [http://purl.org/biotop/biotop.owl#DigitalEntity]
synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] {note="GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual."}
synonym: "data item" RELATED [http://semanticscience.org/resource/SIO_000069] {note="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)."}
synonym: "data item" RELATED [http://purl.obolibrary.org/obo/IAO_0000027] {note="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."}
synonym: "information content entity" RELATED [http://purl.obolibrary.org/obo/IAO_0000030] {note="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."}
synonym: "record" RELATED [http://semanticscience.org/resource/SIO_000088] {note="Data does however not necessarily contain statements and not necessarily about an entity."}
relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option.

[Term]
id: EDAM_topic:0003
name: Topic
namespace: topic
subset: topics
def: "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." [http://edamontology.org]
synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality]
synonym: "continuant" BROAD [snap:Continuant]
synonym: "field of study" RELATED [sumo:FiledOfStudy] ! Related external synonym in EDAM without a note is usually almost exact.
synonym: "Area of Research" RELATED [http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research]
synonym: "Category" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Category] {note="GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated."}
synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] {note="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."}
synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method]
synonym: "quality" RELATED [snap:Quality] {note="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."}
synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] {note="Topic can be a quality of an entity."}


[Term]
id: EDAM_format:1915
name: Format
namespace: format
subset: formats
def: "A specified way or layout of representing, structuring (and in some cases also encoding) data in a computer file, blob, string, message and so on." [http://edamontology.org]
synonym: "Data format" EXACT [http://edamontology.org]
synonym: "File format" NARROW [http://edamontology.org] {note="File format denotes only formats of a computer file, but the same formats apply also to data blobs or messages. Thus the synonym is in practical terms exact."}
synonym: "Format" BROAD [http://purl.org/dc/elements/1.1/format]
synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality]
synonym: "continuant" BROAD [snap:Continuant]
synonym: "data format specification" RELATED [http://purl.obolibrary.org/obo/IAO_0000098] {note="Closely related concept focusing on the specification of a data format."}
synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] {note="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."}
synonym: "Symbol structure" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure]
synonym: "File format" RELATED [http://en.wikipedia.org/wiki/File_format, http://en.wikipedia.org/wiki/List_of_file_formats]
synonym: "machine language" RELATED [http://purl.org/biotop/biotop.owl#MachineLanguage]
synonym: "Compression and encoding" RELATED [http://wsio.org/compression_004] {note="'Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format."}
synonym: "standard" RELATED [http://semanticscience.org/resource/SIO_000618]
synonym: "representation" RELATED [http://semanticscience.org/resource/SIO_000612]
synonym: "quality" RELATED [snap:Quality] {note="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."}
synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] {note="Format can be a quality of a data record."}
relationship: is_format_of EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option.

[Term]
id: EDAM_topic:0077
name: Nucleic acid analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:3046 {since=beta13} ! Not released
def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [http://edamontology.org]
synonym: "Nucleic acids" EXACT [http://edamontology.org]
synonym: "Nucleic acid informatics" EXACT [http://edamontology.org]
synonym: "Nucleic acid bioinformatics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0080
name: Sequence analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:2228
! alt_id: EDAM_topic:0584
def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org]
synonym: "Sequences" EXACT [http://edamontology.org]
xref: BioCatalogue:Sequence Analysis
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0081
name: Structure analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0693
! alt_id: EDAM_topic:2827
! alt_id: EDAM_topic:0585
def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [http://edamontology.org]
comment: This includes related concepts such as structural properties, alignments and structural motifs.
synonym: "Structural bioinformatics" EXACT [http://edamontology.org]
synonym: "Computation structural biology" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0084
! alt_id: EDAM_topic:0192
! alt_id: EDAM_topic:0193
name: Phylogenetics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0636
def: "Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [http://edamontology.org]
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.
xref: BioCatalogue:Phylogeny
xref: BioCatalogue:Statistical Robustness
synonym: "Phylogenetic simulation" EXACT [http://edamontology.org]
synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0085
name: Functional genomics
namespace: topic
subset: topics
def: "Topic concerning the study of gene or protein functions and their interactions." [http://edamontology.org]
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_topic:0217
name: Literature analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0088
! alt_id: EDAM_topic:3058
def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [http://edamontology.org]
xref: BioCatalogue: Document Discovery
xref: BioCatalogue: Literature retrieval
synonym: "Literature search and analysis" EXACT [http://edamontology.org]
synonym: "Literature sources" EXACT [http://edamontology.org]
is_a: EDAM_topic:3068 ! Literature and reference

[Term]
id: EDAM_topic:0091
name: Data handling
namespace: topic
subset: topics
! alt_id: EDAM_topic:2282
def: "Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [http://edamontology.org]
synonym: "Data types, processing and visualisation" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0102
name: Sequencing and mapping
namespace: topic
subset: topics
def: "Topic concerning the determination and mapping of complete (typically nucleotide) sequences." [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_topic:0121
name: Proteomics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0764
def: "Topic concerning the study of whole proteomes of organisms." [http://edamontology.org]
comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues).
synonym: "Protein expression" EXACT [http://edamontology.org]
xref: BioCatalogue:Proteomics
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0200
! alt_id: EDAM_topic:0206
name: Microarrays
namespace: topic
subset: topics
def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org]
xref: BioCatalogue:Microarrays
synonym: "DNA microarrays" EXACT [http://edamontology.org]
is_a: EDAM_topic:0607 ! Laboratory resources

[Term]
id: EDAM_operation:0230
name: Sequence generation
namespace: operation
subset: operations
def: "Generate a molecular sequence by some means." [http://edamontology.org]
is_a: EDAM_operation:2121 ! Sequence file processing

[Term]
id: EDAM_operation:0231
name: Sequence editing
namespace: operation
subset: operations
def: "Edit or change a molecular sequence, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:2121 ! Sequence file processing
is_a: EDAM_operation:3096 ! Editing

[Term]
id: EDAM_operation:0232
name: Sequence merging
namespace: operation
subset: operations
def: "Merge two or more (typically overlapping) molecular sequences." [http://edamontology.org]
synonym: "Sequence splicing" EXACT [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing

[Term]
id: EDAM_operation:0233
name: Sequence conversion
namespace: operation
subset: operations
def: "Convert a molecular sequence from one type to another." [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing

[Term]
id: EDAM_operation:0335
name: File reformatting
namespace: operation
subset: operations
def: "Reformat a file of data (or equivalent entity in memory)." [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing

[Term]
id: EDAM_operation:0561
name: Sequence reformatting
namespace: operation
subset: operations
def: "Reformat (a file or other report of) molecular sequence(s)." [http://edamontology.org]
is_a: EDAM_operation:0335 ! File reformatting
is_a: EDAM_operation:2121 ! Sequence file processing

[Term]
id: EDAM_operation:0562
name: Sequence alignment reformatting
namespace: operation
subset: operations
def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org]
is_a: EDAM_operation:0335 ! File reformatting
is_a: EDAM_operation:2122 ! Sequence alignment file processing

[Term]
id: EDAM_operation:0563
name: Codon usage table reformatting
namespace: operation
subset: operations
def: "Reformat a codon usage table." [http://edamontology.org]
is_a: EDAM_operation:0335 ! File reformatting
is_a: EDAM_operation:2433 ! Codon usage table processing
relationship: has_input EDAM_data:1597 {min_cardinality=1} ! Codon usage table
relationship: has_output EDAM_data:1597 {min_cardinality=1} ! Codon usage table

[Term]
id: EDAM_topic:0078
name: Protein analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0586
def: "Processing and analysis of protein data, typically molecular sequence and structural data." [http://edamontology.org]
synonym: "Protein informatics" EXACT [http://edamontology.org]
synonym: "Protein bioinformatics" EXACT [http://edamontology.org]
synonym: "Proteins" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0602
name: Pathways, networks and models
namespace: topic
subset: topics
! alt_id: EDAM_topic:0198
! alt_id: EDAM_topic:0755
def: "Topic concerning biological pathways, networks and other models." [http://edamontology.org]
xref: BioCatalogue:Pathways
xref: BioCatalogue:Pathway Retrieval
is_a: EDAM_topic:2259 ! Systems biology
is_a: EDAM_topic:3071 ! Biological data resources

[Term]
id: EDAM_topic:0607
name: Laboratory resources
namespace: topic
subset: topics
def: "Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources

[Term]
id: EDAM_topic:0621
name: Genome, proteome and model organisms
namespace: topic
subset: topics
! alt_id: EDAM_topic:0086
! alt_id: EDAM_topic:0591
! alt_id: EDAM_topic:0643
! alt_id: EDAM_topic:0800
! alt_id: EDAM_topic:0795
def: "Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [http://edamontology.org]
comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included.
synonym: "Genome map" EXACT [http://edamontology.org]
is_a: EDAM_topic:0622 ! Genomics
is_a: EDAM_topic:0121 ! Proteomics
is_a: EDAM_topic:0625 ! Genotype and phenotype resources

[Term]
id: EDAM_topic:0622
name: Genomics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0093
! alt_id: EDAM_topic:0794
def: "Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [http://edamontology.org]
xref: BioCatalogue:Genomics
xref: BioCatalogue:Functional Genomics
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0625
name: Genotype and phenotype resources
namespace: topic
subset: topics
! alt_id: EDAM_topic:2231
def: "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." [http://edamontology.org]
is_a: EDAM_topic:2816 ! Gene resources

[Term]
id: EDAM_data:0842
name: Identifier
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:2860
! alt_id: EDAM_data:2861
! alt_id: EDAM_data:2926
def: "Identifier is a datum identifying an entity and serving only the sole purpose of identification." [http://edamontology.org]
comment: An identifier is typically a rather short textual or numerical datum (string or integer). It is usually desired that an identifier identifies the entity uniquely and often also that it is persistent over time.
synonym: "ID" EXACT [http://edamontology.org]
synonym: "Identifier" EXACT [http://wsio.org/data_005]
synonym: "identifier" EXACT [http://semanticscience.org/resource/SIO_000115]
synonym: "Identifier" NARROW [http://purl.org/dc/elements/1.1/identifier] {note="Almost exact but limited to identifying resources."}
is_a: EDAM_data:0006 ! Data
relationship: is_identifier_of EDAM_data:0006 {note="However, NB. that an identifier may identify also other entities than data records."} ! Data

[Term]
id: EDAM_data:0850
name: Sequence set
namespace: data
subset: data
def: "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." [http://edamontology.org]
comment: This concept may be used for arbitrary sequence sets and associated data arising from processing.
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report

[Term]
id: EDAM_data:0912
name: Nucleic acid property
namespace: data
subset: data
def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [http://edamontology.org]
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.
synonym: "Nucleic acid physicochemical property" EXACT [http://edamontology.org]
is_a: EDAM_data:2084 ! Nucleic acid report
is_a: EDAM_data:2087 ! Molecular property

[Term]
id: EDAM_data:1233
name: Sequence set (protein)
namespace: data
subset: data
def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org]
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1234
name: Sequence set (nucleic acid)
namespace: data
subset: data
def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org]
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence

[Term]
id: EDAM_data:1235
name: Sequence cluster
namespace: data
subset: data
def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [http://edamontology.org]
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
is_a: EDAM_data:0850 ! Sequence set
relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification
relationship: has_topic EDAM_topic:0724 ! Protein families

[Term]
id: EDAM_data:1239
name: Restriction digest
namespace: data
subset: data
def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [http://edamontology.org]
xref: SO:0000412
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)

[Term]
id: EDAM_data:1246
name: Sequence cluster (nucleic acid)
namespace: data
subset: data
def: "A cluster of nucleotide sequences." [http://edamontology.org]
comment: The sequences are typically related, for example a family of sequences.
synonym: "Nucleotide sequence cluster" EXACT [http://edamontology.org]
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)
is_a: EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_format:1248
name: EMBL feature location
namespace: format
subset: formats
def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [http://edamontology.org]
synonym: "Feature location" EXACT [http://edamontology.org]
is_a: EDAM_format:2078 ! Sequence range format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_data:1265
name: Sequence composition (base frequencies)
namespace: data
subset: data
def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:3086 ! Nucleic acid sequence composition

[Term]
id: EDAM_data:1276
name: Nucleic acid features
namespace: data
subset: data
! alt_id: EDAM_data:1273
def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [http://edamontology.org]
comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.
synonym: "Nucleic acid feature table" EXACT [http://edamontology.org]
synonym: "Feature table (nucleic acid)" EXACT [http://edamontology.org]
is_a: EDAM_data:2084 ! Nucleic acid report
is_a: EDAM_data:1255 ! Feature record

[Term]
id: EDAM_format:1295
name: quicktandem
namespace: format
subset: formats
def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [http://edamontology.org]
is_a: EDAM_format:2155 ! Sequence features (repeats) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1296
name: Sanger inverted repeats
namespace: format
subset: formats
def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [http://edamontology.org]
is_a: EDAM_format:2155 ! Sequence features (repeats) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1297
name: EMBOSS repeat
namespace: format
subset: formats
def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [http://edamontology.org]
is_a: EDAM_format:2155 ! Sequence features (repeats) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1316
name: est2genome
namespace: format
subset: formats
def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [http://edamontology.org]
is_a: EDAM_format:2159 ! Gene features (coding region) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1318
name: restrict
namespace: format
subset: formats
def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [http://edamontology.org]
is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1319
name: restover
namespace: format
subset: formats
def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [http://edamontology.org]
is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1320
name: REBASE restriction sites
namespace: format
subset: formats
def: "Report format for restriction enzyme recognition sites used by REBASE database." [http://edamontology.org]
is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1334
name: mspcrunch
namespace: format
subset: formats
def: "Format of results of a sequence database search using some variant of MSPCrunch." [http://edamontology.org]
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1335
name: smith-waterman
namespace: format
subset: formats
def: "Format of results of a sequence database search using some variant of Smith Waterman." [http://edamontology.org]
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1336
name: dhf
namespace: format
subset: formats
def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [http://edamontology.org]
comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1337
name: lhf
namespace: format
subset: formats
def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [http://edamontology.org]
comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database.
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1349
name: HMMER Dirichlet prior
namespace: format
subset: formats
def: "Dirichlet distribution HMMER format." [http://edamontology.org]
is_a: EDAM_format:2074 ! Dirichlet distribution format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1350
name: MEME Dirichlet prior
namespace: format
subset: formats
def: "Dirichlet distribution MEME format." [http://edamontology.org]
is_a: EDAM_format:2074 ! Dirichlet distribution format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1351
name: HMMER emission and transition
namespace: format
subset: formats
def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [http://edamontology.org]
is_a: EDAM_format:2075 ! HMM emission and transition counts format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1356
name: prosite-pattern
namespace: format
subset: formats
def: "Format of a regular expression pattern from the Prosite database." [http://edamontology.org]
is_a: EDAM_format:2068 ! Sequence motif format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1357
name: EMBOSS sequence pattern
namespace: format
subset: formats
def: "Format of an EMBOSS sequence pattern." [http://edamontology.org]
is_a: EDAM_format:2068 ! Sequence motif format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1360
name: meme-motif
namespace: format
subset: formats
def: "A motif in the format generated by the MEME program." [http://edamontology.org]
is_a: EDAM_format:2068 ! Sequence motif format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1366
name: prosite-profile
namespace: format
subset: formats
def: "Sequence profile (sequence classifier) format used in the PROSITE database." [http://edamontology.org]
is_a: EDAM_format:2069 ! Sequence profile format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1367
name: jaspar
namespace: format
subset: formats
def: "A profile (sequence classifier) in the format used in the JASPAR database." [http://edamontology.org]
is_a: EDAM_format:2069 ! Sequence profile format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1369
name: MEME background Markov model
namespace: format
subset: formats
def: "Format of the model of random sequences used by MEME." [http://edamontology.org]
is_a: EDAM_format:2072 ! Hidden Markov model format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1370
name: hmmer
namespace: format
subset: formats
def: "Format of a hidden Markov model representation used by the HMMER package." [http://edamontology.org]
is_a: EDAM_format:2072 ! Hidden Markov model format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_data:1383
name: Sequence alignment (nucleic acid)
namespace: data
subset: data
def: "Alignment of multiple nucleotide sequences." [http://edamontology.org]
is_a: EDAM_data:0863 ! Sequence alignment
is_a: EDAM_data:2084 ! Nucleic acid report

[Term]
id: EDAM_format:1419
name: Sequence-MEME profile alignment
namespace: format
subset: formats
def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [http://edamontology.org]
is_a: EDAM_format:2014 ! Sequence-profile alignment format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1421
name: HMMER profile alignment (sequences versus HMMs)
namespace: format
subset: formats
def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [http://edamontology.org]
is_a: EDAM_format:2014 ! Sequence-profile alignment format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1422
name: HMMER profile alignment (HMM versus sequences)
namespace: format
subset: formats
def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [http://edamontology.org]
is_a: EDAM_format:2014 ! Sequence-profile alignment format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1423
name: phylip distance matrix
namespace: format
subset: formats
def: "Format of PHYLIP phylogenetic distance matrix data." [http://edamontology.org]
comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).
is_a: EDAM_format:2067 ! Sequence distance matrix format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1430
name: phylip continuous quantitative characters
namespace: format
subset: formats
def: "PHYLIP file format for continuous quantitative character data." [http://edamontology.org]
is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1432
name: phylip character frequencies
namespace: format
subset: formats
def: "PHYLIP file format for phylogenetics character frequency data." [http://edamontology.org]
is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1433
name: phylip discrete states
namespace: format
subset: formats
def: "Format of PHYLIP discrete states data." [http://edamontology.org]
is_a: EDAM_format:2038 ! Phylogenetic discrete states format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1434
name: phylip cliques
namespace: format
subset: formats
def: "Format of PHYLIP cliques data." [http://edamontology.org]
is_a: EDAM_format:2039 ! Phylogenetic tree report (cliques) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1445
name: phylip tree distance
namespace: format
subset: formats
def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [http://edamontology.org]
is_a: EDAM_format:2049 ! Phylogenetic tree report (tree distances) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1454
name: dssp
namespace: format
subset: formats
def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [http://edamontology.org]
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.
is_a: EDAM_format:2077 ! Protein secondary structure format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1455
name: hssp
namespace: format
subset: formats
def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [http://edamontology.org]
is_a: EDAM_format:2077 ! Protein secondary structure format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1457
name: Vienna RNA secondary structure
namespace: format
subset: formats
def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [http://edamontology.org]
synonym: "Dot-bracket format" EXACT [http://edamontology.org]
is_a: EDAM_format:2076 ! RNA secondary structure format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1458
name: Vienna local RNA secondary structure
namespace: format
subset: formats
def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [http://edamontology.org]
is_a: EDAM_format:1457 ! Vienna RNA secondary structure
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_data:1459
name: Nucleic acid structure
namespace: data
subset: data
def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [http://edamontology.org]
is_a: EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis

[Term]
id: EDAM_format:1476
name: PDB format
namespace: format
subset: formats
def: "Entry format of PDB database in PDB format." [http://edamontology.org]
synonym: "PDB" EXACT [http://edamontology.org]
xref: Moby:PDB-formatted-text
xref: Moby:PDB-Text
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1477
name: mmCIF
namespace: format
subset: formats
def: "Entry format of PDB database in mmCIF format." [http://edamontology.org]
synonym: "mmcif" EXACT [http://edamontology.org]
xref: Moby:mmCIF-Text
xref: Moby:mmCIF_Text
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_data:1482
name: Structure alignment (nucleic acid)
namespace: data
subset: data
def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:0886 ! Structure alignment
is_a: EDAM_data:2084 ! Nucleic acid report

[Term]
id: EDAM_format:1500
name: Domainatrix 3D-1D scoring matrix format
namespace: format
subset: formats
def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [http://edamontology.org]
is_obsolete: true {since=beta12orEarlier}

[Term]
id: EDAM_format:1504
name: aaindex
namespace: format
subset: formats
def: "Amino acid index format used by the AAindex database." [http://edamontology.org]
is_a: EDAM_format:2017 ! Amino acid index format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1551
name: Pcons report format
namespace: format
subset: formats
def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [http://edamontology.org]
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.
is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1552
name: ProQ report format
namespace: format
subset: formats
def: "Format of output of the ProQ protein model quality predictor." [http://edamontology.org]
comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.
is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1582
name: findkm
namespace: format
subset: formats
def: "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)." [http://edamontology.org]
is_a: EDAM_format:2027 ! Enzyme kinetics report format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1627
name: Primer3 primer
namespace: format
subset: formats
def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [http://edamontology.org]
is_a: EDAM_format:2061 ! Nucleic acid features (primers) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1629
name: mira
namespace: format
subset: formats
def: "Format of MIRA sequence trace information file." [http://edamontology.org]
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1630
name: CAF
namespace: format
subset: formats
def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [http://edamontology.org]
xref: http://www.sanger.ac.uk/resources/software/caf/ {documentation=true}
is_a: EDAM_format:2561 ! Sequence assembly format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1633
name: PHD
namespace: format
subset: formats
def: "PHD sequence trace format to store serialised chromatogram data (reads)." [http://edamontology.org]
xref: http://www.bioperl.org/wiki/PHD_sequence_format {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1637
name: dat
namespace: format
subset: formats
def: "Format of Affymetrix data file of raw image data." [http://edamontology.org]
synonym: "Affymetrix image data file format" EXACT [http://edamontology.org]
is_a: EDAM_format:2058 ! Gene expression report format
is_a: EDAM_format:2330 ! Textual format
relationship: is_format_of EDAM_data:1714 ! Microarray spots image

[Term]
id: EDAM_format:1638
name: cel
namespace: format
subset: formats
def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [http://edamontology.org]
synonym: "Affymetrix probe raw data format" EXACT [http://edamontology.org]
is_a: EDAM_format:2058 ! Gene expression report format
is_a: EDAM_format:2330 ! Textual format
relationship: is_format_of EDAM_data:3110 ! Raw microarray data

[Term]
id: EDAM_format:1639
name: affymetrix
namespace: format
subset: formats
def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [http://edamontology.org]
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2172 ! Sequence cluster format (nucleic acid)

[Term]
id: EDAM_format:1641
name: affymetrix-exp
namespace: format
subset: formats
def: "Affymetrix data file format for information about experimental conditions and protocols." [http://edamontology.org]
synonym: "Affymetrix experimental conditions data file format" EXACT [http://edamontology.org]
is_a: EDAM_format:2056 ! Microarray experiment data format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1644
name: CHP
namespace: format
subset: formats
def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [http://edamontology.org]
synonym: "Affymetrix probe normalised data format" EXACT [http://edamontology.org]
is_a: EDAM_format:2058 ! Gene expression report format
is_a: EDAM_format:2330 ! Textual format
relationship: is_format_of EDAM_data:3111 ! Processed microarray data

[Term]
id: EDAM_format:1705
name: HET group dictionary entry format
namespace: format
subset: formats
def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [http://edamontology.org]
is_a: EDAM_format:2030 ! Small molecule report format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1739
name: pmc
namespace: format
subset: formats
def: "Article format of the PubMed Central database." [http://edamontology.org]
is_a: EDAM_format:2020 ! Article format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1740
name: iHOP text mining abstract format
namespace: format
subset: formats
def: "iHOP abstract format." [http://edamontology.org]
is_a: EDAM_format:2021 ! Text mining report format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1741
name: Oscar3
namespace: format
subset: formats
def: "Text mining abstract format from the Oscar 3 application." [http://edamontology.org]
comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.
is_a: EDAM_format:2021 ! Text mining report format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1747
name: PDB atom record format
namespace: format
subset: formats
def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_format:1476 ! PDB format

[Term]
id: EDAM_operation:1848
name: Structure reformatting
namespace: operation
subset: operations
def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org, WHATIF]
xref: WHATIF: PDBasXML
is_a: EDAM_operation:2234 ! Structure file processing
is_a: EDAM_operation:0335 ! File reformatting

[Term]
id: EDAM_format:1861
name: PlasMapper TextMap
namespace: format
subset: formats
def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org]
xref: Moby:PlasMapperTextMap
is_a: EDAM_format:2060 ! Map format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1961
name: stockholm
namespace: format
subset: formats
def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [http://edamontology.org]
xref: http://en.wikipedia.org/wiki/Stockholm_format {documentation=true}
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1974
name: GFF2
namespace: format
subset: formats
def: "General Feature Format (GFF) of sequence features." [http://edamontology.org]
xref: http://www.sanger.ac.uk/resources/software/gff/spec.html {documentation=true}
is_a: EDAM_format:2305 ! GFF

[Term]
id: EDAM_format:1975
name: GFF3
namespace: format
subset: formats
def: "Generic Feature Format version 3 (GFF3) of sequence features." [http://edamontology.org]
xref: http://sequenceontology.org/resources/gff3.html {documentation=true}
is_a: EDAM_format:2305 ! GFF

[Term]
id: EDAM_format:1979
name: debug-feat
namespace: format
subset: formats
def: "EMBOSS debugging trace feature format of full internal data content." [http://edamontology.org]
is_a: EDAM_format:1920 ! Sequence feature annotation format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2035
name: Chemical formula format
namespace: format
subset: formats
def: "Text format of a chemical formula." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0846 ! Chemical formula

[Term]
id: EDAM_data:2070
name: Sequence motif (nucleic acid)
namespace: data
subset: data
def: "A nucleotide sequence motif." [http://edamontology.org]
is_a: EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_data:2084
name: Nucleic acid report
namespace: data
subset: data
def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [http://edamontology.org]
is_a: EDAM_data:2529 ! Molecule report

[Term]
id: EDAM_operation:2121
name: Sequence file processing
namespace: operation
subset: operations
def: "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." [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
is_a: EDAM_operation:2409 ! File processing

[Term]
id: EDAM_format:2181
name: EMBL-like (text)
namespace: format
subset: formats
def: "A text format resembling EMBL entry format." [http://edamontology.org]
comment: This concept may be used for the many non-standard EMBL-like text formats.
is_a: EDAM_format:2543 ! EMBL-like format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2182
name: FASTQ-like format (text)
namespace: format
subset: formats
def: "A text format resembling FASTQ short read format." [http://edamontology.org]
comment: This concept may be used for non-standard FASTQ short read-like formats.
is_a: EDAM_format:2545 ! FASTQ-like format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2187
name: uniprotkb-like (text)
namespace: format
subset: formats
def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org]
is_a: EDAM_format:2547 ! uniprotkb-like format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2194
name: medline
namespace: format
subset: formats
def: "Abstract format used by MedLine database." [http://edamontology.org]
is_a: EDAM_format:2020 ! Article format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2197
name: OWL
namespace: format
subset: formats
def: "OWL ontology format." [http://edamontology.org]
is_a: EDAM_format:2195 ! Ontology format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_data:2198
name: Gene cluster
namespace: data
subset: data
def: "A cluster of similar genes." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_data:1246 ! Sequence cluster (nucleic acid)

[Term]
id: EDAM_format:2200 ! This is the one used for annotation in eSysbio
name: FASTA-like (text)
namespace: format
subset: formats
def: "A text format resembling FASTA format." [http://edamontology.org]
comment: This concept may also be used for the many non-standard FASTA-like formats.
synonym: "DNA and Protein Sequence Alignment" NARROW [http://filext.com/file-extension/FASTA]
is_a: EDAM_format:2546 ! FASTA-like
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2205
name: GenBank-like format (text)
namespace: format
subset: formats
def: "A text format resembling GenBank entry (plain text) format." [http://edamontology.org]
comment: This concept may be used for the non-standard GenBank-like text formats.
is_a: EDAM_format:2559 ! GenBank-like format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2206
name: Sequence feature table format (text)
namespace: format
subset: formats
def: "Text format for a sequence feature table." [http://edamontology.org]
is_a: EDAM_format:2548 ! Sequence feature table format

[Term]
id: EDAM_topic:2230
name: Classification
namespace: topic
subset: topics
def: "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_topic:2829 ! Ontologies, nomenclature and classification

[Term]
id: EDAM_data:2245
name: Sequence set (bootstrapped)
namespace: data
subset: data
def: "A collection of sequences output from a bootstrapping (resampling) procedure." [http://edamontology.org]
comment: Bootstrapping is often performed in phylogenetic analysis.
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_format:2330
name: Textual format
namespace: format
subset: formats
def: "Textual format." [http://edamontology.org]
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 very precisely not plain-textual).
synonym: "Tabular format" NARROW [http://edamontology.org, http://filext.com/file-extension/TSV] {note="Many textual formats used in bioinformatics are tabular (tab-separated values, TSV)."}
synonym: "Plain text" NARROW [http://edamontology.org]
synonym: "TXT" NARROW [http://filext.com/file-extension/TXT]
synonym: "Text File" NARROW [http://filext.com/file-extension/TXT]
synonym: "TSV" NARROW [http://filext.com/file-extension/TSV]
synonym: "Tab-Separated Values" NARROW [http://filext.com/file-extension/TSV]
is_a: EDAM_format:1915 ! Format

[Term]
id: EDAM_format:2334
name: URI format
namespace: format
subset: formats
def: "Typical textual representation of a URI." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_data:1047 ! URI

[Term]
id: EDAM_data:2354
name: RNA family annotation
namespace: data
subset: data
def: "An informative report on a specific RNA family or other group of classified RNA sequences." [http://edamontology.org]
is_a: EDAM_data:2986 ! Nucleic acid classification

[Term]
id: EDAM_data:2525
name: Nucleic acid data
namespace: data
subset: data
def: "Data concerning one or more nucleic acid molecules." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_obsolete: true {since=beta13}
consider: EDAM_data:2084 ! Nucleic acid report

[Term]
id: EDAM_format:2549
name: OBO
namespace: format
subset: formats
def: "OBO ontology text format." [http://edamontology.org]
is_a: EDAM_format:2196 ! OBO format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2551
name: Sequence record format (text)
namespace: format
subset: formats
def: "Data format for a molecular sequence record." [http://edamontology.org]
is_a: EDAM_format:1919 ! Sequence record format

[Term]
id: EDAM_format:2554
name: Alignment format (text)
namespace: format
subset: formats
def: "Text format for molecular sequence alignment information." [http://edamontology.org]
is_a: EDAM_format:1921 ! Alignment format

[Term]
id: EDAM_format:2556
name: Phylogenetic tree format (text)
namespace: format
subset: formats
def: "Text format for a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_format:2006 ! Phylogenetic tree format

[Term]
id: EDAM_format:2562
name: Amino acid identifier format
namespace: format
subset: formats
def: "Text format (representation) of amino acid residues." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_data:0994 ! Amino acid identifier

[Term]
id: EDAM_format:2573
name: SAM
namespace: format
subset: formats
def: "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." [http://edamontology.org]
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.
xref: http://samtools.sourceforge.net/SAM-1.3.pdf {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_topic:2816
name: Gene resources
namespace: topic
subset: topics
! alt_id: EDAM_topic:0630
def: "Informatics resource (typically a database) primarily focussed on genes." [http://edamontology.org]
synonym: "Gene database" EXACT [http://edamontology.org]
synonym: "Gene resource" EXACT [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources
is_a: EDAM_topic:3053 ! Genetics

[Term]
id: EDAM_topic:2829
name: Ontologies, nomenclature and classification
namespace: topic
subset: topics
def: "Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0605
name: Informatics
namespace: topic
subset: topics
! alt_id: EDAM_topic:2841
def: "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." [http://edamontology.org]
is_obsolete: true {since=beta12orEarlier}
consider: EDAM_topic:0091 ! Data handling

[Term]
id: EDAM_data:2874
name: Sequence set (polymorphic)
namespace: data
subset: data
def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [http://edamontology.org]
is_obsolete: true {since=beta13}
consider: EDAM_data:1234 ! Sequence set (nucleic acid)

[Term]
id: EDAM_format:3001
name: ACE
namespace: format
subset: formats
def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [http://edamontology.org]
xref: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt {documentation=true}
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2055 ! Sequence assembly format

[Term]
id: EDAM_format:3003
name: BED
namespace: format
subset: formats
def: "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." [http://edamontology.org]
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).
xref: http://genome.ucsc.edu/FAQ/FAQformat#format1 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3005
name: WIG
namespace: format
subset: formats
def: "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." [http://edamontology.org]
xref: http://genome.ucsc.edu/goldenPath/help/wiggle.html {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3007
name: PSL
namespace: format
subset: formats
def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [http://edamontology.org]
xref: http://genome.ucsc.edu/FAQ/FAQformat#format2 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3008
name: MAF
namespace: format
subset: formats
def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [http://edamontology.org]
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.
xref: http://genome.ucsc.edu/FAQ/FAQformat#format5 {documentation=true}
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2919 ! Sequence annotation track format

[Term]
id: EDAM_format:3011
name: genePred
namespace: format
subset: formats
def: "genePred table format for gene prediction tracks." [http://edamontology.org]
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.
xref: http://genome.ucsc.edu/FAQ/FAQformat#format9 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3012
name: pgSnp
namespace: format
subset: formats
def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [http://edamontology.org] ! UCSC-specific,but also for custom tracks & useful
xref: http://genome.ucsc.edu/FAQ/FAQformat#format10 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3013
name: axt
namespace: format
subset: formats
def: "axt format of alignments, typically produced from BLASTZ." [http://edamontology.org]
xref: http://genome.ucsc.edu/goldenPath/help/axt.html {documentation=true}
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3014
name: LAV
namespace: format
subset: formats
def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://genome.ucsc.edu/goldenPath/help/axt.html] ! Can be used by UCSC and Galaxy
xref: http://www.bx.psu.edu/miller_lab/dist/lav_format.html {documentation=true}
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3015
name: Pileup
namespace: format
subset: formats
def: "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)." [http://edamontology.org]
xref: http://samtools.sourceforge.net/pileup.shtml {documentation=true}
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format
! and of track? (encoded as points, but could be 'function', like wig)

[Term]
id: EDAM_format:3016
name: VCF
namespace: format
subset: formats
def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org]
xref: http://vcftools.sourceforge.net/specs.html {documentation=true}
is_a: EDAM_format:2921 ! Sequence variation annotation format
is_a: EDAM_format:2330 ! Textual format